[Bioc-devel] SPB inconsistencies
Martin Morgan
mtmorg@n@b|oc @end|ng |rom gm@||@com
Mon Mar 4 21:50:04 CET 2019
Thanks Marcel -- when you update this data, do you add a new resource or over-write an existing resource? I think the best practice would be to create a new resource, with updated curateTCGAData package & version bump. Martin
On 3/4/19, 2:31 PM, "Bioc-devel on behalf of Ramos Perez, Marcel" <bioc-devel-bounces using r-project.org on behalf of Marcel.RamosPerez using RoswellPark.org> wrote:
Hi Martin,
I suspect that this is due to caching because I'm unable to reproduce
including after deleting my hub cache.
hb <- ExperimentHub::ExperimentHub()
#> snapshotDate(): 2019-01-25
unlink(
AnnotationHub::hubCache(hb),
recursive = TRUE,
force = TRUE
)
suppressMessages({
gbm <- curatedTCGAData::curatedTCGAData("GBM",
assays=c("GISTIC_Peaks", "CNVSNP", "RNASeq2GeneNorm"),
dry.run=FALSE)
})
gbm
#> A MultiAssayExperiment object of 3 listed
#> experiments with user-defined names and respective classes.
#> Containing an ExperimentList class object of length 3:
#> [1] GBM_CNVSNP-20160128: RaggedExperiment with 146852 rows and 1104 columns
#> [2] GBM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 68 rows and 577 columns
#> [3] GBM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 166 columns
#> Features:
#> experiments() - obtain the ExperimentList instance
#> colData() - the primary/phenotype DataFrame
#> sampleMap() - the sample availability DataFrame
#> `$`, `[`, `[[` - extract colData columns, subset, or experiment
#> *Format() - convert into a long or wide DataFrame
#> assays() - convert ExperimentList to a SimpleList of matrices
sessionInfo()
#> R Under development (unstable) (2019-03-04 r76198)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 18.10
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] parallel stats4 stats graphics grDevices utils datasets
#> [8] methods base
#>
#> other attached packages:
#> [1] RaggedExperiment_1.7.4 curatedTCGAData_1.5.8
#> [3] MultiAssayExperiment_1.9.15 SummarizedExperiment_1.13.0
#> [5] DelayedArray_0.9.8 BiocParallel_1.17.17
#> [7] matrixStats_0.54.0 Biobase_2.43.1
#> [9] GenomicRanges_1.35.1 GenomeInfoDb_1.19.2
#> [11] IRanges_2.17.4 S4Vectors_0.21.10
#> [13] BiocGenerics_0.29.1 nvimcom_0.9-72
#>
#> loaded via a namespace (and not attached):
#> [1] Rcpp_1.0.0 XVector_0.23.0
#> [3] compiler_3.6.0 BiocManager_1.30.4.9003
#> [5] later_0.8.0 highr_0.7
#> [7] AnnotationHub_2.15.7 zlibbioc_1.29.0
#> [9] bitops_1.0-6 tools_3.6.0
#> [11] digest_0.6.18 bit_1.1-14
#> [13] lattice_0.20-38 RSQLite_2.1.1
#> [15] evaluate_0.13 memoise_1.1.0
#> [17] pkgconfig_2.0.2 Matrix_1.2-15
#> [19] shiny_1.2.0 DBI_1.0.0
#> [21] curl_3.3 yaml_2.2.0
#> [23] xfun_0.5 GenomeInfoDbData_1.2.0
#> [25] httr_1.4.0 stringr_1.4.0
#> [27] knitr_1.21 grid_3.6.0
#> [29] bit64_0.9-7 R6_2.4.0
#> [31] AnnotationDbi_1.45.0 rmarkdown_1.11
#> [33] ExperimentHub_1.9.1 blob_1.1.1
#> [35] magrittr_1.5 promises_1.0.1
#> [37] htmltools_0.3.6 mime_0.6
#> [39] interactiveDisplayBase_1.21.0 xtable_1.8-3
#> [41] httpuv_1.4.5.1 stringi_1.3.1
#> [43] RCurl_1.95-4.12
Created on 2019-03-04 by the reprex package<https://reprex.tidyverse.org> (v0.2.1)
Best,
Marcel
On 2/28/19 4:28 PM, Martin Morgan wrote:
In today's R-devel, I install packages required for the vignette, including CNVRanger's Suggests: packages, and ensure that my installation is valid (modulo some irrelevant packages) via BiocManager::valid().
I then Stangle'd the vignette
cd CNVRanger/vignettes
R CMD Stange CNVRanger.Rmd
and then in a new R session sourced the vignette code
source("CNVRanger.R", echo=TRUE, max=Inf)
it runs until
library(curatedTCGAData)
suppressMessages(
+ gbm <- curatedTCGAData("GBM",
+ assays=c("GISTIC_Peaks", "CNVSNP", "RNASeq2GeneNorm"),
+ dry.run=FALSE)
+ )
|======================================================================| 100%
|======================================================================| 100%
|======================================================================| 100%
gbm
A MultiAssayExperiment object of 2 listed
experiments with user-defined names and respective classes.
