Last updated on 2025-04-19 06:50:03 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| CytoSimplex | 8 | 5 | |
| rliger | 7 | 2 | 4 |
Current CRAN status: NOTE: 8, OK: 5
Version: 0.1.1
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
rnaRaw.Rd: dgCMatrix-class
rnaVelo.Rd: dgCMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64
Version: 0.1.1
Check: installed package size
Result: NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
data 1.5Mb
doc 1.1Mb
libs 3.0Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: ERROR: 7, NOTE: 2, OK: 4
Version: 2.1.0
Check: examples
Result: ERROR
Running examples in ‘rliger-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optimizeNewLambda
> ### Title: Perform factorization for new lambda value
> ### Aliases: optimizeNewLambda
>
> ### ** Examples
>
> pbmc <- normalize(pbmc)
ℹ Normalizing datasets "ctrl"
ℹ Normalizing datasets "stim"
✔ Normalizing datasets "stim" ... done
ℹ Normalizing datasets "ctrl"
✔ Normalizing datasets "ctrl" ... done
> pbmc <- selectGenes(pbmc)
ℹ Selecting variable features for dataset "ctrl"
✔ ... 168 features selected out of 249 shared features.
ℹ Selecting variable features for dataset "stim"
✔ ... 166 features selected out of 249 shared features.
✔ Finally 173 shared variable features are selected.
> pbmc <- scaleNotCenter(pbmc)
ℹ Scaling dataset "ctrl"
✔ Scaling dataset "ctrl" ... done
ℹ Scaling dataset "stim"
✔ Scaling dataset "stim" ... done
> if (requireNamespace("RcppPlanc", quietly = TRUE)) {
+ # Only running a few iterations for fast examples
+ pbmc <- runINMF(pbmc, k = 20, nIteration = 2)
+ pbmc <- optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2)
+ }
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 43773
Error: Must provide 2 V matrices
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calcAgreement 9.526 1.466 8.859
createLiger 6.145 0.197 8.617
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [403s/403s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rliger)
Package `rliger` has been updated massively since version 1.99.0, including the object structure which is not compatible with old versions.
We recommand you backup your old analysis before overwriting any existing result.
`readLiger()` is provided for reading an RDS file storing an old object and it converts the object to the up-to-date structure.
>
> test_check("rliger")
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Reading input file...
Number of nodes: 600
Number of edges: 16900
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity: 0.7596
Number of communities: 9
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Reading input file...
Number of nodes: 600
Number of edges: 16701
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity: 0.7658
Number of communities: 10
Elapsed time: 0 seconds
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Dataset 1:
NPM1, SAT1, VIM, FTH1, BTG1, ISG15, GBP1, RSAD2, HSP90AB1
Shared:
NMB, ANXA1, GPR183, NDUFC2, GAPDH, VIM, EIF1, SRGN, JUNB, S100A10, TMSB4X, PABPC1, H3F3B, SAT1, HIST1H2AC, RGCC, ANXA2, RPLP1, LYZ, RPL18, HLA-A, RPS15A, TMEM66, RSAD2, UBC, HSPA8, MALAT1, RPLP0, RPS6, RPS12
Dataset 2
RSAD2, VIM, ISG15, GBP1, HSP90AB1, SAT1, NPM1, FTH1, BTG1
Dataset 1:
CD83, VIM, CXCR4, MARCKSL1, GAPDH, FTL, ISG15, GBP1, SELL, RSAD2, CXCL10, PLAC8, SOD2, SAT1, IFI27, CCL2, CCL8, CCL3, CCL4, APOBEC3A, TYMP
Shared:
RPL23A, RPS2, CD79A, RPL18A, RPL12, RPL13A, RPL3, RPL27A, RPS23, RPL15, RPLP0, RPL10, RPL19, RPS8, RPS4X, RPS5, RPL10A, RPL11, RPS19, RPL18, RPS3A, RPL34, RPS18, PTMA, RPL7, RPS6, RPS27, RPLP1, RPL32, RPL14
Dataset 2
PLAC8, GBP1, IFI27, TYMP, ISG15, SELL, RSAD2, CXCL10, SOD2, SAT1, CCL2, CCL8, CCL3, CCL4, APOBEC3A, MARCKSL1, CXCR4, CD83, VIM, GAPDH, FTL
Dataset 1:
FCGR3A, LGALS1, RPLP0, RPL18, RPS12, RPS3A, RPL23A, S100A4, ACTB, RPL7, ISG15, GBP1, RSAD2, SAT1, CCNH
Shared:
CST7, CHRNB1, NKG7, APOBEC3G, CLIC3, CXCR4, GNLY, HLA-A, CD7, HLA-C, GZMB, SRGN, BAK1, TMSB4X, NDUFC2, HLA-B, B2M, BTG1, JTB, CCNH, FOXN3, H2AFZ, UBC, CREM, MALAT1, PTMA, ANXA1, H3F3B, VIM, RABL5
Dataset 2
CCNH, ISG15, RSAD2, SAT1, GBP1, S100A4, FCGR3A, RPS3A, RPS12, ACTB, RPL7, RPLP0, RPL23A, RPL18, LGALS1
Dataset 1:
CXCL10, GBP1, PTMA, S100A10, CD14, LGALS1, TIMP1, FAM26F, RPS3A, RPL10A, RPL3, S100A6, H2AFZ, CCL3, S100A8, GPX1, IL8, HLA-DQA1, LGALS3, ISG15, RSAD2, CD83, HSPA1A, GIMAP7, IDO1, TXN, MS4A7, IFI27, CCL2, CCL8
Shared:
FCGR3A, MS4A7, VMO1, FAM26F, GBP1, CXCL10, TYROBP, PLAC8, FCER1G, TIMP1, S100A11, FTH1, SAT1, SOD2, JUNB, TMSB4X, TYMP, HLA-C, SRGN, HLA-B, B2M, ACTB, HLA-DPA1, CST3, RPS19, APOBEC3A, MALAT1, TMEM66, S100A4, H3F3B
Dataset 2
ISG15, IFI27, MS4A7, APOBEC3A, HSPA1A, GIMAP7, CD83, RSAD2, GBP1, CXCL10, FAM26F, IDO1, TXN, CCL2, CCL8, CCL3, S100A10, S100A8, S100A6, PTMA, GPX1, IL8, H2AFZ, RPS3A, CD14, HLA-DQA1, RPL10A, TIMP1, LGALS3, LGALS1
Dataset 1:
RPL10A, H2AFZ, GAPDH, PABPC1, ISG15, GBP1, CXCL10, CD83, SAT1, EIF1, HERC6
Shared:
MIR155HG, MYC, ID3, CD83, NPM1, HLA-DQA1, HSP90AB1, CCR7, CCL3, HLA-DRB1, HSPA8, EIF1, HLA-DRA, RPLP0, RPS5, CCL4, JTB, RPL14, RPS23, RPL19, RPL10A, RPL7, RPS12, RPL18A, RPS2, PTMA, CD74, RPL23A, RPS8, RPLP1
Dataset 2
GBP1, EIF1, CD83, CXCL10, HERC6, ISG15, SAT1, H2AFZ, RPL10A, PABPC1, GAPDH
Dataset 1:
RPS8, RPS23, RPL15, RPL21, RPL7, RPL13A, MARCKSL1, RPS3A, TIMP1, RPS6, RPS3, ISG15, GBP1, RSAD2, CXCL10, HSPA1A, FAM26F, HSPB1, IDO1, CREM, CCL8, APOBEC3A, APOBEC3G, TYMP, THRAP3
Shared:
CXCL3, SERPINB2, IL8, CCL7, CCL2, CTSL, CTSB, RABL5, ANXA5, CD63, SOD2, FCER1G, FTL, CSTB, CD14, ANXA2, CCL3, FTH1, VIM, NFKBIA, LGALS1, GAPDH, ANXA1, SRGN, LGALS3, S100A6, S100A9, H3F3B, TYMP, TIMP1
Dataset 2
CCL8, THRAP3, HSPA1A, TYMP, HSPB1, CREM, APOBEC3G, ISG15, GBP1, RSAD2, CXCL10, FAM26F, IDO1, APOBEC3A, MARCKSL1, RPS8, RPL15, RPS3A, RPS23, TIMP1, RPL7, RPS6, RPS3, RPL21, RPL13A
Dataset 1:
RSAD2, ISG15, APOBEC3A, CD14, GPX1, GAPDH, MARCKSL1, RPL10, JTB, RPS3A, RPL21, RPS5, SAT1, RPS27A, RPL3, RPS8, RPL32, RPL7, RPS12, RPL15, PABPC1, RPL11, RPLP0, RPL10A, IL8, RPL19, S100A8, S100A6, DUSP2, CXCR4
Shared:
RSAD2, ISG15, APOBEC3A, CCL8, CXCL10, CCL2, CTSB, IDO1, SOD2, ANXA5, TYMP, FTL, CD63, HSPA1A, GBP1, CSTB, CTSL, IFI27, C15orf48, FAM26F, CCL7, FCER1G, LGALS3, LGALS1, FTH1, S100A11, TYROBP, ANXA2, HSPB1, TIMP1
Dataset 2
IDO1, HSPA1A, CCL4, CCL7, NFKBIA, CCL3, CXCL10, FAM26F, IFI27, RPS19, HERC6, ISG15, RSAD2, HSPB1, SAT1, CCL2, CCL8, APOBEC3A, RPL11, MARCKSL1, RPS8, S100A8, S100A6, RPS27A, DUSP2, CXCR4, PTMA, RPL32, RPL15, RPL14
Dataset 1:
BIRC3, S100A6, FTH1, CCL8, ID3, HLA-DPB1, GAPDH, CD79A, FTL, ISG15, GBP1, SELL, RSAD2, CXCL10, PLAC8, HSP90AB1, GIMAP7, SAT1, CREM, HSPA8, IFI27, CCL2, CCR7, H3F3B, APOBEC3A, TYMP, HERC6
Shared:
TMEM66, RPL13, RPL31, LTB, RPS18, RPL34, RPL32, RPS14, SELL, RPL21, RPS6, RPS15A, RPS27A, RPS12, RPL7, RPL3, RPS4X, RPS3, RPS3A, RPL9, RPL10, RPL11, RPL13A, RPS19, RPL10A, PABPC1, RPS23, RPS8, RPL27A, RPS2
Dataset 2
GIMAP7, PLAC8, CCR7, IFI27, H3F3B, SELL, GBP1, ISG15, RSAD2, CXCL10, HSP90AB1, SAT1, CREM, HSPA8, CCL2, CCL8, APOBEC3A, TYMP, HERC6, ID3, S100A6, HLA-DPB1, FTH1, BIRC3, GAPDH, CD79A, FTL
Dataset 1:
TEX264, FTH1, VIM, CCNH, UBC, RGCC, ISG15, GBP1, RSAD2, CXCL10, PLAC8, CD74, SAT1, CD79A
Shared:
GIMAP7, RGCC, ACAT2, BTG1, THRAP3, RELB, LTB, H2AFZ, EIF2AK1, CXCR4, HERC6, BIRC3, SELL, HSPA8, GPR183, CCR7, BAK1, HIST1H2AC, CHCHD10, EIF1, HSPB1, RPS27, JTB, MALAT1, H3F3B, PTMA, TMEM66, HSP90AB1, ANXA1, HLA-B
Dataset 2
GBP1, RSAD2, RGCC, UBC, ISG15, CXCL10, PLAC8, CD74, SAT1, CD79A, TEX264, VIM, FTH1, CCNH
Dataset 1:
CD14, S100A8, IFI27, RPL31, RPL27A, RPL21, RPL7, GBP1, MARCKSL1, RPS8, S100A6, S100A4, RPS27A, IL1B, PTMA, RPL15, RPL14, GPX1, IL8, CXCL3, H2AFZ, RPL34, RPS3A, RPS23, RPL10A, RPS4X, RPS6, RPS3, GAPDH, RGCC
Shared:
MARCKSL1, TIMP1, C15orf48, SOD2, FTH1, CD63, ANXA5, CSTB, SRGN, GAPDH, FTL, TYROBP, FCER1G, S100A11, EIF1, IL8, LGALS1, TYMP, B2M, LGALS3, ANXA2, CTSB, VIM, TXN, S100A10, ACTB, CCL2, NFKBIA, LYZ, HLA-B
Dataset 2
TXN, CST3, IDO1, APOBEC3A, MARCKSL1, PLAC8, S100A6, S100A4, HERC6, RPL19, RPS3, ISG15, GBP1, SELL, RSAD2, CXCL10, HIST1H2AC, HLA-C, HSPA1A, FAM26F, HSPB1, SAT1, CTSL, BIRC3, IFI27, CCL2, CCL7, CCL8, CCR7, APOBEC3B
Dataset 1:
IDO1, CST7, VMO1, IL8, SAT1, RPS5, TYMP, LAGE3, CXCR4, TIMP1, RGCC, RPL3, ISG15, GBP1, S100A4, SELL, RSAD2, CXCL10, HSPA1A, HSP90AB1, FAM26F, HSPB1, CTSB, ANXA1, HSPA8, IFI27, CCL2, H3F3B, APOBEC3A, APOBEC3B
Shared:
HLA-DPA1, HLA-DPB1, HLA-DRA, CD74, HLA-DRB1, TXN, HLA-DQA1, IDO1, CST3, CCR7, CD83, ANXA2, GPR183, MARCKSL1, ACTB, BIRC3, LYZ, CST7, TMSB4X, C15orf48, S100A10, LGALS1, B2M, GPX1, CD79A, NFKBIA, H2AFZ, RELB, ISG15, HSPA1A
Dataset 2
CXCL10, HSPA1A, ISG15, FAM26F, HSPB1, HERC6, GBP1, S100A4, APOBEC3G, RSAD2, HSP90AB1, HSPA8, SELL, SAT1, CTSB, IDO1, ANXA1, IFI27, CCL2, H3F3B, APOBEC3A, APOBEC3B, TYMP, CXCR4, IL8, TIMP1, RGCC, VMO1, CST7, RPS5
Dataset 1:
H3F3B, BIRC3, ISG15, HLA-C
Shared:
DUSP2, JUNB, GADD45B, HIST1H2AC, MYC, NFKBIA, BIRC3, BTG1, GZMK, CD83, PABPC1, APOBEC3G, TMEM66, H3F3B, EIF1, PTMA, UBC, HLA-C, NDUFC2, RPS19, GPR183, MALAT1, RPS5, RPL18, HLA-A, RPL19, RPS27, SRGN, RPL3, RPL27A
Dataset 2
HLA-C, ISG15, BIRC3, H3F3B
Dataset 1:
GAPDH, RPL12, FTL, ISG15, FCER1G, RSAD2, TYMP
Shared:
GZMH, FGFBP2, CCL5, CLIC3, NKG7, GZMB, CST7, GZMK, HLA-B, APOBEC3G, B2M, HLA-C, PTMA, TMSB4X, NDUFC2, RGCC, ANXA1, HLA-A, GAPDH, ACTN1, PLAC8, RPS19, MALAT1, RPL15, JTB, KLRD1, RPS3, TMEM66, RPS15A, RPL3
Dataset 2
TYMP, FCER1G, ISG15, RSAD2, RPL12, GAPDH, FTL
Dataset 1:
CCL2, H2AFZ, CD14, CTSL, RPL10A, RPS8, RPS6, TIMP1, S100A8, RPS27, RPLP0, RPL21, RPL14, RPL34, RPL7, RPL18A, ID3, RPL11, MARCKSL1, RPL31, IL1B, RPL15, RPL9, IL8, RPS3A, RPS14, NPM1, RPS4X, RPL10, PABPC1
Shared:
S100A4, LGALS3, CTSL, S100A6, GPX1, S100A11, FTL, S100A10, LGALS1, CTSB, CST3, FCER1G, ACTB, VIM, ANXA2, CD63, TYMP, TYROBP, CSTB, HLA-DRB1, CCL2, FCGR3A, ANXA1, ANXA5, SAT1, ACTN1, JTB, HLA-DRA, HLA-DPB1, H3F3B
Dataset 2
HSPB1, FAM26F, LYZ, HSPA1A, RPS14, RPL9, HIST1H2AC, HLA-A, APOBEC3A, ISG15, GBP1, RSAD2, CXCL10, HLA-C, HSP90AB1, SAT1, IDO1, CTSL, TXN, CREM, CCL2, CCL7, CCL8, APOBEC3B, APOBEC3G, TYMP, HERC6, ID3, RPL11, MARCKSL1
Dataset 1:
HSPA1A, H3F3B, CXCR4, FTL, ISG15, GBP1, RSAD2, RPL34, HLA-A, HLA-C, HLA-B, RPLP1, RPS2
Shared:
UBC, HSPA1A, GADD45G, GADD45B, HSP90AB1, HSPA8, HSPB1, H3F3B, PPBP, CREM, SAT1, BIRC3, CCNH, EIF1, NFKBIA, H2AFZ, JUNB, ID3, TMEM66, BTG1, MALAT1, RPS27, HIST1H2AC, NPM1, GBP1, CXCR4, RPS12, RPL14, RELB, CXCL10
Dataset 2
GBP1, RPLP1, HLA-C, RSAD2, HLA-B, ISG15, RPL34, HLA-A, RPS2, CXCR4, HSPA1A, H3F3B, FTL
Dataset 1:
CXCL3, IL8, FTH1, RPL9, GBP1, MARCKSL1, IL1B, H2AFZ, CD14, ISG15, RSAD2, CXCL10, HIST1H2AC, HSPA1A, FAM26F, HSPB1, SAT1, IDO1, CCL8, CST3, APOBEC3A, APOBEC3G
Shared:
IL1B, LYZ, IL8, CST3, NFKBIA, CCL3, S100A10, APOBEC3B, GPX1, ACTB, C15orf48, ANXA2, S100A6, S100A4, HLA-DPB1, CCL4, CXCL3, HLA-DRA, HLA-DRB1, S100A11, TYROBP, IFI27, JTB, HLA-DPA1, VIM, FCER1G, CD74, SRGN, ANXA1, HBA1
Dataset 2
FAM26F, CXCL10, CST3, HSPA1A, IL1B, SAT1, IDO1, ISG15, GBP1, RSAD2, HIST1H2AC, HSPB1, CCL8, APOBEC3A, APOBEC3G, MARCKSL1, RPL9, IL8, CXCL3, H2AFZ, CD14, FTH1
Dataset 1:
APOBEC3B, IL8, S100A4, MARCKSL1, RPS27A, RPL15, RPL7, RPL12, S100A9, PABPC1, S100A8, IL1B, TIMP1, RPS6, BTG1, RPLP0, RGCC, RPL13A, RPL3, ISG15, GBP1, RSAD2, CXCL10, HIST1H2AC, HSPA1A, FAM26F, HSPB1, SAT1, CTSB, IDO1
Shared:
S100A8, S100A9, CD14, GPX1, APOBEC3B, S100A6, TYROBP, LGALS1, S100A4, TYMP, S100A10, IL8, MS4A7, S100A11, FTL, NFKBIA, FTH1, MARCKSL1, APOBEC3A, FCER1G, LYZ, SRGN, SAT1, GAPDH, C15orf48, ANXA5, ACTB, CTSB, ISG15, CD63
Dataset 2
CCL2, HIST1H2AC, S100A8, IDO1, CCL8, CCL7, FAM26F, CTSB, CST3, HSPA1A, APOBEC3G, HSPB1, ISG15, GBP1, RSAD2, CXCL10, SAT1, CTSL, TXN, LGALS3, APOBEC3A, APOBEC3B, MARCKSL1, S100A9, S100A4, RPS27A, IL1B, RPL15, IL8, TIMP1
Dataset 1:
GAPDH, VIM, ACTB, S100A6, TIMP1, RGCC, ISG15, CXCL10, HLA-DPA1, CREM, CD79A
Shared:
RBM10, GZMK, LAGE3, ACAT2, NDUFC2, RPL14, CHCHD10, HSP90AB1, RPLP0, APOBEC3A, RPL12, RSAD2, RPL18A, GAPDH, CSTB, RPS3, RPS6, NPM1, RPL18, RPS15A, RPS19, TMSB4X, RPS12, HLA-A, TYMP, RPS3A, CCL5, RPL15, CD14, LGALS3
Dataset 2
CREM, HLA-DPA1, ISG15, CXCL10, CD79A, S100A6, ACTB, TIMP1, VIM, GAPDH, RGCC
Dataset 1:
TMEM66, BTG1, ISG15, RSAD2, SAT1, ANXA1, HERC6
Shared:
KLRC1, KLRD1, GNLY, APOBEC3G, NKG7, CD7, GZMB, HLA-A, PLAC8, PPBP, LAGE3, CCL5, GPR183, SRGN, HLA-B, TEX264, THRAP3, EIF2AK1, B2M, TMSB4X, CD63, HLA-C, RPL9, XCL2, RPS27A, CXCR4, RPS3, RPLP1, H3F3B, ACTB
Dataset 2
ANXA1, HERC6, ISG15, RSAD2, SAT1, TMEM66, BTG1
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total iterations: 42
Total time: 0 sec
Objective error: 59878.9
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 49910.7
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 41528.3
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 47418.4
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
INMF started, niter=30
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 1 sec
Objective error: 35967.3
INMF started, niter=30
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 1 sec
Objective error: 35967.3
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45479.1
**|
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 49910.7
completed constructor::A::173x300
time taken:4.09253
completed constructor::A::173x300
time taken:3.14566
completed constructor::A::173x300
time taken:3.31607
completed constructor::A::173x300
time taken:3.20268
completed constructor::A::173x300
time taken:3.09251
completed constructor::A::173x300
time taken:4.47727
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpsTMxTT/ctrltest_1026ec61aa139b.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmpsTMxTT/stimtest_1026ec5a3d8b79.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
A liger command record, performed at 04-17-2025 23:30:09 EDT
Call: normalize.liger(object)
Parameters:
useDatasets : "ctrl", "stim"
verbose : TRUE
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpsTMxTT/ctrltest_1026ec2c3eb810.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmpsTMxTT/stimtest_1026ec6d164b36.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
An object of class ligerDataset with 300 cells
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpsTMxTT/ctrltest_1026ec21a6e25d.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmpsTMxTT/stimtest_1026ec3fbfe7e0.h5
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpsTMxTT/ctrltest_1026ec14b94f1f.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmpsTMxTT/stimtest_1026ec23135aa9.h5
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpsTMxTT/ctrltest_1026ec34d7054a.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmpsTMxTT/stimtest_1026ec5e1310bd.h5
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpsTMxTT/ctrltest_1026ec1c6b628e.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmpsTMxTT/stimtest_1026ec62bef07b.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpsTMxTT/ctrltest_1026ec3f776cb7.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmpsTMxTT/stimtest_1026ec18d19dc7.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 1329 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• {DoubletFinder} is not installed (1): 'test_preprocessing.R:112:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_factorization.R:111:5'): UINMF ─────────────────────────────────
<Rcpp::exception/C++Error/error/condition>
Error: k must be <= m
Backtrace:
▆
1. ├─rliger::runUINMF(pbmc, k = 30, nIteration = 2, nRandomStarts = 2) at test_factorization.R:111:5
2. └─rliger:::runUINMF.liger(pbmc, k = 30, nIteration = 2, nRandomStarts = 2)
3. └─rliger:::.runUINMF.list(...)
4. └─RcppPlanc::uinmf(...)
5. └─RcppPlanc:::.uinmf_rcpp(...)
── Error ('test_factorization.R:130:5'): Optimize new parameters ───────────────
<Rcpp::exception/C++Error/error/condition>
Error: Must provide 2 V matrices
Backtrace:
▆
1. └─rliger::optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2) at test_factorization.R:130:5
2. ├─rliger::runINMF(...)
3. └─rliger:::runINMF.liger(...)
4. └─rliger:::.runINMF.list(...)
5. └─RcppPlanc::inmf(...)
6. └─RcppPlanc:::.bppinmf(...)
── Error ('test_factorization.R:180:5'): Online iNMF - in-memory ───────────────
<std::invalid_argument/C++Error/error/condition>
Error: Must provide 2 H matrices
Backtrace:
▆
1. ├─rliger::runOnlineINMF(...) at test_factorization.R:180:5
2. └─rliger:::runOnlineINMF.liger(...)
3. └─rliger:::.runOnlineINMF.list(...)
4. └─RcppPlanc::onlineINMF(...)
5. └─RcppPlanc:::.onlineINMF_withInitial(...)
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 1329 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.1.0
Check: examples
Result: ERROR
Running examples in ‘rliger-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optimizeNewLambda
> ### Title: Perform factorization for new lambda value
> ### Aliases: optimizeNewLambda
>
> ### ** Examples
>
> pbmc <- normalize(pbmc)
ℹ Normalizing datasets "ctrl"
ℹ Normalizing datasets "stim"
✔ Normalizing datasets "stim" ... done
ℹ Normalizing datasets "ctrl"
✔ Normalizing datasets "ctrl" ... done
> pbmc <- selectGenes(pbmc)
ℹ Selecting variable features for dataset "ctrl"
✔ ... 168 features selected out of 249 shared features.
ℹ Selecting variable features for dataset "stim"
✔ ... 166 features selected out of 249 shared features.
✔ Finally 173 shared variable features are selected.
> pbmc <- scaleNotCenter(pbmc)
ℹ Scaling dataset "ctrl"
✔ Scaling dataset "ctrl" ... done
ℹ Scaling dataset "stim"
✔ Scaling dataset "stim" ... done
> if (requireNamespace("RcppPlanc", quietly = TRUE)) {
+ # Only running a few iterations for fast examples
+ pbmc <- runINMF(pbmc, k = 20, nIteration = 2)
+ pbmc <- optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2)
+ }
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 43773
Error: Must provide 2 V matrices
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calcAgreement 5.388 2.878 11.712
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [292s/316s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rliger)
Package `rliger` has been updated massively since version 1.99.0, including the object structure which is not compatible with old versions.
We recommand you backup your old analysis before overwriting any existing result.
`readLiger()` is provided for reading an RDS file storing an old object and it converts the object to the up-to-date structure.
>
> test_check("rliger")
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Reading input file...
Number of nodes: 600
Number of edges: 16900
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity: 0.7596
Number of communities: 9
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Reading input file...
Number of nodes: 600
Number of edges: 16701
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity: 0.7658
Number of communities: 10
Elapsed time: 0 seconds
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Dataset 1:
NPM1, SAT1, VIM, FTH1, BTG1, ISG15, GBP1, RSAD2, HSP90AB1
Shared:
NMB, ANXA1, GPR183, NDUFC2, GAPDH, VIM, EIF1, SRGN, JUNB, S100A10, TMSB4X, PABPC1, H3F3B, SAT1, HIST1H2AC, RGCC, ANXA2, RPLP1, LYZ, RPL18, HLA-A, RPS15A, TMEM66, RSAD2, UBC, HSPA8, MALAT1, RPLP0, RPS6, RPS12
Dataset 2
RSAD2, VIM, ISG15, GBP1, HSP90AB1, SAT1, NPM1, FTH1, BTG1
Dataset 1:
CD83, VIM, CXCR4, MARCKSL1, GAPDH, FTL, ISG15, GBP1, SELL, RSAD2, CXCL10, PLAC8, SOD2, SAT1, IFI27, CCL2, CCL8, CCL3, CCL4, APOBEC3A, TYMP
Shared:
RPL23A, RPS2, CD79A, RPL18A, RPL12, RPL13A, RPL3, RPL27A, RPS23, RPL15, RPLP0, RPL10, RPL19, RPS8, RPS4X, RPS5, RPL10A, RPL11, RPS19, RPL18, RPS3A, RPL34, RPS18, PTMA, RPL7, RPS6, RPS27, RPLP1, RPL32, RPL14
Dataset 2
PLAC8, GBP1, IFI27, TYMP, ISG15, SELL, RSAD2, CXCL10, SOD2, SAT1, CCL2, CCL8, CCL3, CCL4, APOBEC3A, MARCKSL1, CXCR4, CD83, VIM, GAPDH, FTL
Dataset 1:
FCGR3A, LGALS1, RPLP0, RPL18, RPS12, RPS3A, RPL23A, S100A4, ACTB, RPL7, ISG15, GBP1, RSAD2, SAT1, CCNH
Shared:
CST7, CHRNB1, NKG7, APOBEC3G, CLIC3, CXCR4, GNLY, HLA-A, CD7, HLA-C, GZMB, SRGN, BAK1, TMSB4X, NDUFC2, HLA-B, B2M, BTG1, JTB, CCNH, FOXN3, H2AFZ, UBC, CREM, MALAT1, PTMA, ANXA1, H3F3B, VIM, RABL5
Dataset 2
CCNH, ISG15, RSAD2, SAT1, GBP1, S100A4, FCGR3A, RPS3A, RPS12, ACTB, RPL7, RPLP0, RPL23A, RPL18, LGALS1
Dataset 1:
CXCL10, GBP1, PTMA, S100A10, CD14, LGALS1, TIMP1, FAM26F, RPS3A, RPL10A, RPL3, S100A6, H2AFZ, CCL3, S100A8, GPX1, IL8, HLA-DQA1, LGALS3, ISG15, RSAD2, CD83, HSPA1A, GIMAP7, IDO1, TXN, MS4A7, IFI27, CCL2, CCL8
Shared:
FCGR3A, MS4A7, VMO1, FAM26F, GBP1, CXCL10, TYROBP, PLAC8, FCER1G, TIMP1, S100A11, FTH1, SAT1, SOD2, JUNB, TMSB4X, TYMP, HLA-C, SRGN, HLA-B, B2M, ACTB, HLA-DPA1, CST3, RPS19, APOBEC3A, MALAT1, TMEM66, S100A4, H3F3B
Dataset 2
ISG15, IFI27, MS4A7, APOBEC3A, HSPA1A, GIMAP7, CD83, RSAD2, GBP1, CXCL10, FAM26F, IDO1, TXN, CCL2, CCL8, CCL3, S100A10, S100A8, S100A6, PTMA, GPX1, IL8, H2AFZ, RPS3A, CD14, HLA-DQA1, RPL10A, TIMP1, LGALS3, LGALS1
Dataset 1:
RPL10A, H2AFZ, GAPDH, PABPC1, ISG15, GBP1, CXCL10, CD83, SAT1, EIF1, HERC6
Shared:
MIR155HG, MYC, ID3, CD83, NPM1, HLA-DQA1, HSP90AB1, CCR7, CCL3, HLA-DRB1, HSPA8, EIF1, HLA-DRA, RPLP0, RPS5, CCL4, JTB, RPL14, RPS23, RPL19, RPL10A, RPL7, RPS12, RPL18A, RPS2, PTMA, CD74, RPL23A, RPS8, RPLP1
Dataset 2
GBP1, EIF1, CD83, CXCL10, HERC6, ISG15, SAT1, H2AFZ, RPL10A, PABPC1, GAPDH
Dataset 1:
RPS8, RPS23, RPL15, RPL21, RPL7, RPL13A, MARCKSL1, RPS3A, TIMP1, RPS6, RPS3, ISG15, GBP1, RSAD2, CXCL10, HSPA1A, FAM26F, HSPB1, IDO1, CREM, CCL8, APOBEC3A, APOBEC3G, TYMP, THRAP3
Shared:
CXCL3, SERPINB2, IL8, CCL7, CCL2, CTSL, CTSB, RABL5, ANXA5, CD63, SOD2, FCER1G, FTL, CSTB, CD14, ANXA2, CCL3, FTH1, VIM, NFKBIA, LGALS1, GAPDH, ANXA1, SRGN, LGALS3, S100A6, S100A9, H3F3B, TYMP, TIMP1
Dataset 2
CCL8, THRAP3, HSPA1A, TYMP, HSPB1, CREM, APOBEC3G, ISG15, GBP1, RSAD2, CXCL10, FAM26F, IDO1, APOBEC3A, MARCKSL1, RPS8, RPL15, RPS3A, RPS23, TIMP1, RPL7, RPS6, RPS3, RPL21, RPL13A
Dataset 1:
RSAD2, ISG15, APOBEC3A, CD14, GPX1, GAPDH, MARCKSL1, RPL10, JTB, RPS3A, RPL21, RPS5, SAT1, RPS27A, RPL3, RPS8, RPL32, RPL7, RPS12, RPL15, PABPC1, RPL11, RPLP0, RPL10A, IL8, RPL19, S100A8, S100A6, DUSP2, CXCR4
Shared:
RSAD2, ISG15, APOBEC3A, CCL8, CXCL10, CCL2, CTSB, IDO1, SOD2, ANXA5, TYMP, FTL, CD63, HSPA1A, GBP1, CSTB, CTSL, IFI27, C15orf48, FAM26F, CCL7, FCER1G, LGALS3, LGALS1, FTH1, S100A11, TYROBP, ANXA2, HSPB1, TIMP1
Dataset 2
IDO1, HSPA1A, CCL4, CCL7, NFKBIA, CCL3, CXCL10, FAM26F, IFI27, RPS19, HERC6, ISG15, RSAD2, HSPB1, SAT1, CCL2, CCL8, APOBEC3A, RPL11, MARCKSL1, RPS8, S100A8, S100A6, RPS27A, DUSP2, CXCR4, PTMA, RPL32, RPL15, RPL14
Dataset 1:
BIRC3, S100A6, FTH1, CCL8, ID3, HLA-DPB1, GAPDH, CD79A, FTL, ISG15, GBP1, SELL, RSAD2, CXCL10, PLAC8, HSP90AB1, GIMAP7, SAT1, CREM, HSPA8, IFI27, CCL2, CCR7, H3F3B, APOBEC3A, TYMP, HERC6
Shared:
TMEM66, RPL13, RPL31, LTB, RPS18, RPL34, RPL32, RPS14, SELL, RPL21, RPS6, RPS15A, RPS27A, RPS12, RPL7, RPL3, RPS4X, RPS3, RPS3A, RPL9, RPL10, RPL11, RPL13A, RPS19, RPL10A, PABPC1, RPS23, RPS8, RPL27A, RPS2
Dataset 2
GIMAP7, PLAC8, CCR7, IFI27, H3F3B, SELL, GBP1, ISG15, RSAD2, CXCL10, HSP90AB1, SAT1, CREM, HSPA8, CCL2, CCL8, APOBEC3A, TYMP, HERC6, ID3, S100A6, HLA-DPB1, FTH1, BIRC3, GAPDH, CD79A, FTL
Dataset 1:
TEX264, FTH1, VIM, CCNH, UBC, RGCC, ISG15, GBP1, RSAD2, CXCL10, PLAC8, CD74, SAT1, CD79A
Shared:
GIMAP7, RGCC, ACAT2, BTG1, THRAP3, RELB, LTB, H2AFZ, EIF2AK1, CXCR4, HERC6, BIRC3, SELL, HSPA8, GPR183, CCR7, BAK1, HIST1H2AC, CHCHD10, EIF1, HSPB1, RPS27, JTB, MALAT1, H3F3B, PTMA, TMEM66, HSP90AB1, ANXA1, HLA-B
Dataset 2
GBP1, RSAD2, RGCC, UBC, ISG15, CXCL10, PLAC8, CD74, SAT1, CD79A, TEX264, VIM, FTH1, CCNH
Dataset 1:
CD14, S100A8, IFI27, RPL31, RPL27A, RPL21, RPL7, GBP1, MARCKSL1, RPS8, S100A6, S100A4, RPS27A, IL1B, PTMA, RPL15, RPL14, GPX1, IL8, CXCL3, H2AFZ, RPL34, RPS3A, RPS23, RPL10A, RPS4X, RPS6, RPS3, GAPDH, RGCC
Shared:
MARCKSL1, TIMP1, C15orf48, SOD2, FTH1, CD63, ANXA5, CSTB, SRGN, GAPDH, FTL, TYROBP, FCER1G, S100A11, EIF1, IL8, LGALS1, TYMP, B2M, LGALS3, ANXA2, CTSB, VIM, TXN, S100A10, ACTB, CCL2, NFKBIA, LYZ, HLA-B
Dataset 2
TXN, CST3, IDO1, APOBEC3A, MARCKSL1, PLAC8, S100A6, S100A4, HERC6, RPL19, RPS3, ISG15, GBP1, SELL, RSAD2, CXCL10, HIST1H2AC, HLA-C, HSPA1A, FAM26F, HSPB1, SAT1, CTSL, BIRC3, IFI27, CCL2, CCL7, CCL8, CCR7, APOBEC3B
Dataset 1:
IDO1, CST7, VMO1, IL8, SAT1, RPS5, TYMP, LAGE3, CXCR4, TIMP1, RGCC, RPL3, ISG15, GBP1, S100A4, SELL, RSAD2, CXCL10, HSPA1A, HSP90AB1, FAM26F, HSPB1, CTSB, ANXA1, HSPA8, IFI27, CCL2, H3F3B, APOBEC3A, APOBEC3B
Shared:
HLA-DPA1, HLA-DPB1, HLA-DRA, CD74, HLA-DRB1, TXN, HLA-DQA1, IDO1, CST3, CCR7, CD83, ANXA2, GPR183, MARCKSL1, ACTB, BIRC3, LYZ, CST7, TMSB4X, C15orf48, S100A10, LGALS1, B2M, GPX1, CD79A, NFKBIA, H2AFZ, RELB, ISG15, HSPA1A
Dataset 2
CXCL10, HSPA1A, ISG15, FAM26F, HSPB1, HERC6, GBP1, S100A4, APOBEC3G, RSAD2, HSP90AB1, HSPA8, SELL, SAT1, CTSB, IDO1, ANXA1, IFI27, CCL2, H3F3B, APOBEC3A, APOBEC3B, TYMP, CXCR4, IL8, TIMP1, RGCC, VMO1, CST7, RPS5
Dataset 1:
H3F3B, BIRC3, ISG15, HLA-C
Shared:
DUSP2, JUNB, GADD45B, HIST1H2AC, MYC, NFKBIA, BIRC3, BTG1, GZMK, CD83, PABPC1, APOBEC3G, TMEM66, H3F3B, EIF1, PTMA, UBC, HLA-C, NDUFC2, RPS19, GPR183, MALAT1, RPS5, RPL18, HLA-A, RPL19, RPS27, SRGN, RPL3, RPL27A
Dataset 2
HLA-C, ISG15, BIRC3, H3F3B
Dataset 1:
GAPDH, RPL12, FTL, ISG15, FCER1G, RSAD2, TYMP
Shared:
GZMH, FGFBP2, CCL5, CLIC3, NKG7, GZMB, CST7, GZMK, HLA-B, APOBEC3G, B2M, HLA-C, PTMA, TMSB4X, NDUFC2, RGCC, ANXA1, HLA-A, GAPDH, ACTN1, PLAC8, RPS19, MALAT1, RPL15, JTB, KLRD1, RPS3, TMEM66, RPS15A, RPL3
Dataset 2
TYMP, FCER1G, ISG15, RSAD2, RPL12, GAPDH, FTL
Dataset 1:
CCL2, H2AFZ, CD14, CTSL, RPL10A, RPS8, RPS6, TIMP1, S100A8, RPS27, RPLP0, RPL21, RPL14, RPL34, RPL7, RPL18A, ID3, RPL11, MARCKSL1, RPL31, IL1B, RPL15, RPL9, IL8, RPS3A, RPS14, NPM1, RPS4X, RPL10, PABPC1
Shared:
S100A4, LGALS3, CTSL, S100A6, GPX1, S100A11, FTL, S100A10, LGALS1, CTSB, CST3, FCER1G, ACTB, VIM, ANXA2, CD63, TYMP, TYROBP, CSTB, HLA-DRB1, CCL2, FCGR3A, ANXA1, ANXA5, SAT1, ACTN1, JTB, HLA-DRA, HLA-DPB1, H3F3B
Dataset 2
HSPB1, FAM26F, LYZ, HSPA1A, RPS14, RPL9, HIST1H2AC, HLA-A, APOBEC3A, ISG15, GBP1, RSAD2, CXCL10, HLA-C, HSP90AB1, SAT1, IDO1, CTSL, TXN, CREM, CCL2, CCL7, CCL8, APOBEC3B, APOBEC3G, TYMP, HERC6, ID3, RPL11, MARCKSL1
Dataset 1:
HSPA1A, H3F3B, CXCR4, FTL, ISG15, GBP1, RSAD2, RPL34, HLA-A, HLA-C, HLA-B, RPLP1, RPS2
Shared:
UBC, HSPA1A, GADD45G, GADD45B, HSP90AB1, HSPA8, HSPB1, H3F3B, PPBP, CREM, SAT1, BIRC3, CCNH, EIF1, NFKBIA, H2AFZ, JUNB, ID3, TMEM66, BTG1, MALAT1, RPS27, HIST1H2AC, NPM1, GBP1, CXCR4, RPS12, RPL14, RELB, CXCL10
Dataset 2
GBP1, RPLP1, HLA-C, RSAD2, HLA-B, ISG15, RPL34, HLA-A, RPS2, CXCR4, HSPA1A, H3F3B, FTL
Dataset 1:
CXCL3, IL8, FTH1, RPL9, GBP1, MARCKSL1, IL1B, H2AFZ, CD14, ISG15, RSAD2, CXCL10, HIST1H2AC, HSPA1A, FAM26F, HSPB1, SAT1, IDO1, CCL8, CST3, APOBEC3A, APOBEC3G
Shared:
IL1B, LYZ, IL8, CST3, NFKBIA, CCL3, S100A10, APOBEC3B, GPX1, ACTB, C15orf48, ANXA2, S100A6, S100A4, HLA-DPB1, CCL4, CXCL3, HLA-DRA, HLA-DRB1, S100A11, TYROBP, IFI27, JTB, HLA-DPA1, VIM, FCER1G, CD74, SRGN, ANXA1, HBA1
Dataset 2
FAM26F, CXCL10, CST3, HSPA1A, IL1B, SAT1, IDO1, ISG15, GBP1, RSAD2, HIST1H2AC, HSPB1, CCL8, APOBEC3A, APOBEC3G, MARCKSL1, RPL9, IL8, CXCL3, H2AFZ, CD14, FTH1
Dataset 1:
APOBEC3B, IL8, S100A4, MARCKSL1, RPS27A, RPL15, RPL7, RPL12, S100A9, PABPC1, S100A8, IL1B, TIMP1, RPS6, BTG1, RPLP0, RGCC, RPL13A, RPL3, ISG15, GBP1, RSAD2, CXCL10, HIST1H2AC, HSPA1A, FAM26F, HSPB1, SAT1, CTSB, IDO1
Shared:
S100A8, S100A9, CD14, GPX1, APOBEC3B, S100A6, TYROBP, LGALS1, S100A4, TYMP, S100A10, IL8, MS4A7, S100A11, FTL, NFKBIA, FTH1, MARCKSL1, APOBEC3A, FCER1G, LYZ, SRGN, SAT1, GAPDH, C15orf48, ANXA5, ACTB, CTSB, ISG15, CD63
Dataset 2
CCL2, HIST1H2AC, S100A8, IDO1, CCL8, CCL7, FAM26F, CTSB, CST3, HSPA1A, APOBEC3G, HSPB1, ISG15, GBP1, RSAD2, CXCL10, SAT1, CTSL, TXN, LGALS3, APOBEC3A, APOBEC3B, MARCKSL1, S100A9, S100A4, RPS27A, IL1B, RPL15, IL8, TIMP1
Dataset 1:
GAPDH, VIM, ACTB, S100A6, TIMP1, RGCC, ISG15, CXCL10, HLA-DPA1, CREM, CD79A
Shared:
RBM10, GZMK, LAGE3, ACAT2, NDUFC2, RPL14, CHCHD10, HSP90AB1, RPLP0, APOBEC3A, RPL12, RSAD2, RPL18A, GAPDH, CSTB, RPS3, RPS6, NPM1, RPL18, RPS15A, RPS19, TMSB4X, RPS12, HLA-A, TYMP, RPS3A, CCL5, RPL15, CD14, LGALS3
Dataset 2
CREM, HLA-DPA1, ISG15, CXCL10, CD79A, S100A6, ACTB, TIMP1, VIM, GAPDH, RGCC
Dataset 1:
TMEM66, BTG1, ISG15, RSAD2, SAT1, ANXA1, HERC6
Shared:
KLRC1, KLRD1, GNLY, APOBEC3G, NKG7, CD7, GZMB, HLA-A, PLAC8, PPBP, LAGE3, CCL5, GPR183, SRGN, HLA-B, TEX264, THRAP3, EIF2AK1, B2M, TMSB4X, CD63, HLA-C, RPL9, XCL2, RPS27A, CXCR4, RPS3, RPLP1, H3F3B, ACTB
Dataset 2
ANXA1, HERC6, ISG15, RSAD2, SAT1, TMEM66, BTG1
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total iterations: 42
Total time: 0 sec
Objective error: 59878.9
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 49910.7
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 41528.3
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 47418.4
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
INMF started, niter=30
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 35967.3
INMF started, niter=30
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 35967.3
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45479.1
**|
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 49910.7
completed constructor::A::173x300
time taken:4.62086
completed constructor::A::173x300
time taken:4.43021
completed constructor::A::173x300
time taken:4.60853
completed constructor::A::173x300
time taken:4.52858
completed constructor::A::173x300
time taken:4.63708
completed constructor::A::173x300
time taken:4.73855
Working ctrl H5 file path: /tmp/RtmpUA4XzR/ctrltest_e1c97478cf903.h5
Working stim H5 file path: /tmp/RtmpUA4XzR/stimtest_e1c975bc1f515.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
A liger command record, performed at 04-18-2025 11:44:48 EDT
Call: normalize.liger(object)
Parameters:
useDatasets : "ctrl", "stim"
verbose : TRUE
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
Working ctrl H5 file path: /tmp/RtmpUA4XzR/ctrltest_e1c971378955e.h5
Working stim H5 file path: /tmp/RtmpUA4XzR/stimtest_e1c972d70e8c.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
An object of class ligerDataset with 300 cells
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Working ctrl H5 file path: /tmp/RtmpUA4XzR/ctrltest_e1c9740045d2.h5
Working stim H5 file path: /tmp/RtmpUA4XzR/stimtest_e1c97701922f7.h5
Working ctrl H5 file path: /tmp/RtmpUA4XzR/ctrltest_e1c977a3e2f33.h5
Working stim H5 file path: /tmp/RtmpUA4XzR/stimtest_e1c97311f2422.h5
Working ctrl H5 file path: /tmp/RtmpUA4XzR/ctrltest_e1c971babfc8d.h5
Working stim H5 file path: /tmp/RtmpUA4XzR/stimtest_e1c97ffdc3aa.h5
Working ctrl H5 file path: /tmp/RtmpUA4XzR/ctrltest_e1c975e434f3.h5
Working stim H5 file path: /tmp/RtmpUA4XzR/stimtest_e1c976c16706d.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Working ctrl H5 file path: /tmp/RtmpUA4XzR/ctrltest_e1c972ece34ff.h5
Working stim H5 file path: /tmp/RtmpUA4XzR/stimtest_e1c97551cabb.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 1329 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• {DoubletFinder} is not installed (1): 'test_preprocessing.R:112:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_factorization.R:111:5'): UINMF ─────────────────────────────────
<Rcpp::exception/C++Error/error/condition>
Error: k must be <= m
Backtrace:
▆
1. ├─rliger::runUINMF(pbmc, k = 30, nIteration = 2, nRandomStarts = 2) at test_factorization.R:111:5
2. └─rliger:::runUINMF.liger(pbmc, k = 30, nIteration = 2, nRandomStarts = 2)
3. └─rliger:::.runUINMF.list(...)
4. └─RcppPlanc::uinmf(...)
5. └─RcppPlanc:::.uinmf_rcpp(...)
── Error ('test_factorization.R:130:5'): Optimize new parameters ───────────────
<Rcpp::exception/C++Error/error/condition>
Error: Must provide 2 V matrices
Backtrace:
▆
1. └─rliger::optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2) at test_factorization.R:130:5
2. ├─rliger::runINMF(...)
3. └─rliger:::runINMF.liger(...)
4. └─rliger:::.runINMF.list(...)
5. └─RcppPlanc::inmf(...)
6. └─RcppPlanc:::.bppinmf(...)
── Error ('test_factorization.R:180:5'): Online iNMF - in-memory ───────────────
<std::invalid_argument/C++Error/error/condition>
Error: Must provide 2 H matrices
Backtrace:
▆
1. ├─rliger::runOnlineINMF(...) at test_factorization.R:180:5
2. └─rliger:::runOnlineINMF.liger(...)
3. └─rliger:::.runOnlineINMF.list(...)
4. └─RcppPlanc::onlineINMF(...)
5. └─RcppPlanc:::.onlineINMF_withInitial(...)
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 1329 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.0
Check: examples
Result: ERROR
Running examples in 'rliger-Ex.R' failed
The error most likely occurred in:
> ### Name: optimizeNewLambda
> ### Title: Perform factorization for new lambda value
> ### Aliases: optimizeNewLambda
>
> ### ** Examples
>
> pbmc <- normalize(pbmc)
ℹ Normalizing datasets "ctrl"
ℹ Normalizing datasets "stim"
✔ Normalizing datasets "stim" ... done
ℹ Normalizing datasets "ctrl"
✔ Normalizing datasets "ctrl" ... done
> pbmc <- selectGenes(pbmc)
ℹ Selecting variable features for dataset "ctrl"
✔ ... 168 features selected out of 249 shared features.
ℹ Selecting variable features for dataset "stim"
✔ ... 166 features selected out of 249 shared features.
✔ Finally 173 shared variable features are selected.
> pbmc <- scaleNotCenter(pbmc)
ℹ Scaling dataset "ctrl"
✔ Scaling dataset "ctrl" ... done
ℹ Scaling dataset "stim"
✔ Scaling dataset "stim" ... done
> if (requireNamespace("RcppPlanc", quietly = TRUE)) {
+ # Only running a few iterations for fast examples
+ pbmc <- runINMF(pbmc, k = 20, nIteration = 2)
+ pbmc <- optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2)
+ }
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 43773
Error: Must provide 2 V matrices
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 2.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [14m]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(rliger)
Package `rliger` has been updated massively since version 1.99.0, including the object structure which is not compatible with old versions.
We recommand you backup your old analysis before overwriting any existing result.
`readLiger()` is provided for reading an RDS file storing an old object and it converts the object to the up-to-date structure.
>
> test_check("rliger")
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Reading input file...
Number of nodes: 600
Number of edges: 16900
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity: 0.7596
Number of communities: 9
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Reading input file...
Number of nodes: 600
Number of edges: 16701
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity: 0.7658
Number of communities: 10
Elapsed time: 0 seconds
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Dataset 1:
NPM1, SAT1, VIM, FTH1, BTG1, ISG15, GBP1, RSAD2, HSP90AB1
Shared:
NMB, ANXA1, GPR183, NDUFC2, GAPDH, VIM, EIF1, SRGN, JUNB, S100A10, TMSB4X, PABPC1, H3F3B, SAT1, HIST1H2AC, RGCC, ANXA2, RPLP1, LYZ, RPL18, HLA-A, RPS15A, TMEM66, RSAD2, UBC, HSPA8, MALAT1, RPLP0, RPS6, RPS12
Dataset 2
RSAD2, VIM, ISG15, GBP1, HSP90AB1, SAT1, NPM1, FTH1, BTG1
Dataset 1:
CD83, VIM, CXCR4, MARCKSL1, GAPDH, FTL, ISG15, GBP1, SELL, RSAD2, CXCL10, PLAC8, SOD2, SAT1, IFI27, CCL2, CCL8, CCL3, CCL4, APOBEC3A, TYMP
Shared:
RPL23A, RPS2, CD79A, RPL18A, RPL12, RPL13A, RPL3, RPL27A, RPS23, RPL15, RPLP0, RPL10, RPL19, RPS8, RPS4X, RPS5, RPL10A, RPL11, RPS19, RPL18, RPS3A, RPL34, RPS18, PTMA, RPL7, RPS6, RPS27, RPLP1, RPL32, RPL14
Dataset 2
PLAC8, GBP1, IFI27, TYMP, ISG15, SELL, RSAD2, CXCL10, SOD2, SAT1, CCL2, CCL8, CCL3, CCL4, APOBEC3A, MARCKSL1, CXCR4, CD83, VIM, GAPDH, FTL
Dataset 1:
FCGR3A, LGALS1, RPLP0, RPL18, RPS12, RPS3A, RPL23A, S100A4, ACTB, RPL7, ISG15, GBP1, RSAD2, SAT1, CCNH
Shared:
CST7, CHRNB1, NKG7, APOBEC3G, CLIC3, CXCR4, GNLY, HLA-A, CD7, HLA-C, GZMB, SRGN, BAK1, TMSB4X, NDUFC2, HLA-B, B2M, BTG1, JTB, CCNH, FOXN3, H2AFZ, UBC, CREM, MALAT1, PTMA, ANXA1, H3F3B, VIM, RABL5
Dataset 2
CCNH, ISG15, RSAD2, SAT1, GBP1, S100A4, FCGR3A, RPS3A, RPS12, ACTB, RPL7, RPLP0, RPL23A, RPL18, LGALS1
Dataset 1:
CXCL10, GBP1, PTMA, S100A10, CD14, LGALS1, TIMP1, FAM26F, RPS3A, RPL10A, RPL3, S100A6, H2AFZ, CCL3, S100A8, GPX1, IL8, HLA-DQA1, LGALS3, ISG15, RSAD2, CD83, HSPA1A, GIMAP7, IDO1, TXN, MS4A7, IFI27, CCL2, CCL8
Shared:
FCGR3A, MS4A7, VMO1, FAM26F, GBP1, CXCL10, TYROBP, PLAC8, FCER1G, TIMP1, S100A11, FTH1, SAT1, SOD2, JUNB, TMSB4X, TYMP, HLA-C, SRGN, HLA-B, B2M, ACTB, HLA-DPA1, CST3, RPS19, APOBEC3A, MALAT1, TMEM66, S100A4, H3F3B
Dataset 2
ISG15, IFI27, MS4A7, APOBEC3A, HSPA1A, GIMAP7, CD83, RSAD2, GBP1, CXCL10, FAM26F, IDO1, TXN, CCL2, CCL8, CCL3, S100A10, S100A8, S100A6, PTMA, GPX1, IL8, H2AFZ, RPS3A, CD14, HLA-DQA1, RPL10A, TIMP1, LGALS3, LGALS1
Dataset 1:
RPL10A, H2AFZ, GAPDH, PABPC1, ISG15, GBP1, CXCL10, CD83, SAT1, EIF1, HERC6
Shared:
MIR155HG, MYC, ID3, CD83, NPM1, HLA-DQA1, HSP90AB1, CCR7, CCL3, HLA-DRB1, HSPA8, EIF1, HLA-DRA, RPLP0, RPS5, CCL4, JTB, RPL14, RPS23, RPL19, RPL10A, RPL7, RPS12, RPL18A, RPS2, PTMA, CD74, RPL23A, RPS8, RPLP1
Dataset 2
GBP1, EIF1, CD83, CXCL10, HERC6, ISG15, SAT1, H2AFZ, RPL10A, PABPC1, GAPDH
Dataset 1:
RPS8, RPS23, RPL15, RPL21, RPL7, RPL13A, MARCKSL1, RPS3A, TIMP1, RPS6, RPS3, ISG15, GBP1, RSAD2, CXCL10, HSPA1A, FAM26F, HSPB1, IDO1, CREM, CCL8, APOBEC3A, APOBEC3G, TYMP, THRAP3
Shared:
CXCL3, SERPINB2, IL8, CCL7, CCL2, CTSL, CTSB, RABL5, ANXA5, CD63, SOD2, FCER1G, FTL, CSTB, CD14, ANXA2, CCL3, FTH1, VIM, NFKBIA, LGALS1, GAPDH, ANXA1, SRGN, LGALS3, S100A6, S100A9, H3F3B, TYMP, TIMP1
Dataset 2
CCL8, THRAP3, HSPA1A, TYMP, HSPB1, CREM, APOBEC3G, ISG15, GBP1, RSAD2, CXCL10, FAM26F, IDO1, APOBEC3A, MARCKSL1, RPS8, RPL15, RPS3A, RPS23, TIMP1, RPL7, RPS6, RPS3, RPL21, RPL13A
Dataset 1:
RSAD2, ISG15, APOBEC3A, CD14, GPX1, GAPDH, MARCKSL1, RPL10, JTB, RPS3A, RPL21, RPS5, SAT1, RPS27A, RPL3, RPS8, RPL32, RPL7, RPS12, RPL15, PABPC1, RPL11, RPLP0, RPL10A, IL8, RPL19, S100A8, S100A6, DUSP2, CXCR4
Shared:
RSAD2, ISG15, APOBEC3A, CCL8, CXCL10, CCL2, CTSB, IDO1, SOD2, ANXA5, TYMP, FTL, CD63, HSPA1A, GBP1, CSTB, CTSL, IFI27, C15orf48, FAM26F, CCL7, FCER1G, LGALS3, LGALS1, FTH1, S100A11, TYROBP, ANXA2, HSPB1, TIMP1
Dataset 2
IDO1, HSPA1A, CCL4, CCL7, NFKBIA, CCL3, CXCL10, FAM26F, IFI27, RPS19, HERC6, ISG15, RSAD2, HSPB1, SAT1, CCL2, CCL8, APOBEC3A, RPL11, MARCKSL1, RPS8, S100A8, S100A6, RPS27A, DUSP2, CXCR4, PTMA, RPL32, RPL15, RPL14
Dataset 1:
BIRC3, S100A6, FTH1, CCL8, ID3, HLA-DPB1, GAPDH, CD79A, FTL, ISG15, GBP1, SELL, RSAD2, CXCL10, PLAC8, HSP90AB1, GIMAP7, SAT1, CREM, HSPA8, IFI27, CCL2, CCR7, H3F3B, APOBEC3A, TYMP, HERC6
Shared:
TMEM66, RPL13, RPL31, LTB, RPS18, RPL34, RPL32, RPS14, SELL, RPL21, RPS6, RPS15A, RPS27A, RPS12, RPL7, RPL3, RPS4X, RPS3, RPS3A, RPL9, RPL10, RPL11, RPL13A, RPS19, RPL10A, PABPC1, RPS23, RPS8, RPL27A, RPS2
Dataset 2
GIMAP7, PLAC8, CCR7, IFI27, H3F3B, SELL, GBP1, ISG15, RSAD2, CXCL10, HSP90AB1, SAT1, CREM, HSPA8, CCL2, CCL8, APOBEC3A, TYMP, HERC6, ID3, S100A6, HLA-DPB1, FTH1, BIRC3, GAPDH, CD79A, FTL
Dataset 1:
TEX264, FTH1, VIM, CCNH, UBC, RGCC, ISG15, GBP1, RSAD2, CXCL10, PLAC8, CD74, SAT1, CD79A
Shared:
GIMAP7, RGCC, ACAT2, BTG1, THRAP3, RELB, LTB, H2AFZ, EIF2AK1, CXCR4, HERC6, BIRC3, SELL, HSPA8, GPR183, CCR7, BAK1, HIST1H2AC, CHCHD10, EIF1, HSPB1, RPS27, JTB, MALAT1, H3F3B, PTMA, TMEM66, HSP90AB1, ANXA1, HLA-B
Dataset 2
GBP1, RSAD2, RGCC, UBC, ISG15, CXCL10, PLAC8, CD74, SAT1, CD79A, TEX264, VIM, FTH1, CCNH
Dataset 1:
CD14, S100A8, IFI27, RPL31, RPL27A, RPL21, RPL7, GBP1, MARCKSL1, RPS8, S100A6, S100A4, RPS27A, IL1B, PTMA, RPL15, RPL14, GPX1, IL8, CXCL3, H2AFZ, RPL34, RPS3A, RPS23, RPL10A, RPS4X, RPS6, RPS3, GAPDH, RGCC
Shared:
MARCKSL1, TIMP1, C15orf48, SOD2, FTH1, CD63, ANXA5, CSTB, SRGN, GAPDH, FTL, TYROBP, FCER1G, S100A11, EIF1, IL8, LGALS1, TYMP, B2M, LGALS3, ANXA2, CTSB, VIM, TXN, S100A10, ACTB, CCL2, NFKBIA, LYZ, HLA-B
Dataset 2
TXN, CST3, IDO1, APOBEC3A, MARCKSL1, PLAC8, S100A6, S100A4, HERC6, RPL19, RPS3, ISG15, GBP1, SELL, RSAD2, CXCL10, HIST1H2AC, HLA-C, HSPA1A, FAM26F, HSPB1, SAT1, CTSL, BIRC3, IFI27, CCL2, CCL7, CCL8, CCR7, APOBEC3B
Dataset 1:
IDO1, CST7, VMO1, IL8, SAT1, RPS5, TYMP, LAGE3, CXCR4, TIMP1, RGCC, RPL3, ISG15, GBP1, S100A4, SELL, RSAD2, CXCL10, HSPA1A, HSP90AB1, FAM26F, HSPB1, CTSB, ANXA1, HSPA8, IFI27, CCL2, H3F3B, APOBEC3A, APOBEC3B
Shared:
HLA-DPA1, HLA-DPB1, HLA-DRA, CD74, HLA-DRB1, TXN, HLA-DQA1, IDO1, CST3, CCR7, CD83, ANXA2, GPR183, MARCKSL1, ACTB, BIRC3, LYZ, CST7, TMSB4X, C15orf48, S100A10, LGALS1, B2M, GPX1, CD79A, NFKBIA, H2AFZ, RELB, ISG15, HSPA1A
Dataset 2
CXCL10, HSPA1A, ISG15, FAM26F, HSPB1, HERC6, GBP1, S100A4, APOBEC3G, RSAD2, HSP90AB1, HSPA8, SELL, SAT1, CTSB, IDO1, ANXA1, IFI27, CCL2, H3F3B, APOBEC3A, APOBEC3B, TYMP, CXCR4, IL8, TIMP1, RGCC, VMO1, CST7, RPS5
Dataset 1:
H3F3B, BIRC3, ISG15, HLA-C
Shared:
DUSP2, JUNB, GADD45B, HIST1H2AC, MYC, NFKBIA, BIRC3, BTG1, GZMK, CD83, PABPC1, APOBEC3G, TMEM66, H3F3B, EIF1, PTMA, UBC, HLA-C, NDUFC2, RPS19, GPR183, MALAT1, RPS5, RPL18, HLA-A, RPL19, RPS27, SRGN, RPL3, RPL27A
Dataset 2
HLA-C, ISG15, BIRC3, H3F3B
Dataset 1:
GAPDH, RPL12, FTL, ISG15, FCER1G, RSAD2, TYMP
Shared:
GZMH, FGFBP2, CCL5, CLIC3, NKG7, GZMB, CST7, GZMK, HLA-B, APOBEC3G, B2M, HLA-C, PTMA, TMSB4X, NDUFC2, RGCC, ANXA1, HLA-A, GAPDH, ACTN1, PLAC8, RPS19, MALAT1, RPL15, JTB, KLRD1, RPS3, TMEM66, RPS15A, RPL3
Dataset 2
TYMP, FCER1G, ISG15, RSAD2, RPL12, GAPDH, FTL
Dataset 1:
CCL2, H2AFZ, CD14, CTSL, RPL10A, RPS8, RPS6, TIMP1, S100A8, RPS27, RPLP0, RPL21, RPL14, RPL34, RPL7, RPL18A, ID3, RPL11, MARCKSL1, RPL31, IL1B, RPL15, RPL9, IL8, RPS3A, RPS14, NPM1, RPS4X, RPL10, PABPC1
Shared:
S100A4, LGALS3, CTSL, S100A6, GPX1, S100A11, FTL, S100A10, LGALS1, CTSB, CST3, FCER1G, ACTB, VIM, ANXA2, CD63, TYMP, TYROBP, CSTB, HLA-DRB1, CCL2, FCGR3A, ANXA1, ANXA5, SAT1, ACTN1, JTB, HLA-DRA, HLA-DPB1, H3F3B
Dataset 2
HSPB1, FAM26F, LYZ, HSPA1A, RPS14, RPL9, HIST1H2AC, HLA-A, APOBEC3A, ISG15, GBP1, RSAD2, CXCL10, HLA-C, HSP90AB1, SAT1, IDO1, CTSL, TXN, CREM, CCL2, CCL7, CCL8, APOBEC3B, APOBEC3G, TYMP, HERC6, ID3, RPL11, MARCKSL1
Dataset 1:
HSPA1A, H3F3B, CXCR4, FTL, ISG15, GBP1, RSAD2, RPL34, HLA-A, HLA-C, HLA-B, RPLP1, RPS2
Shared:
UBC, HSPA1A, GADD45G, GADD45B, HSP90AB1, HSPA8, HSPB1, H3F3B, PPBP, CREM, SAT1, BIRC3, CCNH, EIF1, NFKBIA, H2AFZ, JUNB, ID3, TMEM66, BTG1, MALAT1, RPS27, HIST1H2AC, NPM1, GBP1, CXCR4, RPS12, RPL14, RELB, CXCL10
Dataset 2
GBP1, RPLP1, HLA-C, RSAD2, HLA-B, ISG15, RPL34, HLA-A, RPS2, CXCR4, HSPA1A, H3F3B, FTL
Dataset 1:
CXCL3, IL8, FTH1, RPL9, GBP1, MARCKSL1, IL1B, H2AFZ, CD14, ISG15, RSAD2, CXCL10, HIST1H2AC, HSPA1A, FAM26F, HSPB1, SAT1, IDO1, CCL8, CST3, APOBEC3A, APOBEC3G
Shared:
IL1B, LYZ, IL8, CST3, NFKBIA, CCL3, S100A10, APOBEC3B, GPX1, ACTB, C15orf48, ANXA2, S100A6, S100A4, HLA-DPB1, CCL4, CXCL3, HLA-DRA, HLA-DRB1, S100A11, TYROBP, IFI27, JTB, HLA-DPA1, VIM, FCER1G, CD74, SRGN, ANXA1, HBA1
Dataset 2
FAM26F, CXCL10, CST3, HSPA1A, IL1B, SAT1, IDO1, ISG15, GBP1, RSAD2, HIST1H2AC, HSPB1, CCL8, APOBEC3A, APOBEC3G, MARCKSL1, RPL9, IL8, CXCL3, H2AFZ, CD14, FTH1
Dataset 1:
APOBEC3B, IL8, S100A4, MARCKSL1, RPS27A, RPL15, RPL7, RPL12, S100A9, PABPC1, S100A8, IL1B, TIMP1, RPS6, BTG1, RPLP0, RGCC, RPL13A, RPL3, ISG15, GBP1, RSAD2, CXCL10, HIST1H2AC, HSPA1A, FAM26F, HSPB1, SAT1, CTSB, IDO1
Shared:
S100A8, S100A9, CD14, GPX1, APOBEC3B, S100A6, TYROBP, LGALS1, S100A4, TYMP, S100A10, IL8, MS4A7, S100A11, FTL, NFKBIA, FTH1, MARCKSL1, APOBEC3A, FCER1G, LYZ, SRGN, SAT1, GAPDH, C15orf48, ANXA5, ACTB, CTSB, ISG15, CD63
Dataset 2
CCL2, HIST1H2AC, S100A8, IDO1, CCL8, CCL7, FAM26F, CTSB, CST3, HSPA1A, APOBEC3G, HSPB1, ISG15, GBP1, RSAD2, CXCL10, SAT1, CTSL, TXN, LGALS3, APOBEC3A, APOBEC3B, MARCKSL1, S100A9, S100A4, RPS27A, IL1B, RPL15, IL8, TIMP1
Dataset 1:
GAPDH, VIM, ACTB, S100A6, TIMP1, RGCC, ISG15, CXCL10, HLA-DPA1, CREM, CD79A
Shared:
RBM10, GZMK, LAGE3, ACAT2, NDUFC2, RPL14, CHCHD10, HSP90AB1, RPLP0, APOBEC3A, RPL12, RSAD2, RPL18A, GAPDH, CSTB, RPS3, RPS6, NPM1, RPL18, RPS15A, RPS19, TMSB4X, RPS12, HLA-A, TYMP, RPS3A, CCL5, RPL15, CD14, LGALS3
Dataset 2
CREM, HLA-DPA1, ISG15, CXCL10, CD79A, S100A6, ACTB, TIMP1, VIM, GAPDH, RGCC
Dataset 1:
TMEM66, BTG1, ISG15, RSAD2, SAT1, ANXA1, HERC6
Shared:
KLRC1, KLRD1, GNLY, APOBEC3G, NKG7, CD7, GZMB, HLA-A, PLAC8, PPBP, LAGE3, CCL5, GPR183, SRGN, HLA-B, TEX264, THRAP3, EIF2AK1, B2M, TMSB4X, CD63, HLA-C, RPL9, XCL2, RPS27A, CXCR4, RPS3, RPLP1, H3F3B, ACTB
Dataset 2
ANXA1, HERC6, ISG15, RSAD2, SAT1, TMEM66, BTG1
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total iterations: 42
Total time: 0 sec
Objective error: 59878.9
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 49910.7
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 41528.3
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 47418.4
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
INMF started, niter=30
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 35967.3
INMF started, niter=30
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 35967.3
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45479.1
**|
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 49910.7
completed constructor::A::173x300
time taken:33.7158
completed constructor::A::173x300
time taken:32.0428
completed constructor::A::173x300
time taken:35.1065
completed constructor::A::173x300
time taken:26.1075
completed constructor::A::173x300
time taken:35.0407
completed constructor::A::173x300
time taken:30.8037
Working ctrl H5 file path: D:\temp\2025_04_17_01_50_00_8240\RtmpmeVxTe\ctrltest_225987c6a3c3d.h5
Working stim H5 file path: D:\temp\2025_04_17_01_50_00_8240\RtmpmeVxTe\stimtest_22598622e390f.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
A liger command record, performed at 04-17-2025 07:26:27 EDT
Call: normalize.liger(object)
Parameters:
useDatasets : "ctrl", "stim"
verbose : TRUE
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
Working ctrl H5 file path: D:\temp\2025_04_17_01_50_00_8240\RtmpmeVxTe\ctrltest_22598f044009.h5
Working stim H5 file path: D:\temp\2025_04_17_01_50_00_8240\RtmpmeVxTe\stimtest_2259828bd614e.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
An object of class ligerDataset with 300 cells
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Working ctrl H5 file path: D:\temp\2025_04_17_01_50_00_8240\RtmpmeVxTe\ctrltest_2259856977b55.h5
Working stim H5 file path: D:\temp\2025_04_17_01_50_00_8240\RtmpmeVxTe\stimtest_225984e4841de.h5
Working ctrl H5 file path: D:\temp\2025_04_17_01_50_00_8240\RtmpmeVxTe\ctrltest_225981f762963.h5
Working stim H5 file path: D:\temp\2025_04_17_01_50_00_8240\RtmpmeVxTe\stimtest_2259866e6596c.h5
Working ctrl H5 file path: D:\temp\2025_04_17_01_50_00_8240\RtmpmeVxTe\ctrltest_22598202559fb.h5
Working stim H5 file path: D:\temp\2025_04_17_01_50_00_8240\RtmpmeVxTe\stimtest_2259820ea1cb5.h5
Working ctrl H5 file path: D:\temp\2025_04_17_01_50_00_8240\RtmpmeVxTe\ctrltest_22598696e16a9.h5
Working stim H5 file path: D:\temp\2025_04_17_01_50_00_8240\RtmpmeVxTe\stimtest_225981787502c.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Working ctrl H5 file path: D:\temp\2025_04_17_01_50_00_8240\RtmpmeVxTe\ctrltest_22598744e3f04.h5
Working stim H5 file path: D:\temp\2025_04_17_01_50_00_8240\RtmpmeVxTe\stimtest_225983b602642.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 1329 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• {DoubletFinder} is not installed (1): 'test_preprocessing.R:112:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_factorization.R:111:5'): UINMF ─────────────────────────────────
<Rcpp::exception/C++Error/error/condition>
Error: k must be <= m
Backtrace:
▆
1. ├─rliger::runUINMF(pbmc, k = 30, nIteration = 2, nRandomStarts = 2) at test_factorization.R:111:5
2. └─rliger:::runUINMF.liger(pbmc, k = 30, nIteration = 2, nRandomStarts = 2)
3. └─rliger:::.runUINMF.list(...)
4. └─RcppPlanc::uinmf(...)
5. └─RcppPlanc:::.uinmf_rcpp(...)
── Error ('test_factorization.R:130:5'): Optimize new parameters ───────────────
<Rcpp::exception/C++Error/error/condition>
Error: Must provide 2 V matrices
Backtrace:
▆
1. └─rliger::optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2) at test_factorization.R:130:5
2. ├─rliger::runINMF(...)
3. └─rliger:::runINMF.liger(...)
4. └─rliger:::.runINMF.list(...)
5. └─RcppPlanc::inmf(...)
6. └─RcppPlanc:::.bppinmf(...)
── Error ('test_factorization.R:180:5'): Online iNMF - in-memory ───────────────
<std::invalid_argument/C++Error/error/condition>
Error: Must provide 2 H matrices
Backtrace:
▆
1. ├─rliger::runOnlineINMF(...) at test_factorization.R:180:5
2. └─rliger:::runOnlineINMF.liger(...)
3. └─rliger:::.runOnlineINMF.list(...)
4. └─RcppPlanc::onlineINMF(...)
5. └─RcppPlanc:::.onlineINMF_withInitial(...)
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 1329 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 2.1.0
Check: examples
Result: ERROR
Running examples in ‘rliger-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optimizeNewLambda
> ### Title: Perform factorization for new lambda value
> ### Aliases: optimizeNewLambda
>
> ### ** Examples
>
> pbmc <- normalize(pbmc)
ℹ Normalizing datasets "ctrl"
ℹ Normalizing datasets "stim"
✔ Normalizing datasets "stim" ... done
ℹ Normalizing datasets "ctrl"
✔ Normalizing datasets "ctrl" ... done
> pbmc <- selectGenes(pbmc)
ℹ Selecting variable features for dataset "ctrl"
✔ ... 168 features selected out of 249 shared features.
ℹ Selecting variable features for dataset "stim"
✔ ... 166 features selected out of 249 shared features.
✔ Finally 173 shared variable features are selected.
> pbmc <- scaleNotCenter(pbmc)
ℹ Scaling dataset "ctrl"
✔ Scaling dataset "ctrl" ... done
ℹ Scaling dataset "stim"
✔ Scaling dataset "stim" ... done
> if (requireNamespace("RcppPlanc", quietly = TRUE)) {
+ # Only running a few iterations for fast examples
+ pbmc <- runINMF(pbmc, k = 20, nIteration = 2)
+ pbmc <- optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2)
+ }
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 43773
Error: Must provide 2 V matrices
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
createLiger 5.510 0.221 6.130
calcAgreement 4.725 1.003 8.165
Flavor: r-patched-linux-x86_64
Version: 2.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [439s/413s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rliger)
Package `rliger` has been updated massively since version 1.99.0, including the object structure which is not compatible with old versions.
We recommand you backup your old analysis before overwriting any existing result.
`readLiger()` is provided for reading an RDS file storing an old object and it converts the object to the up-to-date structure.
>
> test_check("rliger")
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Reading input file...
Number of nodes: 600
Number of edges: 16900
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity: 0.7596
Number of communities: 9
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Reading input file...
Number of nodes: 600
Number of edges: 16701
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity: 0.7658
Number of communities: 10
Elapsed time: 0 seconds
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Dataset 1:
NPM1, SAT1, VIM, FTH1, BTG1, ISG15, GBP1, RSAD2, HSP90AB1
Shared:
NMB, ANXA1, GPR183, NDUFC2, GAPDH, VIM, EIF1, SRGN, JUNB, S100A10, TMSB4X, PABPC1, H3F3B, SAT1, HIST1H2AC, RGCC, ANXA2, RPLP1, LYZ, RPL18, HLA-A, RPS15A, TMEM66, RSAD2, UBC, HSPA8, MALAT1, RPLP0, RPS6, RPS12
Dataset 2
RSAD2, VIM, ISG15, GBP1, HSP90AB1, SAT1, NPM1, FTH1, BTG1
Dataset 1:
CD83, VIM, CXCR4, MARCKSL1, GAPDH, FTL, ISG15, GBP1, SELL, RSAD2, CXCL10, PLAC8, SOD2, SAT1, IFI27, CCL2, CCL8, CCL3, CCL4, APOBEC3A, TYMP
Shared:
RPL23A, RPS2, CD79A, RPL18A, RPL12, RPL13A, RPL3, RPL27A, RPS23, RPL15, RPLP0, RPL10, RPL19, RPS8, RPS4X, RPS5, RPL10A, RPL11, RPS19, RPL18, RPS3A, RPL34, RPS18, PTMA, RPL7, RPS6, RPS27, RPLP1, RPL32, RPL14
Dataset 2
PLAC8, GBP1, IFI27, TYMP, ISG15, SELL, RSAD2, CXCL10, SOD2, SAT1, CCL2, CCL8, CCL3, CCL4, APOBEC3A, MARCKSL1, CXCR4, CD83, VIM, GAPDH, FTL
Dataset 1:
FCGR3A, LGALS1, RPLP0, RPL18, RPS12, RPS3A, RPL23A, S100A4, ACTB, RPL7, ISG15, GBP1, RSAD2, SAT1, CCNH
Shared:
CST7, CHRNB1, NKG7, APOBEC3G, CLIC3, CXCR4, GNLY, HLA-A, CD7, HLA-C, GZMB, SRGN, BAK1, TMSB4X, NDUFC2, HLA-B, B2M, BTG1, JTB, CCNH, FOXN3, H2AFZ, UBC, CREM, MALAT1, PTMA, ANXA1, H3F3B, VIM, RABL5
Dataset 2
CCNH, ISG15, RSAD2, SAT1, GBP1, S100A4, FCGR3A, RPS3A, RPS12, ACTB, RPL7, RPLP0, RPL23A, RPL18, LGALS1
Dataset 1:
CXCL10, GBP1, PTMA, S100A10, CD14, LGALS1, TIMP1, FAM26F, RPS3A, RPL10A, RPL3, S100A6, H2AFZ, CCL3, S100A8, GPX1, IL8, HLA-DQA1, LGALS3, ISG15, RSAD2, CD83, HSPA1A, GIMAP7, IDO1, TXN, MS4A7, IFI27, CCL2, CCL8
Shared:
FCGR3A, MS4A7, VMO1, FAM26F, GBP1, CXCL10, TYROBP, PLAC8, FCER1G, TIMP1, S100A11, FTH1, SAT1, SOD2, JUNB, TMSB4X, TYMP, HLA-C, SRGN, HLA-B, B2M, ACTB, HLA-DPA1, CST3, RPS19, APOBEC3A, MALAT1, TMEM66, S100A4, H3F3B
Dataset 2
ISG15, IFI27, MS4A7, APOBEC3A, HSPA1A, GIMAP7, CD83, RSAD2, GBP1, CXCL10, FAM26F, IDO1, TXN, CCL2, CCL8, CCL3, S100A10, S100A8, S100A6, PTMA, GPX1, IL8, H2AFZ, RPS3A, CD14, HLA-DQA1, RPL10A, TIMP1, LGALS3, LGALS1
Dataset 1:
RPL10A, H2AFZ, GAPDH, PABPC1, ISG15, GBP1, CXCL10, CD83, SAT1, EIF1, HERC6
Shared:
MIR155HG, MYC, ID3, CD83, NPM1, HLA-DQA1, HSP90AB1, CCR7, CCL3, HLA-DRB1, HSPA8, EIF1, HLA-DRA, RPLP0, RPS5, CCL4, JTB, RPL14, RPS23, RPL19, RPL10A, RPL7, RPS12, RPL18A, RPS2, PTMA, CD74, RPL23A, RPS8, RPLP1
Dataset 2
GBP1, EIF1, CD83, CXCL10, HERC6, ISG15, SAT1, H2AFZ, RPL10A, PABPC1, GAPDH
Dataset 1:
RPS8, RPS23, RPL15, RPL21, RPL7, RPL13A, MARCKSL1, RPS3A, TIMP1, RPS6, RPS3, ISG15, GBP1, RSAD2, CXCL10, HSPA1A, FAM26F, HSPB1, IDO1, CREM, CCL8, APOBEC3A, APOBEC3G, TYMP, THRAP3
Shared:
CXCL3, SERPINB2, IL8, CCL7, CCL2, CTSL, CTSB, RABL5, ANXA5, CD63, SOD2, FCER1G, FTL, CSTB, CD14, ANXA2, CCL3, FTH1, VIM, NFKBIA, LGALS1, GAPDH, ANXA1, SRGN, LGALS3, S100A6, S100A9, H3F3B, TYMP, TIMP1
Dataset 2
CCL8, THRAP3, HSPA1A, TYMP, HSPB1, CREM, APOBEC3G, ISG15, GBP1, RSAD2, CXCL10, FAM26F, IDO1, APOBEC3A, MARCKSL1, RPS8, RPL15, RPS3A, RPS23, TIMP1, RPL7, RPS6, RPS3, RPL21, RPL13A
Dataset 1:
RSAD2, ISG15, APOBEC3A, CD14, GPX1, GAPDH, MARCKSL1, RPL10, JTB, RPS3A, RPL21, RPS5, SAT1, RPS27A, RPL3, RPS8, RPL32, RPL7, RPS12, RPL15, PABPC1, RPL11, RPLP0, RPL10A, IL8, RPL19, S100A8, S100A6, DUSP2, CXCR4
Shared:
RSAD2, ISG15, APOBEC3A, CCL8, CXCL10, CCL2, CTSB, IDO1, SOD2, ANXA5, TYMP, FTL, CD63, HSPA1A, GBP1, CSTB, CTSL, IFI27, C15orf48, FAM26F, CCL7, FCER1G, LGALS3, LGALS1, FTH1, S100A11, TYROBP, ANXA2, HSPB1, TIMP1
Dataset 2
IDO1, HSPA1A, CCL4, CCL7, NFKBIA, CCL3, CXCL10, FAM26F, IFI27, RPS19, HERC6, ISG15, RSAD2, HSPB1, SAT1, CCL2, CCL8, APOBEC3A, RPL11, MARCKSL1, RPS8, S100A8, S100A6, RPS27A, DUSP2, CXCR4, PTMA, RPL32, RPL15, RPL14
Dataset 1:
BIRC3, S100A6, FTH1, CCL8, ID3, HLA-DPB1, GAPDH, CD79A, FTL, ISG15, GBP1, SELL, RSAD2, CXCL10, PLAC8, HSP90AB1, GIMAP7, SAT1, CREM, HSPA8, IFI27, CCL2, CCR7, H3F3B, APOBEC3A, TYMP, HERC6
Shared:
TMEM66, RPL13, RPL31, LTB, RPS18, RPL34, RPL32, RPS14, SELL, RPL21, RPS6, RPS15A, RPS27A, RPS12, RPL7, RPL3, RPS4X, RPS3, RPS3A, RPL9, RPL10, RPL11, RPL13A, RPS19, RPL10A, PABPC1, RPS23, RPS8, RPL27A, RPS2
Dataset 2
GIMAP7, PLAC8, CCR7, IFI27, H3F3B, SELL, GBP1, ISG15, RSAD2, CXCL10, HSP90AB1, SAT1, CREM, HSPA8, CCL2, CCL8, APOBEC3A, TYMP, HERC6, ID3, S100A6, HLA-DPB1, FTH1, BIRC3, GAPDH, CD79A, FTL
Dataset 1:
TEX264, FTH1, VIM, CCNH, UBC, RGCC, ISG15, GBP1, RSAD2, CXCL10, PLAC8, CD74, SAT1, CD79A
Shared:
GIMAP7, RGCC, ACAT2, BTG1, THRAP3, RELB, LTB, H2AFZ, EIF2AK1, CXCR4, HERC6, BIRC3, SELL, HSPA8, GPR183, CCR7, BAK1, HIST1H2AC, CHCHD10, EIF1, HSPB1, RPS27, JTB, MALAT1, H3F3B, PTMA, TMEM66, HSP90AB1, ANXA1, HLA-B
Dataset 2
GBP1, RSAD2, RGCC, UBC, ISG15, CXCL10, PLAC8, CD74, SAT1, CD79A, TEX264, VIM, FTH1, CCNH
Dataset 1:
CD14, S100A8, IFI27, RPL31, RPL27A, RPL21, RPL7, GBP1, MARCKSL1, RPS8, S100A6, S100A4, RPS27A, IL1B, PTMA, RPL15, RPL14, GPX1, IL8, CXCL3, H2AFZ, RPL34, RPS3A, RPS23, RPL10A, RPS4X, RPS6, RPS3, GAPDH, RGCC
Shared:
MARCKSL1, TIMP1, C15orf48, SOD2, FTH1, CD63, ANXA5, CSTB, SRGN, GAPDH, FTL, TYROBP, FCER1G, S100A11, EIF1, IL8, LGALS1, TYMP, B2M, LGALS3, ANXA2, CTSB, VIM, TXN, S100A10, ACTB, CCL2, NFKBIA, LYZ, HLA-B
Dataset 2
TXN, CST3, IDO1, APOBEC3A, MARCKSL1, PLAC8, S100A6, S100A4, HERC6, RPL19, RPS3, ISG15, GBP1, SELL, RSAD2, CXCL10, HIST1H2AC, HLA-C, HSPA1A, FAM26F, HSPB1, SAT1, CTSL, BIRC3, IFI27, CCL2, CCL7, CCL8, CCR7, APOBEC3B
Dataset 1:
IDO1, CST7, VMO1, IL8, SAT1, RPS5, TYMP, LAGE3, CXCR4, TIMP1, RGCC, RPL3, ISG15, GBP1, S100A4, SELL, RSAD2, CXCL10, HSPA1A, HSP90AB1, FAM26F, HSPB1, CTSB, ANXA1, HSPA8, IFI27, CCL2, H3F3B, APOBEC3A, APOBEC3B
Shared:
HLA-DPA1, HLA-DPB1, HLA-DRA, CD74, HLA-DRB1, TXN, HLA-DQA1, IDO1, CST3, CCR7, CD83, ANXA2, GPR183, MARCKSL1, ACTB, BIRC3, LYZ, CST7, TMSB4X, C15orf48, S100A10, LGALS1, B2M, GPX1, CD79A, NFKBIA, H2AFZ, RELB, ISG15, HSPA1A
Dataset 2
CXCL10, HSPA1A, ISG15, FAM26F, HSPB1, HERC6, GBP1, S100A4, APOBEC3G, RSAD2, HSP90AB1, HSPA8, SELL, SAT1, CTSB, IDO1, ANXA1, IFI27, CCL2, H3F3B, APOBEC3A, APOBEC3B, TYMP, CXCR4, IL8, TIMP1, RGCC, VMO1, CST7, RPS5
Dataset 1:
H3F3B, BIRC3, ISG15, HLA-C
Shared:
DUSP2, JUNB, GADD45B, HIST1H2AC, MYC, NFKBIA, BIRC3, BTG1, GZMK, CD83, PABPC1, APOBEC3G, TMEM66, H3F3B, EIF1, PTMA, UBC, HLA-C, NDUFC2, RPS19, GPR183, MALAT1, RPS5, RPL18, HLA-A, RPL19, RPS27, SRGN, RPL3, RPL27A
Dataset 2
HLA-C, ISG15, BIRC3, H3F3B
Dataset 1:
GAPDH, RPL12, FTL, ISG15, FCER1G, RSAD2, TYMP
Shared:
GZMH, FGFBP2, CCL5, CLIC3, NKG7, GZMB, CST7, GZMK, HLA-B, APOBEC3G, B2M, HLA-C, PTMA, TMSB4X, NDUFC2, RGCC, ANXA1, HLA-A, GAPDH, ACTN1, PLAC8, RPS19, MALAT1, RPL15, JTB, KLRD1, RPS3, TMEM66, RPS15A, RPL3
Dataset 2
TYMP, FCER1G, ISG15, RSAD2, RPL12, GAPDH, FTL
Dataset 1:
CCL2, H2AFZ, CD14, CTSL, RPL10A, RPS8, RPS6, TIMP1, S100A8, RPS27, RPLP0, RPL21, RPL14, RPL34, RPL7, RPL18A, ID3, RPL11, MARCKSL1, RPL31, IL1B, RPL15, RPL9, IL8, RPS3A, RPS14, NPM1, RPS4X, RPL10, PABPC1
Shared:
S100A4, LGALS3, CTSL, S100A6, GPX1, S100A11, FTL, S100A10, LGALS1, CTSB, CST3, FCER1G, ACTB, VIM, ANXA2, CD63, TYMP, TYROBP, CSTB, HLA-DRB1, CCL2, FCGR3A, ANXA1, ANXA5, SAT1, ACTN1, JTB, HLA-DRA, HLA-DPB1, H3F3B
Dataset 2
HSPB1, FAM26F, LYZ, HSPA1A, RPS14, RPL9, HIST1H2AC, HLA-A, APOBEC3A, ISG15, GBP1, RSAD2, CXCL10, HLA-C, HSP90AB1, SAT1, IDO1, CTSL, TXN, CREM, CCL2, CCL7, CCL8, APOBEC3B, APOBEC3G, TYMP, HERC6, ID3, RPL11, MARCKSL1
Dataset 1:
HSPA1A, H3F3B, CXCR4, FTL, ISG15, GBP1, RSAD2, RPL34, HLA-A, HLA-C, HLA-B, RPLP1, RPS2
Shared:
UBC, HSPA1A, GADD45G, GADD45B, HSP90AB1, HSPA8, HSPB1, H3F3B, PPBP, CREM, SAT1, BIRC3, CCNH, EIF1, NFKBIA, H2AFZ, JUNB, ID3, TMEM66, BTG1, MALAT1, RPS27, HIST1H2AC, NPM1, GBP1, CXCR4, RPS12, RPL14, RELB, CXCL10
Dataset 2
GBP1, RPLP1, HLA-C, RSAD2, HLA-B, ISG15, RPL34, HLA-A, RPS2, CXCR4, HSPA1A, H3F3B, FTL
Dataset 1:
CXCL3, IL8, FTH1, RPL9, GBP1, MARCKSL1, IL1B, H2AFZ, CD14, ISG15, RSAD2, CXCL10, HIST1H2AC, HSPA1A, FAM26F, HSPB1, SAT1, IDO1, CCL8, CST3, APOBEC3A, APOBEC3G
Shared:
IL1B, LYZ, IL8, CST3, NFKBIA, CCL3, S100A10, APOBEC3B, GPX1, ACTB, C15orf48, ANXA2, S100A6, S100A4, HLA-DPB1, CCL4, CXCL3, HLA-DRA, HLA-DRB1, S100A11, TYROBP, IFI27, JTB, HLA-DPA1, VIM, FCER1G, CD74, SRGN, ANXA1, HBA1
Dataset 2
FAM26F, CXCL10, CST3, HSPA1A, IL1B, SAT1, IDO1, ISG15, GBP1, RSAD2, HIST1H2AC, HSPB1, CCL8, APOBEC3A, APOBEC3G, MARCKSL1, RPL9, IL8, CXCL3, H2AFZ, CD14, FTH1
Dataset 1:
APOBEC3B, IL8, S100A4, MARCKSL1, RPS27A, RPL15, RPL7, RPL12, S100A9, PABPC1, S100A8, IL1B, TIMP1, RPS6, BTG1, RPLP0, RGCC, RPL13A, RPL3, ISG15, GBP1, RSAD2, CXCL10, HIST1H2AC, HSPA1A, FAM26F, HSPB1, SAT1, CTSB, IDO1
Shared:
S100A8, S100A9, CD14, GPX1, APOBEC3B, S100A6, TYROBP, LGALS1, S100A4, TYMP, S100A10, IL8, MS4A7, S100A11, FTL, NFKBIA, FTH1, MARCKSL1, APOBEC3A, FCER1G, LYZ, SRGN, SAT1, GAPDH, C15orf48, ANXA5, ACTB, CTSB, ISG15, CD63
Dataset 2
CCL2, HIST1H2AC, S100A8, IDO1, CCL8, CCL7, FAM26F, CTSB, CST3, HSPA1A, APOBEC3G, HSPB1, ISG15, GBP1, RSAD2, CXCL10, SAT1, CTSL, TXN, LGALS3, APOBEC3A, APOBEC3B, MARCKSL1, S100A9, S100A4, RPS27A, IL1B, RPL15, IL8, TIMP1
Dataset 1:
GAPDH, VIM, ACTB, S100A6, TIMP1, RGCC, ISG15, CXCL10, HLA-DPA1, CREM, CD79A
Shared:
RBM10, GZMK, LAGE3, ACAT2, NDUFC2, RPL14, CHCHD10, HSP90AB1, RPLP0, APOBEC3A, RPL12, RSAD2, RPL18A, GAPDH, CSTB, RPS3, RPS6, NPM1, RPL18, RPS15A, RPS19, TMSB4X, RPS12, HLA-A, TYMP, RPS3A, CCL5, RPL15, CD14, LGALS3
Dataset 2
CREM, HLA-DPA1, ISG15, CXCL10, CD79A, S100A6, ACTB, TIMP1, VIM, GAPDH, RGCC
Dataset 1:
TMEM66, BTG1, ISG15, RSAD2, SAT1, ANXA1, HERC6
Shared:
KLRC1, KLRD1, GNLY, APOBEC3G, NKG7, CD7, GZMB, HLA-A, PLAC8, PPBP, LAGE3, CCL5, GPR183, SRGN, HLA-B, TEX264, THRAP3, EIF2AK1, B2M, TMSB4X, CD63, HLA-C, RPL9, XCL2, RPS27A, CXCR4, RPS3, RPLP1, H3F3B, ACTB
Dataset 2
ANXA1, HERC6, ISG15, RSAD2, SAT1, TMEM66, BTG1
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total iterations: 42
Total time: 0 sec
Objective error: 59878.9
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 49910.7
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 41528.3
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 47418.4
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
INMF started, niter=30
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 1 sec
Objective error: 35967.3
INMF started, niter=30
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 1 sec
Objective error: 35967.3
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45479.1
**|
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 49910.7
completed constructor::A::173x300
time taken:3.07134
completed constructor::A::173x300
time taken:2.83118
completed constructor::A::173x300
time taken:2.97946
completed constructor::A::173x300
time taken:2.832
completed constructor::A::173x300
time taken:3.32876
completed constructor::A::173x300
time taken:2.83529
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmphBCDR0/ctrltest_3f6a997f95982.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmphBCDR0/stimtest_3f6a99648b28a8.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
A liger command record, performed at 04-15-2025 23:18:29 EDT
Call: normalize.liger(object)
Parameters:
useDatasets : "ctrl", "stim"
verbose : TRUE
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmphBCDR0/ctrltest_3f6a9963c9528e.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmphBCDR0/stimtest_3f6a991f037448.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
An object of class ligerDataset with 300 cells
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmphBCDR0/ctrltest_3f6a9957e010cd.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmphBCDR0/stimtest_3f6a9973cf7015.h5
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmphBCDR0/ctrltest_3f6a9926ab33ec.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmphBCDR0/stimtest_3f6a9917b74132.h5
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmphBCDR0/ctrltest_3f6a994e45bbb5.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmphBCDR0/stimtest_3f6a9950197951.h5
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmphBCDR0/ctrltest_3f6a99711a06b3.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmphBCDR0/stimtest_3f6a996e399166.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmphBCDR0/ctrltest_3f6a99748309a7.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmphBCDR0/stimtest_3f6a99421bc97.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 1329 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• {DoubletFinder} is not installed (1): 'test_preprocessing.R:112:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_factorization.R:111:5'): UINMF ─────────────────────────────────
<Rcpp::exception/C++Error/error/condition>
Error: k must be <= m
Backtrace:
▆
1. ├─rliger::runUINMF(pbmc, k = 30, nIteration = 2, nRandomStarts = 2) at test_factorization.R:111:5
2. └─rliger:::runUINMF.liger(pbmc, k = 30, nIteration = 2, nRandomStarts = 2)
3. └─rliger:::.runUINMF.list(...)
4. └─RcppPlanc::uinmf(...)
5. └─RcppPlanc:::.uinmf_rcpp(...)
── Error ('test_factorization.R:130:5'): Optimize new parameters ───────────────
<Rcpp::exception/C++Error/error/condition>
Error: Must provide 2 V matrices
Backtrace:
▆
1. └─rliger::optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2) at test_factorization.R:130:5
2. ├─rliger::runINMF(...)
3. └─rliger:::runINMF.liger(...)
4. └─rliger:::.runINMF.list(...)
5. └─RcppPlanc::inmf(...)
6. └─RcppPlanc:::.bppinmf(...)
── Error ('test_factorization.R:180:5'): Online iNMF - in-memory ───────────────
<std::invalid_argument/C++Error/error/condition>
Error: Must provide 2 H matrices
Backtrace:
▆
1. ├─rliger::runOnlineINMF(...) at test_factorization.R:180:5
2. └─rliger:::runOnlineINMF.liger(...)
3. └─rliger:::.runOnlineINMF.list(...)
4. └─RcppPlanc::onlineINMF(...)
5. └─RcppPlanc:::.onlineINMF_withInitial(...)
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 1329 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 2.1.0
Check: examples
Result: ERROR
Running examples in ‘rliger-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optimizeNewLambda
> ### Title: Perform factorization for new lambda value
> ### Aliases: optimizeNewLambda
>
> ### ** Examples
>
> pbmc <- normalize(pbmc)
ℹ Normalizing datasets "ctrl"
ℹ Normalizing datasets "stim"
✔ Normalizing datasets "stim" ... done
ℹ Normalizing datasets "ctrl"
✔ Normalizing datasets "ctrl" ... done
> pbmc <- selectGenes(pbmc)
ℹ Selecting variable features for dataset "ctrl"
✔ ... 168 features selected out of 249 shared features.
ℹ Selecting variable features for dataset "stim"
✔ ... 166 features selected out of 249 shared features.
✔ Finally 173 shared variable features are selected.
> pbmc <- scaleNotCenter(pbmc)
ℹ Scaling dataset "ctrl"
✔ Scaling dataset "ctrl" ... done
ℹ Scaling dataset "stim"
✔ Scaling dataset "stim" ... done
> if (requireNamespace("RcppPlanc", quietly = TRUE)) {
+ # Only running a few iterations for fast examples
+ pbmc <- runINMF(pbmc, k = 20, nIteration = 2)
+ pbmc <- optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2)
+ }
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 43773
Error: Must provide 2 V matrices
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
createLiger 5.659 0.197 7.074
calcAgreement 4.726 1.103 8.372
Flavor: r-release-linux-x86_64
Version: 2.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [367s/391s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rliger)
Package `rliger` has been updated massively since version 1.99.0, including the object structure which is not compatible with old versions.
We recommand you backup your old analysis before overwriting any existing result.
`readLiger()` is provided for reading an RDS file storing an old object and it converts the object to the up-to-date structure.
>
> test_check("rliger")
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Reading input file...
Number of nodes: 600
Number of edges: 16900
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity: 0.7596
Number of communities: 9
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Reading input file...
Number of nodes: 600
Number of edges: 16701
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity: 0.7658
Number of communities: 10
Elapsed time: 0 seconds
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Dataset 1:
NPM1, SAT1, VIM, FTH1, BTG1, ISG15, GBP1, RSAD2, HSP90AB1
Shared:
NMB, ANXA1, GPR183, NDUFC2, GAPDH, VIM, EIF1, SRGN, JUNB, S100A10, TMSB4X, PABPC1, H3F3B, SAT1, HIST1H2AC, RGCC, ANXA2, RPLP1, LYZ, RPL18, HLA-A, RPS15A, TMEM66, RSAD2, UBC, HSPA8, MALAT1, RPLP0, RPS6, RPS12
Dataset 2
RSAD2, VIM, ISG15, GBP1, HSP90AB1, SAT1, NPM1, FTH1, BTG1
Dataset 1:
CD83, VIM, CXCR4, MARCKSL1, GAPDH, FTL, ISG15, GBP1, SELL, RSAD2, CXCL10, PLAC8, SOD2, SAT1, IFI27, CCL2, CCL8, CCL3, CCL4, APOBEC3A, TYMP
Shared:
RPL23A, RPS2, CD79A, RPL18A, RPL12, RPL13A, RPL3, RPL27A, RPS23, RPL15, RPLP0, RPL10, RPL19, RPS8, RPS4X, RPS5, RPL10A, RPL11, RPS19, RPL18, RPS3A, RPL34, RPS18, PTMA, RPL7, RPS6, RPS27, RPLP1, RPL32, RPL14
Dataset 2
PLAC8, GBP1, IFI27, TYMP, ISG15, SELL, RSAD2, CXCL10, SOD2, SAT1, CCL2, CCL8, CCL3, CCL4, APOBEC3A, MARCKSL1, CXCR4, CD83, VIM, GAPDH, FTL
Dataset 1:
FCGR3A, LGALS1, RPLP0, RPL18, RPS12, RPS3A, RPL23A, S100A4, ACTB, RPL7, ISG15, GBP1, RSAD2, SAT1, CCNH
Shared:
CST7, CHRNB1, NKG7, APOBEC3G, CLIC3, CXCR4, GNLY, HLA-A, CD7, HLA-C, GZMB, SRGN, BAK1, TMSB4X, NDUFC2, HLA-B, B2M, BTG1, JTB, CCNH, FOXN3, H2AFZ, UBC, CREM, MALAT1, PTMA, ANXA1, H3F3B, VIM, RABL5
Dataset 2
CCNH, ISG15, RSAD2, SAT1, GBP1, S100A4, FCGR3A, RPS3A, RPS12, ACTB, RPL7, RPLP0, RPL23A, RPL18, LGALS1
Dataset 1:
CXCL10, GBP1, PTMA, S100A10, CD14, LGALS1, TIMP1, FAM26F, RPS3A, RPL10A, RPL3, S100A6, H2AFZ, CCL3, S100A8, GPX1, IL8, HLA-DQA1, LGALS3, ISG15, RSAD2, CD83, HSPA1A, GIMAP7, IDO1, TXN, MS4A7, IFI27, CCL2, CCL8
Shared:
FCGR3A, MS4A7, VMO1, FAM26F, GBP1, CXCL10, TYROBP, PLAC8, FCER1G, TIMP1, S100A11, FTH1, SAT1, SOD2, JUNB, TMSB4X, TYMP, HLA-C, SRGN, HLA-B, B2M, ACTB, HLA-DPA1, CST3, RPS19, APOBEC3A, MALAT1, TMEM66, S100A4, H3F3B
Dataset 2
ISG15, IFI27, MS4A7, APOBEC3A, HSPA1A, GIMAP7, CD83, RSAD2, GBP1, CXCL10, FAM26F, IDO1, TXN, CCL2, CCL8, CCL3, S100A10, S100A8, S100A6, PTMA, GPX1, IL8, H2AFZ, RPS3A, CD14, HLA-DQA1, RPL10A, TIMP1, LGALS3, LGALS1
Dataset 1:
RPL10A, H2AFZ, GAPDH, PABPC1, ISG15, GBP1, CXCL10, CD83, SAT1, EIF1, HERC6
Shared:
MIR155HG, MYC, ID3, CD83, NPM1, HLA-DQA1, HSP90AB1, CCR7, CCL3, HLA-DRB1, HSPA8, EIF1, HLA-DRA, RPLP0, RPS5, CCL4, JTB, RPL14, RPS23, RPL19, RPL10A, RPL7, RPS12, RPL18A, RPS2, PTMA, CD74, RPL23A, RPS8, RPLP1
Dataset 2
GBP1, EIF1, CD83, CXCL10, HERC6, ISG15, SAT1, H2AFZ, RPL10A, PABPC1, GAPDH
Dataset 1:
RPS8, RPS23, RPL15, RPL21, RPL7, RPL13A, MARCKSL1, RPS3A, TIMP1, RPS6, RPS3, ISG15, GBP1, RSAD2, CXCL10, HSPA1A, FAM26F, HSPB1, IDO1, CREM, CCL8, APOBEC3A, APOBEC3G, TYMP, THRAP3
Shared:
CXCL3, SERPINB2, IL8, CCL7, CCL2, CTSL, CTSB, RABL5, ANXA5, CD63, SOD2, FCER1G, FTL, CSTB, CD14, ANXA2, CCL3, FTH1, VIM, NFKBIA, LGALS1, GAPDH, ANXA1, SRGN, LGALS3, S100A6, S100A9, H3F3B, TYMP, TIMP1
Dataset 2
CCL8, THRAP3, HSPA1A, TYMP, HSPB1, CREM, APOBEC3G, ISG15, GBP1, RSAD2, CXCL10, FAM26F, IDO1, APOBEC3A, MARCKSL1, RPS8, RPL15, RPS3A, RPS23, TIMP1, RPL7, RPS6, RPS3, RPL21, RPL13A
Dataset 1:
RSAD2, ISG15, APOBEC3A, CD14, GPX1, GAPDH, MARCKSL1, RPL10, JTB, RPS3A, RPL21, RPS5, SAT1, RPS27A, RPL3, RPS8, RPL32, RPL7, RPS12, RPL15, PABPC1, RPL11, RPLP0, RPL10A, IL8, RPL19, S100A8, S100A6, DUSP2, CXCR4
Shared:
RSAD2, ISG15, APOBEC3A, CCL8, CXCL10, CCL2, CTSB, IDO1, SOD2, ANXA5, TYMP, FTL, CD63, HSPA1A, GBP1, CSTB, CTSL, IFI27, C15orf48, FAM26F, CCL7, FCER1G, LGALS3, LGALS1, FTH1, S100A11, TYROBP, ANXA2, HSPB1, TIMP1
Dataset 2
IDO1, HSPA1A, CCL4, CCL7, NFKBIA, CCL3, CXCL10, FAM26F, IFI27, RPS19, HERC6, ISG15, RSAD2, HSPB1, SAT1, CCL2, CCL8, APOBEC3A, RPL11, MARCKSL1, RPS8, S100A8, S100A6, RPS27A, DUSP2, CXCR4, PTMA, RPL32, RPL15, RPL14
Dataset 1:
BIRC3, S100A6, FTH1, CCL8, ID3, HLA-DPB1, GAPDH, CD79A, FTL, ISG15, GBP1, SELL, RSAD2, CXCL10, PLAC8, HSP90AB1, GIMAP7, SAT1, CREM, HSPA8, IFI27, CCL2, CCR7, H3F3B, APOBEC3A, TYMP, HERC6
Shared:
TMEM66, RPL13, RPL31, LTB, RPS18, RPL34, RPL32, RPS14, SELL, RPL21, RPS6, RPS15A, RPS27A, RPS12, RPL7, RPL3, RPS4X, RPS3, RPS3A, RPL9, RPL10, RPL11, RPL13A, RPS19, RPL10A, PABPC1, RPS23, RPS8, RPL27A, RPS2
Dataset 2
GIMAP7, PLAC8, CCR7, IFI27, H3F3B, SELL, GBP1, ISG15, RSAD2, CXCL10, HSP90AB1, SAT1, CREM, HSPA8, CCL2, CCL8, APOBEC3A, TYMP, HERC6, ID3, S100A6, HLA-DPB1, FTH1, BIRC3, GAPDH, CD79A, FTL
Dataset 1:
TEX264, FTH1, VIM, CCNH, UBC, RGCC, ISG15, GBP1, RSAD2, CXCL10, PLAC8, CD74, SAT1, CD79A
Shared:
GIMAP7, RGCC, ACAT2, BTG1, THRAP3, RELB, LTB, H2AFZ, EIF2AK1, CXCR4, HERC6, BIRC3, SELL, HSPA8, GPR183, CCR7, BAK1, HIST1H2AC, CHCHD10, EIF1, HSPB1, RPS27, JTB, MALAT1, H3F3B, PTMA, TMEM66, HSP90AB1, ANXA1, HLA-B
Dataset 2
GBP1, RSAD2, RGCC, UBC, ISG15, CXCL10, PLAC8, CD74, SAT1, CD79A, TEX264, VIM, FTH1, CCNH
Dataset 1:
CD14, S100A8, IFI27, RPL31, RPL27A, RPL21, RPL7, GBP1, MARCKSL1, RPS8, S100A6, S100A4, RPS27A, IL1B, PTMA, RPL15, RPL14, GPX1, IL8, CXCL3, H2AFZ, RPL34, RPS3A, RPS23, RPL10A, RPS4X, RPS6, RPS3, GAPDH, RGCC
Shared:
MARCKSL1, TIMP1, C15orf48, SOD2, FTH1, CD63, ANXA5, CSTB, SRGN, GAPDH, FTL, TYROBP, FCER1G, S100A11, EIF1, IL8, LGALS1, TYMP, B2M, LGALS3, ANXA2, CTSB, VIM, TXN, S100A10, ACTB, CCL2, NFKBIA, LYZ, HLA-B
Dataset 2
TXN, CST3, IDO1, APOBEC3A, MARCKSL1, PLAC8, S100A6, S100A4, HERC6, RPL19, RPS3, ISG15, GBP1, SELL, RSAD2, CXCL10, HIST1H2AC, HLA-C, HSPA1A, FAM26F, HSPB1, SAT1, CTSL, BIRC3, IFI27, CCL2, CCL7, CCL8, CCR7, APOBEC3B
Dataset 1:
IDO1, CST7, VMO1, IL8, SAT1, RPS5, TYMP, LAGE3, CXCR4, TIMP1, RGCC, RPL3, ISG15, GBP1, S100A4, SELL, RSAD2, CXCL10, HSPA1A, HSP90AB1, FAM26F, HSPB1, CTSB, ANXA1, HSPA8, IFI27, CCL2, H3F3B, APOBEC3A, APOBEC3B
Shared:
HLA-DPA1, HLA-DPB1, HLA-DRA, CD74, HLA-DRB1, TXN, HLA-DQA1, IDO1, CST3, CCR7, CD83, ANXA2, GPR183, MARCKSL1, ACTB, BIRC3, LYZ, CST7, TMSB4X, C15orf48, S100A10, LGALS1, B2M, GPX1, CD79A, NFKBIA, H2AFZ, RELB, ISG15, HSPA1A
Dataset 2
CXCL10, HSPA1A, ISG15, FAM26F, HSPB1, HERC6, GBP1, S100A4, APOBEC3G, RSAD2, HSP90AB1, HSPA8, SELL, SAT1, CTSB, IDO1, ANXA1, IFI27, CCL2, H3F3B, APOBEC3A, APOBEC3B, TYMP, CXCR4, IL8, TIMP1, RGCC, VMO1, CST7, RPS5
Dataset 1:
H3F3B, BIRC3, ISG15, HLA-C
Shared:
DUSP2, JUNB, GADD45B, HIST1H2AC, MYC, NFKBIA, BIRC3, BTG1, GZMK, CD83, PABPC1, APOBEC3G, TMEM66, H3F3B, EIF1, PTMA, UBC, HLA-C, NDUFC2, RPS19, GPR183, MALAT1, RPS5, RPL18, HLA-A, RPL19, RPS27, SRGN, RPL3, RPL27A
Dataset 2
HLA-C, ISG15, BIRC3, H3F3B
Dataset 1:
GAPDH, RPL12, FTL, ISG15, FCER1G, RSAD2, TYMP
Shared:
GZMH, FGFBP2, CCL5, CLIC3, NKG7, GZMB, CST7, GZMK, HLA-B, APOBEC3G, B2M, HLA-C, PTMA, TMSB4X, NDUFC2, RGCC, ANXA1, HLA-A, GAPDH, ACTN1, PLAC8, RPS19, MALAT1, RPL15, JTB, KLRD1, RPS3, TMEM66, RPS15A, RPL3
Dataset 2
TYMP, FCER1G, ISG15, RSAD2, RPL12, GAPDH, FTL
Dataset 1:
CCL2, H2AFZ, CD14, CTSL, RPL10A, RPS8, RPS6, TIMP1, S100A8, RPS27, RPLP0, RPL21, RPL14, RPL34, RPL7, RPL18A, ID3, RPL11, MARCKSL1, RPL31, IL1B, RPL15, RPL9, IL8, RPS3A, RPS14, NPM1, RPS4X, RPL10, PABPC1
Shared:
S100A4, LGALS3, CTSL, S100A6, GPX1, S100A11, FTL, S100A10, LGALS1, CTSB, CST3, FCER1G, ACTB, VIM, ANXA2, CD63, TYMP, TYROBP, CSTB, HLA-DRB1, CCL2, FCGR3A, ANXA1, ANXA5, SAT1, ACTN1, JTB, HLA-DRA, HLA-DPB1, H3F3B
Dataset 2
HSPB1, FAM26F, LYZ, HSPA1A, RPS14, RPL9, HIST1H2AC, HLA-A, APOBEC3A, ISG15, GBP1, RSAD2, CXCL10, HLA-C, HSP90AB1, SAT1, IDO1, CTSL, TXN, CREM, CCL2, CCL7, CCL8, APOBEC3B, APOBEC3G, TYMP, HERC6, ID3, RPL11, MARCKSL1
Dataset 1:
HSPA1A, H3F3B, CXCR4, FTL, ISG15, GBP1, RSAD2, RPL34, HLA-A, HLA-C, HLA-B, RPLP1, RPS2
Shared:
UBC, HSPA1A, GADD45G, GADD45B, HSP90AB1, HSPA8, HSPB1, H3F3B, PPBP, CREM, SAT1, BIRC3, CCNH, EIF1, NFKBIA, H2AFZ, JUNB, ID3, TMEM66, BTG1, MALAT1, RPS27, HIST1H2AC, NPM1, GBP1, CXCR4, RPS12, RPL14, RELB, CXCL10
Dataset 2
GBP1, RPLP1, HLA-C, RSAD2, HLA-B, ISG15, RPL34, HLA-A, RPS2, CXCR4, HSPA1A, H3F3B, FTL
Dataset 1:
CXCL3, IL8, FTH1, RPL9, GBP1, MARCKSL1, IL1B, H2AFZ, CD14, ISG15, RSAD2, CXCL10, HIST1H2AC, HSPA1A, FAM26F, HSPB1, SAT1, IDO1, CCL8, CST3, APOBEC3A, APOBEC3G
Shared:
IL1B, LYZ, IL8, CST3, NFKBIA, CCL3, S100A10, APOBEC3B, GPX1, ACTB, C15orf48, ANXA2, S100A6, S100A4, HLA-DPB1, CCL4, CXCL3, HLA-DRA, HLA-DRB1, S100A11, TYROBP, IFI27, JTB, HLA-DPA1, VIM, FCER1G, CD74, SRGN, ANXA1, HBA1
Dataset 2
FAM26F, CXCL10, CST3, HSPA1A, IL1B, SAT1, IDO1, ISG15, GBP1, RSAD2, HIST1H2AC, HSPB1, CCL8, APOBEC3A, APOBEC3G, MARCKSL1, RPL9, IL8, CXCL3, H2AFZ, CD14, FTH1
Dataset 1:
APOBEC3B, IL8, S100A4, MARCKSL1, RPS27A, RPL15, RPL7, RPL12, S100A9, PABPC1, S100A8, IL1B, TIMP1, RPS6, BTG1, RPLP0, RGCC, RPL13A, RPL3, ISG15, GBP1, RSAD2, CXCL10, HIST1H2AC, HSPA1A, FAM26F, HSPB1, SAT1, CTSB, IDO1
Shared:
S100A8, S100A9, CD14, GPX1, APOBEC3B, S100A6, TYROBP, LGALS1, S100A4, TYMP, S100A10, IL8, MS4A7, S100A11, FTL, NFKBIA, FTH1, MARCKSL1, APOBEC3A, FCER1G, LYZ, SRGN, SAT1, GAPDH, C15orf48, ANXA5, ACTB, CTSB, ISG15, CD63
Dataset 2
CCL2, HIST1H2AC, S100A8, IDO1, CCL8, CCL7, FAM26F, CTSB, CST3, HSPA1A, APOBEC3G, HSPB1, ISG15, GBP1, RSAD2, CXCL10, SAT1, CTSL, TXN, LGALS3, APOBEC3A, APOBEC3B, MARCKSL1, S100A9, S100A4, RPS27A, IL1B, RPL15, IL8, TIMP1
Dataset 1:
GAPDH, VIM, ACTB, S100A6, TIMP1, RGCC, ISG15, CXCL10, HLA-DPA1, CREM, CD79A
Shared:
RBM10, GZMK, LAGE3, ACAT2, NDUFC2, RPL14, CHCHD10, HSP90AB1, RPLP0, APOBEC3A, RPL12, RSAD2, RPL18A, GAPDH, CSTB, RPS3, RPS6, NPM1, RPL18, RPS15A, RPS19, TMSB4X, RPS12, HLA-A, TYMP, RPS3A, CCL5, RPL15, CD14, LGALS3
Dataset 2
CREM, HLA-DPA1, ISG15, CXCL10, CD79A, S100A6, ACTB, TIMP1, VIM, GAPDH, RGCC
Dataset 1:
TMEM66, BTG1, ISG15, RSAD2, SAT1, ANXA1, HERC6
Shared:
KLRC1, KLRD1, GNLY, APOBEC3G, NKG7, CD7, GZMB, HLA-A, PLAC8, PPBP, LAGE3, CCL5, GPR183, SRGN, HLA-B, TEX264, THRAP3, EIF2AK1, B2M, TMSB4X, CD63, HLA-C, RPL9, XCL2, RPS27A, CXCR4, RPS3, RPLP1, H3F3B, ACTB
Dataset 2
ANXA1, HERC6, ISG15, RSAD2, SAT1, TMEM66, BTG1
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total iterations: 42
Total time: 0 sec
Objective error: 59878.9
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 49910.7
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 41528.3
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 47418.4
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
INMF started, niter=30
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 1 sec
Objective error: 35967.3
INMF started, niter=30
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 1 sec
Objective error: 35967.3
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45479.1
**|
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 49910.7
completed constructor::A::173x300
time taken:3.13126
completed constructor::A::173x300
time taken:2.94756
completed constructor::A::173x300
time taken:3.11866
completed constructor::A::173x300
time taken:3.1275
completed constructor::A::173x300
time taken:3.09841
completed constructor::A::173x300
time taken:3.03418
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpZlqiJd/ctrltest_84e765c436ede.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmpZlqiJd/stimtest_84e76219aec2c.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
A liger command record, performed at 04-16-2025 23:08:31 EDT
Call: normalize.liger(object)
Parameters:
useDatasets : "ctrl", "stim"
verbose : TRUE
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpZlqiJd/ctrltest_84e76e3c7ae8.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmpZlqiJd/stimtest_84e763c8393bc.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
An object of class ligerDataset with 300 cells
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpZlqiJd/ctrltest_84e76cfc2d2d.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmpZlqiJd/stimtest_84e7679dd540f.h5
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpZlqiJd/ctrltest_84e76b42e23d.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmpZlqiJd/stimtest_84e761389e4ff.h5
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpZlqiJd/ctrltest_84e769e46433.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmpZlqiJd/stimtest_84e7631ab0d5b.h5
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpZlqiJd/ctrltest_84e76248e9e65.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmpZlqiJd/stimtest_84e76233b04a0.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpZlqiJd/ctrltest_84e7656bd161f.h5
Working stim H5 file path: /home/hornik/tmp/scratch/RtmpZlqiJd/stimtest_84e7617b3cced.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 1329 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• {DoubletFinder} is not installed (1): 'test_preprocessing.R:112:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_factorization.R:111:5'): UINMF ─────────────────────────────────
<Rcpp::exception/C++Error/error/condition>
Error: k must be <= m
Backtrace:
▆
1. ├─rliger::runUINMF(pbmc, k = 30, nIteration = 2, nRandomStarts = 2) at test_factorization.R:111:5
2. └─rliger:::runUINMF.liger(pbmc, k = 30, nIteration = 2, nRandomStarts = 2)
3. └─rliger:::.runUINMF.list(...)
4. └─RcppPlanc::uinmf(...)
5. └─RcppPlanc:::.uinmf_rcpp(...)
── Error ('test_factorization.R:130:5'): Optimize new parameters ───────────────
<Rcpp::exception/C++Error/error/condition>
Error: Must provide 2 V matrices
Backtrace:
▆
1. └─rliger::optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2) at test_factorization.R:130:5
2. ├─rliger::runINMF(...)
3. └─rliger:::runINMF.liger(...)
4. └─rliger:::.runINMF.list(...)
5. └─RcppPlanc::inmf(...)
6. └─RcppPlanc:::.bppinmf(...)
── Error ('test_factorization.R:180:5'): Online iNMF - in-memory ───────────────
<std::invalid_argument/C++Error/error/condition>
Error: Must provide 2 H matrices
Backtrace:
▆
1. ├─rliger::runOnlineINMF(...) at test_factorization.R:180:5
2. └─rliger:::runOnlineINMF.liger(...)
3. └─rliger:::.runOnlineINMF.list(...)
4. └─RcppPlanc::onlineINMF(...)
5. └─RcppPlanc:::.onlineINMF_withInitial(...)
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 1329 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 2.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [13m]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(rliger)
Package `rliger` has been updated massively since version 1.99.0, including the object structure which is not compatible with old versions.
We recommand you backup your old analysis before overwriting any existing result.
`readLiger()` is provided for reading an RDS file storing an old object and it converts the object to the up-to-date structure.
>
> test_check("rliger")
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Reading input file...
Number of nodes: 600
Number of edges: 16900
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity: 0.7596
Number of communities: 9
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Reading input file...
Number of nodes: 600
Number of edges: 16701
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity: 0.7658
Number of communities: 10
Elapsed time: 0 seconds
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Dataset 1:
NPM1, SAT1, VIM, FTH1, BTG1, ISG15, GBP1, RSAD2, HSP90AB1
Shared:
NMB, ANXA1, GPR183, NDUFC2, GAPDH, VIM, EIF1, SRGN, JUNB, S100A10, TMSB4X, PABPC1, H3F3B, SAT1, HIST1H2AC, RGCC, ANXA2, RPLP1, LYZ, RPL18, HLA-A, RPS15A, TMEM66, RSAD2, UBC, HSPA8, MALAT1, RPLP0, RPS6, RPS12
Dataset 2
RSAD2, VIM, ISG15, GBP1, HSP90AB1, SAT1, NPM1, FTH1, BTG1
Dataset 1:
CD83, VIM, CXCR4, MARCKSL1, GAPDH, FTL, ISG15, GBP1, SELL, RSAD2, CXCL10, PLAC8, SOD2, SAT1, IFI27, CCL2, CCL8, CCL3, CCL4, APOBEC3A, TYMP
Shared:
RPL23A, RPS2, CD79A, RPL18A, RPL12, RPL13A, RPL3, RPL27A, RPS23, RPL15, RPLP0, RPL10, RPL19, RPS8, RPS4X, RPS5, RPL10A, RPL11, RPS19, RPL18, RPS3A, RPL34, RPS18, PTMA, RPL7, RPS6, RPS27, RPLP1, RPL32, RPL14
Dataset 2
PLAC8, GBP1, IFI27, TYMP, ISG15, SELL, RSAD2, CXCL10, SOD2, SAT1, CCL2, CCL8, CCL3, CCL4, APOBEC3A, MARCKSL1, CXCR4, CD83, VIM, GAPDH, FTL
Dataset 1:
FCGR3A, LGALS1, RPLP0, RPL18, RPS12, RPS3A, RPL23A, S100A4, ACTB, RPL7, ISG15, GBP1, RSAD2, SAT1, CCNH
Shared:
CST7, CHRNB1, NKG7, APOBEC3G, CLIC3, CXCR4, GNLY, HLA-A, CD7, HLA-C, GZMB, SRGN, BAK1, TMSB4X, NDUFC2, HLA-B, B2M, BTG1, JTB, CCNH, FOXN3, H2AFZ, UBC, CREM, MALAT1, PTMA, ANXA1, H3F3B, VIM, RABL5
Dataset 2
CCNH, ISG15, RSAD2, SAT1, GBP1, S100A4, FCGR3A, RPS3A, RPS12, ACTB, RPL7, RPLP0, RPL23A, RPL18, LGALS1
Dataset 1:
CXCL10, GBP1, PTMA, S100A10, CD14, LGALS1, TIMP1, FAM26F, RPS3A, RPL10A, RPL3, S100A6, H2AFZ, CCL3, S100A8, GPX1, IL8, HLA-DQA1, LGALS3, ISG15, RSAD2, CD83, HSPA1A, GIMAP7, IDO1, TXN, MS4A7, IFI27, CCL2, CCL8
Shared:
FCGR3A, MS4A7, VMO1, FAM26F, GBP1, CXCL10, TYROBP, PLAC8, FCER1G, TIMP1, S100A11, FTH1, SAT1, SOD2, JUNB, TMSB4X, TYMP, HLA-C, SRGN, HLA-B, B2M, ACTB, HLA-DPA1, CST3, RPS19, APOBEC3A, MALAT1, TMEM66, S100A4, H3F3B
Dataset 2
ISG15, IFI27, MS4A7, APOBEC3A, HSPA1A, GIMAP7, CD83, RSAD2, GBP1, CXCL10, FAM26F, IDO1, TXN, CCL2, CCL8, CCL3, S100A10, S100A8, S100A6, PTMA, GPX1, IL8, H2AFZ, RPS3A, CD14, HLA-DQA1, RPL10A, TIMP1, LGALS3, LGALS1
Dataset 1:
RPL10A, H2AFZ, GAPDH, PABPC1, ISG15, GBP1, CXCL10, CD83, SAT1, EIF1, HERC6
Shared:
MIR155HG, MYC, ID3, CD83, NPM1, HLA-DQA1, HSP90AB1, CCR7, CCL3, HLA-DRB1, HSPA8, EIF1, HLA-DRA, RPLP0, RPS5, CCL4, JTB, RPL14, RPS23, RPL19, RPL10A, RPL7, RPS12, RPL18A, RPS2, PTMA, CD74, RPL23A, RPS8, RPLP1
Dataset 2
GBP1, EIF1, CD83, CXCL10, HERC6, ISG15, SAT1, H2AFZ, RPL10A, PABPC1, GAPDH
Dataset 1:
RPS8, RPS23, RPL15, RPL21, RPL7, RPL13A, MARCKSL1, RPS3A, TIMP1, RPS6, RPS3, ISG15, GBP1, RSAD2, CXCL10, HSPA1A, FAM26F, HSPB1, IDO1, CREM, CCL8, APOBEC3A, APOBEC3G, TYMP, THRAP3
Shared:
CXCL3, SERPINB2, IL8, CCL7, CCL2, CTSL, CTSB, RABL5, ANXA5, CD63, SOD2, FCER1G, FTL, CSTB, CD14, ANXA2, CCL3, FTH1, VIM, NFKBIA, LGALS1, GAPDH, ANXA1, SRGN, LGALS3, S100A6, S100A9, H3F3B, TYMP, TIMP1
Dataset 2
CCL8, THRAP3, HSPA1A, TYMP, HSPB1, CREM, APOBEC3G, ISG15, GBP1, RSAD2, CXCL10, FAM26F, IDO1, APOBEC3A, MARCKSL1, RPS8, RPL15, RPS3A, RPS23, TIMP1, RPL7, RPS6, RPS3, RPL21, RPL13A
Dataset 1:
RSAD2, ISG15, APOBEC3A, CD14, GPX1, GAPDH, MARCKSL1, RPL10, JTB, RPS3A, RPL21, RPS5, SAT1, RPS27A, RPL3, RPS8, RPL32, RPL7, RPS12, RPL15, PABPC1, RPL11, RPLP0, RPL10A, IL8, RPL19, S100A8, S100A6, DUSP2, CXCR4
Shared:
RSAD2, ISG15, APOBEC3A, CCL8, CXCL10, CCL2, CTSB, IDO1, SOD2, ANXA5, TYMP, FTL, CD63, HSPA1A, GBP1, CSTB, CTSL, IFI27, C15orf48, FAM26F, CCL7, FCER1G, LGALS3, LGALS1, FTH1, S100A11, TYROBP, ANXA2, HSPB1, TIMP1
Dataset 2
IDO1, HSPA1A, CCL4, CCL7, NFKBIA, CCL3, CXCL10, FAM26F, IFI27, RPS19, HERC6, ISG15, RSAD2, HSPB1, SAT1, CCL2, CCL8, APOBEC3A, RPL11, MARCKSL1, RPS8, S100A8, S100A6, RPS27A, DUSP2, CXCR4, PTMA, RPL32, RPL15, RPL14
Dataset 1:
BIRC3, S100A6, FTH1, CCL8, ID3, HLA-DPB1, GAPDH, CD79A, FTL, ISG15, GBP1, SELL, RSAD2, CXCL10, PLAC8, HSP90AB1, GIMAP7, SAT1, CREM, HSPA8, IFI27, CCL2, CCR7, H3F3B, APOBEC3A, TYMP, HERC6
Shared:
TMEM66, RPL13, RPL31, LTB, RPS18, RPL34, RPL32, RPS14, SELL, RPL21, RPS6, RPS15A, RPS27A, RPS12, RPL7, RPL3, RPS4X, RPS3, RPS3A, RPL9, RPL10, RPL11, RPL13A, RPS19, RPL10A, PABPC1, RPS23, RPS8, RPL27A, RPS2
Dataset 2
GIMAP7, PLAC8, CCR7, IFI27, H3F3B, SELL, GBP1, ISG15, RSAD2, CXCL10, HSP90AB1, SAT1, CREM, HSPA8, CCL2, CCL8, APOBEC3A, TYMP, HERC6, ID3, S100A6, HLA-DPB1, FTH1, BIRC3, GAPDH, CD79A, FTL
Dataset 1:
TEX264, FTH1, VIM, CCNH, UBC, RGCC, ISG15, GBP1, RSAD2, CXCL10, PLAC8, CD74, SAT1, CD79A
Shared:
GIMAP7, RGCC, ACAT2, BTG1, THRAP3, RELB, LTB, H2AFZ, EIF2AK1, CXCR4, HERC6, BIRC3, SELL, HSPA8, GPR183, CCR7, BAK1, HIST1H2AC, CHCHD10, EIF1, HSPB1, RPS27, JTB, MALAT1, H3F3B, PTMA, TMEM66, HSP90AB1, ANXA1, HLA-B
Dataset 2
GBP1, RSAD2, RGCC, UBC, ISG15, CXCL10, PLAC8, CD74, SAT1, CD79A, TEX264, VIM, FTH1, CCNH
Dataset 1:
CD14, S100A8, IFI27, RPL31, RPL27A, RPL21, RPL7, GBP1, MARCKSL1, RPS8, S100A6, S100A4, RPS27A, IL1B, PTMA, RPL15, RPL14, GPX1, IL8, CXCL3, H2AFZ, RPL34, RPS3A, RPS23, RPL10A, RPS4X, RPS6, RPS3, GAPDH, RGCC
Shared:
MARCKSL1, TIMP1, C15orf48, SOD2, FTH1, CD63, ANXA5, CSTB, SRGN, GAPDH, FTL, TYROBP, FCER1G, S100A11, EIF1, IL8, LGALS1, TYMP, B2M, LGALS3, ANXA2, CTSB, VIM, TXN, S100A10, ACTB, CCL2, NFKBIA, LYZ, HLA-B
Dataset 2
TXN, CST3, IDO1, APOBEC3A, MARCKSL1, PLAC8, S100A6, S100A4, HERC6, RPL19, RPS3, ISG15, GBP1, SELL, RSAD2, CXCL10, HIST1H2AC, HLA-C, HSPA1A, FAM26F, HSPB1, SAT1, CTSL, BIRC3, IFI27, CCL2, CCL7, CCL8, CCR7, APOBEC3B
Dataset 1:
IDO1, CST7, VMO1, IL8, SAT1, RPS5, TYMP, LAGE3, CXCR4, TIMP1, RGCC, RPL3, ISG15, GBP1, S100A4, SELL, RSAD2, CXCL10, HSPA1A, HSP90AB1, FAM26F, HSPB1, CTSB, ANXA1, HSPA8, IFI27, CCL2, H3F3B, APOBEC3A, APOBEC3B
Shared:
HLA-DPA1, HLA-DPB1, HLA-DRA, CD74, HLA-DRB1, TXN, HLA-DQA1, IDO1, CST3, CCR7, CD83, ANXA2, GPR183, MARCKSL1, ACTB, BIRC3, LYZ, CST7, TMSB4X, C15orf48, S100A10, LGALS1, B2M, GPX1, CD79A, NFKBIA, H2AFZ, RELB, ISG15, HSPA1A
Dataset 2
CXCL10, HSPA1A, ISG15, FAM26F, HSPB1, HERC6, GBP1, S100A4, APOBEC3G, RSAD2, HSP90AB1, HSPA8, SELL, SAT1, CTSB, IDO1, ANXA1, IFI27, CCL2, H3F3B, APOBEC3A, APOBEC3B, TYMP, CXCR4, IL8, TIMP1, RGCC, VMO1, CST7, RPS5
Dataset 1:
H3F3B, BIRC3, ISG15, HLA-C
Shared:
DUSP2, JUNB, GADD45B, HIST1H2AC, MYC, NFKBIA, BIRC3, BTG1, GZMK, CD83, PABPC1, APOBEC3G, TMEM66, H3F3B, EIF1, PTMA, UBC, HLA-C, NDUFC2, RPS19, GPR183, MALAT1, RPS5, RPL18, HLA-A, RPL19, RPS27, SRGN, RPL3, RPL27A
Dataset 2
HLA-C, ISG15, BIRC3, H3F3B
Dataset 1:
GAPDH, RPL12, FTL, ISG15, FCER1G, RSAD2, TYMP
Shared:
GZMH, FGFBP2, CCL5, CLIC3, NKG7, GZMB, CST7, GZMK, HLA-B, APOBEC3G, B2M, HLA-C, PTMA, TMSB4X, NDUFC2, RGCC, ANXA1, HLA-A, GAPDH, ACTN1, PLAC8, RPS19, MALAT1, RPL15, JTB, KLRD1, RPS3, TMEM66, RPS15A, RPL3
Dataset 2
TYMP, FCER1G, ISG15, RSAD2, RPL12, GAPDH, FTL
Dataset 1:
CCL2, H2AFZ, CD14, CTSL, RPL10A, RPS8, RPS6, TIMP1, S100A8, RPS27, RPLP0, RPL21, RPL14, RPL34, RPL7, RPL18A, ID3, RPL11, MARCKSL1, RPL31, IL1B, RPL15, RPL9, IL8, RPS3A, RPS14, NPM1, RPS4X, RPL10, PABPC1
Shared:
S100A4, LGALS3, CTSL, S100A6, GPX1, S100A11, FTL, S100A10, LGALS1, CTSB, CST3, FCER1G, ACTB, VIM, ANXA2, CD63, TYMP, TYROBP, CSTB, HLA-DRB1, CCL2, FCGR3A, ANXA1, ANXA5, SAT1, ACTN1, JTB, HLA-DRA, HLA-DPB1, H3F3B
Dataset 2
HSPB1, FAM26F, LYZ, HSPA1A, RPS14, RPL9, HIST1H2AC, HLA-A, APOBEC3A, ISG15, GBP1, RSAD2, CXCL10, HLA-C, HSP90AB1, SAT1, IDO1, CTSL, TXN, CREM, CCL2, CCL7, CCL8, APOBEC3B, APOBEC3G, TYMP, HERC6, ID3, RPL11, MARCKSL1
Dataset 1:
HSPA1A, H3F3B, CXCR4, FTL, ISG15, GBP1, RSAD2, RPL34, HLA-A, HLA-C, HLA-B, RPLP1, RPS2
Shared:
UBC, HSPA1A, GADD45G, GADD45B, HSP90AB1, HSPA8, HSPB1, H3F3B, PPBP, CREM, SAT1, BIRC3, CCNH, EIF1, NFKBIA, H2AFZ, JUNB, ID3, TMEM66, BTG1, MALAT1, RPS27, HIST1H2AC, NPM1, GBP1, CXCR4, RPS12, RPL14, RELB, CXCL10
Dataset 2
GBP1, RPLP1, HLA-C, RSAD2, HLA-B, ISG15, RPL34, HLA-A, RPS2, CXCR4, HSPA1A, H3F3B, FTL
Dataset 1:
CXCL3, IL8, FTH1, RPL9, GBP1, MARCKSL1, IL1B, H2AFZ, CD14, ISG15, RSAD2, CXCL10, HIST1H2AC, HSPA1A, FAM26F, HSPB1, SAT1, IDO1, CCL8, CST3, APOBEC3A, APOBEC3G
Shared:
IL1B, LYZ, IL8, CST3, NFKBIA, CCL3, S100A10, APOBEC3B, GPX1, ACTB, C15orf48, ANXA2, S100A6, S100A4, HLA-DPB1, CCL4, CXCL3, HLA-DRA, HLA-DRB1, S100A11, TYROBP, IFI27, JTB, HLA-DPA1, VIM, FCER1G, CD74, SRGN, ANXA1, HBA1
Dataset 2
FAM26F, CXCL10, CST3, HSPA1A, IL1B, SAT1, IDO1, ISG15, GBP1, RSAD2, HIST1H2AC, HSPB1, CCL8, APOBEC3A, APOBEC3G, MARCKSL1, RPL9, IL8, CXCL3, H2AFZ, CD14, FTH1
Dataset 1:
APOBEC3B, IL8, S100A4, MARCKSL1, RPS27A, RPL15, RPL7, RPL12, S100A9, PABPC1, S100A8, IL1B, TIMP1, RPS6, BTG1, RPLP0, RGCC, RPL13A, RPL3, ISG15, GBP1, RSAD2, CXCL10, HIST1H2AC, HSPA1A, FAM26F, HSPB1, SAT1, CTSB, IDO1
Shared:
S100A8, S100A9, CD14, GPX1, APOBEC3B, S100A6, TYROBP, LGALS1, S100A4, TYMP, S100A10, IL8, MS4A7, S100A11, FTL, NFKBIA, FTH1, MARCKSL1, APOBEC3A, FCER1G, LYZ, SRGN, SAT1, GAPDH, C15orf48, ANXA5, ACTB, CTSB, ISG15, CD63
Dataset 2
CCL2, HIST1H2AC, S100A8, IDO1, CCL8, CCL7, FAM26F, CTSB, CST3, HSPA1A, APOBEC3G, HSPB1, ISG15, GBP1, RSAD2, CXCL10, SAT1, CTSL, TXN, LGALS3, APOBEC3A, APOBEC3B, MARCKSL1, S100A9, S100A4, RPS27A, IL1B, RPL15, IL8, TIMP1
Dataset 1:
GAPDH, VIM, ACTB, S100A6, TIMP1, RGCC, ISG15, CXCL10, HLA-DPA1, CREM, CD79A
Shared:
RBM10, GZMK, LAGE3, ACAT2, NDUFC2, RPL14, CHCHD10, HSP90AB1, RPLP0, APOBEC3A, RPL12, RSAD2, RPL18A, GAPDH, CSTB, RPS3, RPS6, NPM1, RPL18, RPS15A, RPS19, TMSB4X, RPS12, HLA-A, TYMP, RPS3A, CCL5, RPL15, CD14, LGALS3
Dataset 2
CREM, HLA-DPA1, ISG15, CXCL10, CD79A, S100A6, ACTB, TIMP1, VIM, GAPDH, RGCC
Dataset 1:
TMEM66, BTG1, ISG15, RSAD2, SAT1, ANXA1, HERC6
Shared:
KLRC1, KLRD1, GNLY, APOBEC3G, NKG7, CD7, GZMB, HLA-A, PLAC8, PPBP, LAGE3, CCL5, GPR183, SRGN, HLA-B, TEX264, THRAP3, EIF2AK1, B2M, TMSB4X, CD63, HLA-C, RPL9, XCL2, RPS27A, CXCR4, RPS3, RPLP1, H3F3B, ACTB
Dataset 2
ANXA1, HERC6, ISG15, RSAD2, SAT1, TMEM66, BTG1
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total iterations: 42
Total time: 0 sec
Objective error: 59878.9
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 49910.7
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 41528.3
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 47418.4
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
INMF started, niter=30
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 35967.3
INMF started, niter=30
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 35967.3
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45479.1
**|
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 49910.7
completed constructor::A::173x300
time taken:27.1988
completed constructor::A::173x300
time taken:29.0374
completed constructor::A::173x300
time taken:34.1374
completed constructor::A::173x300
time taken:33.5615
completed constructor::A::173x300
time taken:28.7722
completed constructor::A::173x300
time taken:28.3759
Working ctrl H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpUBnIlo\ctrltest_830c1b1667f8.h5
Working stim H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpUBnIlo\stimtest_830c32cf4a87.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
A liger command record, performed at 04-16-2025 01:02:15 EDT
Call: normalize.liger(object)
Parameters:
useDatasets : "ctrl", "stim"
verbose : TRUE
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
Working ctrl H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpUBnIlo\ctrltest_830c5e397784.h5
Working stim H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpUBnIlo\stimtest_830c51121ca.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
An object of class ligerDataset with 300 cells
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Working ctrl H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpUBnIlo\ctrltest_830c34671f4.h5
Working stim H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpUBnIlo\stimtest_830c4e5169df.h5
Working ctrl H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpUBnIlo\ctrltest_830c6656c5f.h5
Working stim H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpUBnIlo\stimtest_830c3e251de2.h5
Working ctrl H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpUBnIlo\ctrltest_830c610c732b.h5
Working stim H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpUBnIlo\stimtest_830c37b9f01.h5
Working ctrl H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpUBnIlo\ctrltest_830c19367428.h5
Working stim H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpUBnIlo\stimtest_830c47927947.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Working ctrl H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpUBnIlo\ctrltest_830c77e36166.h5
Working stim H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpUBnIlo\stimtest_830c1b6350e.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 1329 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• {DoubletFinder} is not installed (1): 'test_preprocessing.R:112:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_factorization.R:111:5'): UINMF ─────────────────────────────────
<Rcpp::exception/C++Error/error/condition>
Error: k must be <= m
Backtrace:
▆
1. ├─rliger::runUINMF(pbmc, k = 30, nIteration = 2, nRandomStarts = 2) at test_factorization.R:111:5
2. └─rliger:::runUINMF.liger(pbmc, k = 30, nIteration = 2, nRandomStarts = 2)
3. └─rliger:::.runUINMF.list(...)
4. └─RcppPlanc::uinmf(...)
5. └─RcppPlanc:::.uinmf_rcpp(...)
── Error ('test_factorization.R:130:5'): Optimize new parameters ───────────────
<Rcpp::exception/C++Error/error/condition>
Error: Must provide 2 V matrices
Backtrace:
▆
1. └─rliger::optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2) at test_factorization.R:130:5
2. ├─rliger::runINMF(...)
3. └─rliger:::runINMF.liger(...)
4. └─rliger:::.runINMF.list(...)
5. └─RcppPlanc::inmf(...)
6. └─RcppPlanc:::.bppinmf(...)
── Error ('test_factorization.R:180:5'): Online iNMF - in-memory ───────────────
<std::invalid_argument/C++Error/error/condition>
Error: Must provide 2 H matrices
Backtrace:
▆
1. ├─rliger::runOnlineINMF(...) at test_factorization.R:180:5
2. └─rliger:::runOnlineINMF.liger(...)
3. └─rliger:::.runOnlineINMF.list(...)
4. └─RcppPlanc::onlineINMF(...)
5. └─RcppPlanc:::.onlineINMF_withInitial(...)
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 1329 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 2.1.0
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'DoubletFinder', 'RcppPlanc', 'reactome.db'
Flavor: r-oldrel-macos-arm64
Version: 2.1.0
Check: installed package size
Result: NOTE
installed size is 9.5Mb
sub-directories of 1Mb or more:
R 1.0Mb
libs 6.4Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 2.1.0
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'DoubletFinder', 'RcppPlanc'
Flavor: r-oldrel-macos-x86_64
Version: 2.1.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: 'DoubletFinder'
Flavor: r-oldrel-windows-x86_64
Version: 2.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [17m]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(rliger)
Package `rliger` has been updated massively since version 1.99.0, including the object structure which is not compatible with old versions.
We recommand you backup your old analysis before overwriting any existing result.
`readLiger()` is provided for reading an RDS file storing an old object and it converts the object to the up-to-date structure.
>
> test_check("rliger")
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Reading input file...
Number of nodes: 600
Number of edges: 16900
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity: 0.7596
Number of communities: 9
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Reading input file...
Number of nodes: 600
Number of edges: 16701
Running Louvain algorithm...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity: 0.7658
Number of communities: 10
Elapsed time: 0 seconds
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Dataset 1:
NPM1, SAT1, VIM, FTH1, BTG1, ISG15, GBP1, RSAD2, HSP90AB1
Shared:
NMB, ANXA1, GPR183, NDUFC2, GAPDH, VIM, EIF1, SRGN, JUNB, S100A10, TMSB4X, PABPC1, H3F3B, SAT1, HIST1H2AC, RGCC, ANXA2, RPLP1, LYZ, RPL18, HLA-A, RPS15A, TMEM66, RSAD2, UBC, HSPA8, MALAT1, RPLP0, RPS6, RPS12
Dataset 2
RSAD2, VIM, ISG15, GBP1, HSP90AB1, SAT1, NPM1, FTH1, BTG1
Dataset 1:
CD83, VIM, CXCR4, MARCKSL1, GAPDH, FTL, ISG15, GBP1, SELL, RSAD2, CXCL10, PLAC8, SOD2, SAT1, IFI27, CCL2, CCL8, CCL3, CCL4, APOBEC3A, TYMP
Shared:
RPL23A, RPS2, CD79A, RPL18A, RPL12, RPL13A, RPL3, RPL27A, RPS23, RPL15, RPLP0, RPL10, RPL19, RPS8, RPS4X, RPS5, RPL10A, RPL11, RPS19, RPL18, RPS3A, RPL34, RPS18, PTMA, RPL7, RPS6, RPS27, RPLP1, RPL32, RPL14
Dataset 2
PLAC8, GBP1, IFI27, TYMP, ISG15, SELL, RSAD2, CXCL10, SOD2, SAT1, CCL2, CCL8, CCL3, CCL4, APOBEC3A, MARCKSL1, CXCR4, CD83, VIM, GAPDH, FTL
Dataset 1:
FCGR3A, LGALS1, RPLP0, RPL18, RPS12, RPS3A, RPL23A, S100A4, ACTB, RPL7, ISG15, GBP1, RSAD2, SAT1, CCNH
Shared:
CST7, CHRNB1, NKG7, APOBEC3G, CLIC3, CXCR4, GNLY, HLA-A, CD7, HLA-C, GZMB, SRGN, BAK1, TMSB4X, NDUFC2, HLA-B, B2M, BTG1, JTB, CCNH, FOXN3, H2AFZ, UBC, CREM, MALAT1, PTMA, ANXA1, H3F3B, VIM, RABL5
Dataset 2
CCNH, ISG15, RSAD2, SAT1, GBP1, S100A4, FCGR3A, RPS3A, RPS12, ACTB, RPL7, RPLP0, RPL23A, RPL18, LGALS1
Dataset 1:
CXCL10, GBP1, PTMA, S100A10, CD14, LGALS1, TIMP1, FAM26F, RPS3A, RPL10A, RPL3, S100A6, H2AFZ, CCL3, S100A8, GPX1, IL8, HLA-DQA1, LGALS3, ISG15, RSAD2, CD83, HSPA1A, GIMAP7, IDO1, TXN, MS4A7, IFI27, CCL2, CCL8
Shared:
FCGR3A, MS4A7, VMO1, FAM26F, GBP1, CXCL10, TYROBP, PLAC8, FCER1G, TIMP1, S100A11, FTH1, SAT1, SOD2, JUNB, TMSB4X, TYMP, HLA-C, SRGN, HLA-B, B2M, ACTB, HLA-DPA1, CST3, RPS19, APOBEC3A, MALAT1, TMEM66, S100A4, H3F3B
Dataset 2
ISG15, IFI27, MS4A7, APOBEC3A, HSPA1A, GIMAP7, CD83, RSAD2, GBP1, CXCL10, FAM26F, IDO1, TXN, CCL2, CCL8, CCL3, S100A10, S100A8, S100A6, PTMA, GPX1, IL8, H2AFZ, RPS3A, CD14, HLA-DQA1, RPL10A, TIMP1, LGALS3, LGALS1
Dataset 1:
RPL10A, H2AFZ, GAPDH, PABPC1, ISG15, GBP1, CXCL10, CD83, SAT1, EIF1, HERC6
Shared:
MIR155HG, MYC, ID3, CD83, NPM1, HLA-DQA1, HSP90AB1, CCR7, CCL3, HLA-DRB1, HSPA8, EIF1, HLA-DRA, RPLP0, RPS5, CCL4, JTB, RPL14, RPS23, RPL19, RPL10A, RPL7, RPS12, RPL18A, RPS2, PTMA, CD74, RPL23A, RPS8, RPLP1
Dataset 2
GBP1, EIF1, CD83, CXCL10, HERC6, ISG15, SAT1, H2AFZ, RPL10A, PABPC1, GAPDH
Dataset 1:
RPS8, RPS23, RPL15, RPL21, RPL7, RPL13A, MARCKSL1, RPS3A, TIMP1, RPS6, RPS3, ISG15, GBP1, RSAD2, CXCL10, HSPA1A, FAM26F, HSPB1, IDO1, CREM, CCL8, APOBEC3A, APOBEC3G, TYMP, THRAP3
Shared:
CXCL3, SERPINB2, IL8, CCL7, CCL2, CTSL, CTSB, RABL5, ANXA5, CD63, SOD2, FCER1G, FTL, CSTB, CD14, ANXA2, CCL3, FTH1, VIM, NFKBIA, LGALS1, GAPDH, ANXA1, SRGN, LGALS3, S100A6, S100A9, H3F3B, TYMP, TIMP1
Dataset 2
CCL8, THRAP3, HSPA1A, TYMP, HSPB1, CREM, APOBEC3G, ISG15, GBP1, RSAD2, CXCL10, FAM26F, IDO1, APOBEC3A, MARCKSL1, RPS8, RPL15, RPS3A, RPS23, TIMP1, RPL7, RPS6, RPS3, RPL21, RPL13A
Dataset 1:
RSAD2, ISG15, APOBEC3A, CD14, GPX1, GAPDH, MARCKSL1, RPL10, JTB, RPS3A, RPL21, RPS5, SAT1, RPS27A, RPL3, RPS8, RPL32, RPL7, RPS12, RPL15, PABPC1, RPL11, RPLP0, RPL10A, IL8, RPL19, S100A8, S100A6, DUSP2, CXCR4
Shared:
RSAD2, ISG15, APOBEC3A, CCL8, CXCL10, CCL2, CTSB, IDO1, SOD2, ANXA5, TYMP, FTL, CD63, HSPA1A, GBP1, CSTB, CTSL, IFI27, C15orf48, FAM26F, CCL7, FCER1G, LGALS3, LGALS1, FTH1, S100A11, TYROBP, ANXA2, HSPB1, TIMP1
Dataset 2
IDO1, HSPA1A, CCL4, CCL7, NFKBIA, CCL3, CXCL10, FAM26F, IFI27, RPS19, HERC6, ISG15, RSAD2, HSPB1, SAT1, CCL2, CCL8, APOBEC3A, RPL11, MARCKSL1, RPS8, S100A8, S100A6, RPS27A, DUSP2, CXCR4, PTMA, RPL32, RPL15, RPL14
Dataset 1:
BIRC3, S100A6, FTH1, CCL8, ID3, HLA-DPB1, GAPDH, CD79A, FTL, ISG15, GBP1, SELL, RSAD2, CXCL10, PLAC8, HSP90AB1, GIMAP7, SAT1, CREM, HSPA8, IFI27, CCL2, CCR7, H3F3B, APOBEC3A, TYMP, HERC6
Shared:
TMEM66, RPL13, RPL31, LTB, RPS18, RPL34, RPL32, RPS14, SELL, RPL21, RPS6, RPS15A, RPS27A, RPS12, RPL7, RPL3, RPS4X, RPS3, RPS3A, RPL9, RPL10, RPL11, RPL13A, RPS19, RPL10A, PABPC1, RPS23, RPS8, RPL27A, RPS2
Dataset 2
GIMAP7, PLAC8, CCR7, IFI27, H3F3B, SELL, GBP1, ISG15, RSAD2, CXCL10, HSP90AB1, SAT1, CREM, HSPA8, CCL2, CCL8, APOBEC3A, TYMP, HERC6, ID3, S100A6, HLA-DPB1, FTH1, BIRC3, GAPDH, CD79A, FTL
Dataset 1:
TEX264, FTH1, VIM, CCNH, UBC, RGCC, ISG15, GBP1, RSAD2, CXCL10, PLAC8, CD74, SAT1, CD79A
Shared:
GIMAP7, RGCC, ACAT2, BTG1, THRAP3, RELB, LTB, H2AFZ, EIF2AK1, CXCR4, HERC6, BIRC3, SELL, HSPA8, GPR183, CCR7, BAK1, HIST1H2AC, CHCHD10, EIF1, HSPB1, RPS27, JTB, MALAT1, H3F3B, PTMA, TMEM66, HSP90AB1, ANXA1, HLA-B
Dataset 2
GBP1, RSAD2, RGCC, UBC, ISG15, CXCL10, PLAC8, CD74, SAT1, CD79A, TEX264, VIM, FTH1, CCNH
Dataset 1:
CD14, S100A8, IFI27, RPL31, RPL27A, RPL21, RPL7, GBP1, MARCKSL1, RPS8, S100A6, S100A4, RPS27A, IL1B, PTMA, RPL15, RPL14, GPX1, IL8, CXCL3, H2AFZ, RPL34, RPS3A, RPS23, RPL10A, RPS4X, RPS6, RPS3, GAPDH, RGCC
Shared:
MARCKSL1, TIMP1, C15orf48, SOD2, FTH1, CD63, ANXA5, CSTB, SRGN, GAPDH, FTL, TYROBP, FCER1G, S100A11, EIF1, IL8, LGALS1, TYMP, B2M, LGALS3, ANXA2, CTSB, VIM, TXN, S100A10, ACTB, CCL2, NFKBIA, LYZ, HLA-B
Dataset 2
TXN, CST3, IDO1, APOBEC3A, MARCKSL1, PLAC8, S100A6, S100A4, HERC6, RPL19, RPS3, ISG15, GBP1, SELL, RSAD2, CXCL10, HIST1H2AC, HLA-C, HSPA1A, FAM26F, HSPB1, SAT1, CTSL, BIRC3, IFI27, CCL2, CCL7, CCL8, CCR7, APOBEC3B
Dataset 1:
IDO1, CST7, VMO1, IL8, SAT1, RPS5, TYMP, LAGE3, CXCR4, TIMP1, RGCC, RPL3, ISG15, GBP1, S100A4, SELL, RSAD2, CXCL10, HSPA1A, HSP90AB1, FAM26F, HSPB1, CTSB, ANXA1, HSPA8, IFI27, CCL2, H3F3B, APOBEC3A, APOBEC3B
Shared:
HLA-DPA1, HLA-DPB1, HLA-DRA, CD74, HLA-DRB1, TXN, HLA-DQA1, IDO1, CST3, CCR7, CD83, ANXA2, GPR183, MARCKSL1, ACTB, BIRC3, LYZ, CST7, TMSB4X, C15orf48, S100A10, LGALS1, B2M, GPX1, CD79A, NFKBIA, H2AFZ, RELB, ISG15, HSPA1A
Dataset 2
CXCL10, HSPA1A, ISG15, FAM26F, HSPB1, HERC6, GBP1, S100A4, APOBEC3G, RSAD2, HSP90AB1, HSPA8, SELL, SAT1, CTSB, IDO1, ANXA1, IFI27, CCL2, H3F3B, APOBEC3A, APOBEC3B, TYMP, CXCR4, IL8, TIMP1, RGCC, VMO1, CST7, RPS5
Dataset 1:
H3F3B, BIRC3, ISG15, HLA-C
Shared:
DUSP2, JUNB, GADD45B, HIST1H2AC, MYC, NFKBIA, BIRC3, BTG1, GZMK, CD83, PABPC1, APOBEC3G, TMEM66, H3F3B, EIF1, PTMA, UBC, HLA-C, NDUFC2, RPS19, GPR183, MALAT1, RPS5, RPL18, HLA-A, RPL19, RPS27, SRGN, RPL3, RPL27A
Dataset 2
HLA-C, ISG15, BIRC3, H3F3B
Dataset 1:
GAPDH, RPL12, FTL, ISG15, FCER1G, RSAD2, TYMP
Shared:
GZMH, FGFBP2, CCL5, CLIC3, NKG7, GZMB, CST7, GZMK, HLA-B, APOBEC3G, B2M, HLA-C, PTMA, TMSB4X, NDUFC2, RGCC, ANXA1, HLA-A, GAPDH, ACTN1, PLAC8, RPS19, MALAT1, RPL15, JTB, KLRD1, RPS3, TMEM66, RPS15A, RPL3
Dataset 2
TYMP, FCER1G, ISG15, RSAD2, RPL12, GAPDH, FTL
Dataset 1:
CCL2, H2AFZ, CD14, CTSL, RPL10A, RPS8, RPS6, TIMP1, S100A8, RPS27, RPLP0, RPL21, RPL14, RPL34, RPL7, RPL18A, ID3, RPL11, MARCKSL1, RPL31, IL1B, RPL15, RPL9, IL8, RPS3A, RPS14, NPM1, RPS4X, RPL10, PABPC1
Shared:
S100A4, LGALS3, CTSL, S100A6, GPX1, S100A11, FTL, S100A10, LGALS1, CTSB, CST3, FCER1G, ACTB, VIM, ANXA2, CD63, TYMP, TYROBP, CSTB, HLA-DRB1, CCL2, FCGR3A, ANXA1, ANXA5, SAT1, ACTN1, JTB, HLA-DRA, HLA-DPB1, H3F3B
Dataset 2
HSPB1, FAM26F, LYZ, HSPA1A, RPS14, RPL9, HIST1H2AC, HLA-A, APOBEC3A, ISG15, GBP1, RSAD2, CXCL10, HLA-C, HSP90AB1, SAT1, IDO1, CTSL, TXN, CREM, CCL2, CCL7, CCL8, APOBEC3B, APOBEC3G, TYMP, HERC6, ID3, RPL11, MARCKSL1
Dataset 1:
HSPA1A, H3F3B, CXCR4, FTL, ISG15, GBP1, RSAD2, RPL34, HLA-A, HLA-C, HLA-B, RPLP1, RPS2
Shared:
UBC, HSPA1A, GADD45G, GADD45B, HSP90AB1, HSPA8, HSPB1, H3F3B, PPBP, CREM, SAT1, BIRC3, CCNH, EIF1, NFKBIA, H2AFZ, JUNB, ID3, TMEM66, BTG1, MALAT1, RPS27, HIST1H2AC, NPM1, GBP1, CXCR4, RPS12, RPL14, RELB, CXCL10
Dataset 2
GBP1, RPLP1, HLA-C, RSAD2, HLA-B, ISG15, RPL34, HLA-A, RPS2, CXCR4, HSPA1A, H3F3B, FTL
Dataset 1:
CXCL3, IL8, FTH1, RPL9, GBP1, MARCKSL1, IL1B, H2AFZ, CD14, ISG15, RSAD2, CXCL10, HIST1H2AC, HSPA1A, FAM26F, HSPB1, SAT1, IDO1, CCL8, CST3, APOBEC3A, APOBEC3G
Shared:
IL1B, LYZ, IL8, CST3, NFKBIA, CCL3, S100A10, APOBEC3B, GPX1, ACTB, C15orf48, ANXA2, S100A6, S100A4, HLA-DPB1, CCL4, CXCL3, HLA-DRA, HLA-DRB1, S100A11, TYROBP, IFI27, JTB, HLA-DPA1, VIM, FCER1G, CD74, SRGN, ANXA1, HBA1
Dataset 2
FAM26F, CXCL10, CST3, HSPA1A, IL1B, SAT1, IDO1, ISG15, GBP1, RSAD2, HIST1H2AC, HSPB1, CCL8, APOBEC3A, APOBEC3G, MARCKSL1, RPL9, IL8, CXCL3, H2AFZ, CD14, FTH1
Dataset 1:
APOBEC3B, IL8, S100A4, MARCKSL1, RPS27A, RPL15, RPL7, RPL12, S100A9, PABPC1, S100A8, IL1B, TIMP1, RPS6, BTG1, RPLP0, RGCC, RPL13A, RPL3, ISG15, GBP1, RSAD2, CXCL10, HIST1H2AC, HSPA1A, FAM26F, HSPB1, SAT1, CTSB, IDO1
Shared:
S100A8, S100A9, CD14, GPX1, APOBEC3B, S100A6, TYROBP, LGALS1, S100A4, TYMP, S100A10, IL8, MS4A7, S100A11, FTL, NFKBIA, FTH1, MARCKSL1, APOBEC3A, FCER1G, LYZ, SRGN, SAT1, GAPDH, C15orf48, ANXA5, ACTB, CTSB, ISG15, CD63
Dataset 2
CCL2, HIST1H2AC, S100A8, IDO1, CCL8, CCL7, FAM26F, CTSB, CST3, HSPA1A, APOBEC3G, HSPB1, ISG15, GBP1, RSAD2, CXCL10, SAT1, CTSL, TXN, LGALS3, APOBEC3A, APOBEC3B, MARCKSL1, S100A9, S100A4, RPS27A, IL1B, RPL15, IL8, TIMP1
Dataset 1:
GAPDH, VIM, ACTB, S100A6, TIMP1, RGCC, ISG15, CXCL10, HLA-DPA1, CREM, CD79A
Shared:
RBM10, GZMK, LAGE3, ACAT2, NDUFC2, RPL14, CHCHD10, HSP90AB1, RPLP0, APOBEC3A, RPL12, RSAD2, RPL18A, GAPDH, CSTB, RPS3, RPS6, NPM1, RPL18, RPS15A, RPS19, TMSB4X, RPS12, HLA-A, TYMP, RPS3A, CCL5, RPL15, CD14, LGALS3
Dataset 2
CREM, HLA-DPA1, ISG15, CXCL10, CD79A, S100A6, ACTB, TIMP1, VIM, GAPDH, RGCC
Dataset 1:
TMEM66, BTG1, ISG15, RSAD2, SAT1, ANXA1, HERC6
Shared:
KLRC1, KLRD1, GNLY, APOBEC3G, NKG7, CD7, GZMB, HLA-A, PLAC8, PPBP, LAGE3, CCL5, GPR183, SRGN, HLA-B, TEX264, THRAP3, EIF2AK1, B2M, TMSB4X, CD63, HLA-C, RPL9, XCL2, RPS27A, CXCR4, RPS3, RPLP1, H3F3B, ACTB
Dataset 2
ANXA1, HERC6, ISG15, RSAD2, SAT1, TMEM66, BTG1
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total iterations: 42
Total time: 0 sec
Objective error: 59878.9
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 49910.7
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 41528.3
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 47418.4
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
INMF started, niter=30
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 1 sec
Objective error: 35967.3
INMF started, niter=30
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 1 sec
Objective error: 35967.3
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45479.1
**|
INMF started, niter=2
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time: 0 sec
Objective error: 49910.7
completed constructor::A::173x300
time taken:35.6457
completed constructor::A::173x300
time taken:37.6061
completed constructor::A::173x300
time taken:36.7154
completed constructor::A::173x300
time taken:42.695
completed constructor::A::173x300
time taken:38.6121
completed constructor::A::173x300
time taken:32.3453
Working ctrl H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpqqBSpR\ctrltest_1544c11b537a4.h5
Working stim H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpqqBSpR\stimtest_1544c68927cc8.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
A liger command record, performed at 04-16-2025 01:59:03 EDT
Call: normalize.liger(object)
Parameters:
useDatasets : "ctrl", "stim"
verbose : TRUE
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
Working ctrl H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpqqBSpR\ctrltest_1544c1a8435b.h5
Working stim H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpqqBSpR\stimtest_1544ccc34cf5.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 45414.7
**|
An object of class ligerDataset with 300 cells
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Working ctrl H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpqqBSpR\ctrltest_1544c4350592b.h5
Working stim H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpqqBSpR\stimtest_1544c2355171.h5
Working ctrl H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpqqBSpR\ctrltest_1544c7f201df4.h5
Working stim H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpqqBSpR\stimtest_1544c5cf010c5.h5
Working ctrl H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpqqBSpR\ctrltest_1544c6368504.h5
Working stim H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpqqBSpR\stimtest_1544c28c773eb.h5
Working ctrl H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpqqBSpR\ctrltest_1544c240c616.h5
Working stim H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpqqBSpR\stimtest_1544c51dc140a.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
Working ctrl H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpqqBSpR\ctrltest_1544c43564bbf.h5
Working stim H5 file path: D:\temp\2025_04_16_01_50_00_21006\RtmpqqBSpR\stimtest_1544c62ab5721.h5
Starting online iNMF scenario 1, factorize all datasets
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations: 30
Total time: 0 sec
Objective error: 37129
**|
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 1329 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• {DoubletFinder} is not installed (1): 'test_preprocessing.R:112:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_factorization.R:111:5'): UINMF ─────────────────────────────────
<Rcpp::exception/C++Error/error/condition>
Error: k must be <= m
Backtrace:
▆
1. ├─rliger::runUINMF(pbmc, k = 30, nIteration = 2, nRandomStarts = 2) at test_factorization.R:111:5
2. └─rliger:::runUINMF.liger(pbmc, k = 30, nIteration = 2, nRandomStarts = 2)
3. └─rliger:::.runUINMF.list(...)
4. └─RcppPlanc::uinmf(...)
5. └─RcppPlanc:::.uinmf_rcpp(...)
── Error ('test_factorization.R:130:5'): Optimize new parameters ───────────────
<Rcpp::exception/C++Error/error/condition>
Error: Must provide 2 V matrices
Backtrace:
▆
1. └─rliger::optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2) at test_factorization.R:130:5
2. ├─rliger::runINMF(...)
3. └─rliger:::runINMF.liger(...)
4. └─rliger:::.runINMF.list(...)
5. └─RcppPlanc::inmf(...)
6. └─RcppPlanc:::.bppinmf(...)
── Error ('test_factorization.R:180:5'): Online iNMF - in-memory ───────────────
<std::invalid_argument/C++Error/error/condition>
Error: Must provide 2 H matrices
Backtrace:
▆
1. ├─rliger::runOnlineINMF(...) at test_factorization.R:180:5
2. └─rliger:::runOnlineINMF.liger(...)
3. └─rliger:::.runOnlineINMF.list(...)
4. └─RcppPlanc::onlineINMF(...)
5. └─RcppPlanc:::.onlineINMF_withInitial(...)
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 1329 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64