Containing an ExperimentList class object of length 2:
[1] GBM_CNVSNP-20160128: RaggedExperiment with 146852 rows and 1104 columns
[2] GBM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 166 columns
Features:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample availability DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
## ----gisticPeaks---------------------------------------------------------
peaks <- granges(rowRanges(gbm[["GBM_GISTIC_Peaks-20160128"]]))
Error in matrixStats::rowRanges(x, ...) :
Argument 'x' must be a matrix or a vector.
In addition: Warning message:
call dbDisconnect() when finished working with a connection
where the problem is apparent
gbm[["GBM_GISTIC_Peaks-20160128"]]
NULL
The MultiAssayExperiment doesn't contain GBM_GISTIC_Peaks-20160128.
If I try something simpler it also fails...
curatedTCGAData("GBM", assays = "GISTIC_Peaks", dry.run=FALSE)
snapshotDate(): 2019-01-25
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
downloading 0 resources
loading from cache
'/Users/ma38727//.ExperimentHub/2143'
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
downloading 0 resources
loading from cache
'/Users/ma38727//.ExperimentHub/671'
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
downloading 0 resources
loading from cache
'/Users/ma38727//.ExperimentHub/674'
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
downloading 0 resources
loading from cache
'/Users/ma38727//.ExperimentHub/685'
harmonizing input:
removing 6149 sampleMap rows not in names(experiments)
removing 599 colData rownames not in sampleMap 'primary'
A MultiAssayExperiment object of 0 listed
experiments with no user-defined names and respective classes.
Containing an ExperimentList class object of length 0:
Features:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample availability DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
So perhaps the problem is with the curated* package?
Here's my sessionInfo() (yikes!)
sessionInfo()
R Under development (unstable) (2019-02-28 r76173)
Platform: x86_64-apple-darwin17.7.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /Users/ma38727/bin/R-devel/lib/libRblas.dylib
LAPACK: /Users/ma38727/bin/R-devel/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] ensembldb_2.7.9
[2] AnnotationFilter_1.7.0
[3] GenomicFeatures_1.35.7
[4] AnnotationDbi_1.45.0
[5] TCGAutils_1.3.20
[6] curatedTCGAData_1.5.8
[7] MultiAssayExperiment_1.9.15
[8] SummarizedExperiment_1.13.0
[9] DelayedArray_0.9.8
[10] BiocParallel_1.17.17
[11] matrixStats_0.54.0
[12] Biobase_2.43.1
[13] BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99
[14] BSgenome.Btaurus.UCSC.bosTau6_1.4.0
[15] BSgenome_1.51.0
[16] rtracklayer_1.43.2
[17] Biostrings_2.51.2
[18] XVector_0.23.0
[19] regioneR_1.15.2
[20] AnnotationHub_2.15.7
[21] CNVRanger_0.99.18
[22] RaggedExperiment_1.7.4
[23] GenomicRanges_1.35.1
[24] GenomeInfoDb_1.19.2
[25] IRanges_2.17.4
[26] S4Vectors_0.21.10
[27] BiocGenerics_0.29.1
loaded via a namespace (and not attached):
[1] httr_1.4.0 edgeR_3.25.3
[3] splines_3.6.0 bit64_0.9-7
[5] jsonlite_1.6 shiny_1.2.0
[7] assertthat_0.2.0 statmod_1.4.30
[9] interactiveDisplayBase_1.21.0 BiocManager_1.30.4
[11] blob_1.1.1 GenomeInfoDbData_1.2.0
[13] Rsamtools_1.99.2 yaml_2.2.0
[15] progress_1.2.0 pillar_1.3.1
[17] RSQLite_2.1.1 lattice_0.20-38
[19] limma_3.39.12 glue_1.3.0
[21] digest_0.6.18 promises_1.0.1
[23] rvest_0.3.2 htmltools_0.3.6
[25] httpuv_1.4.5.1 Matrix_1.2-15
[27] XML_3.98-1.17 pkgconfig_2.0.2
[29] biomaRt_2.39.3 zlibbioc_1.29.0
[31] purrr_0.3.0 xtable_1.8-3
[33] later_0.8.0 tibble_2.0.1
[35] lazyeval_0.2.1 magrittr_1.5
[37] crayon_1.3.4 mime_0.6
[39] memoise_1.1.0 xml2_1.2.0
[41] tools_3.6.0 prettyunits_1.0.2
[43] hms_0.4.2 stringr_1.4.0
[45] locfit_1.5-9.1 compiler_3.6.0
[47] rlang_0.3.1 grid_3.6.0
[49] GenomicDataCommons_1.7.3 RCurl_1.95-4.11
[51] rappdirs_0.3.1 bitops_1.0-6
[53] ExperimentHub_1.9.1 DBI_1.0.0
[55] curl_3.3 R6_2.4.0
[57] GenomicAlignments_1.19.1 dplyr_0.8.0.1
[59] bit_1.1-14 ProtGenerics_1.15.0
[61] readr_1.3.1 stringi_1.3.1
[63] Rcpp_1.0.0 tidyselect_0.2.5
On 2/28/19, 2:19 PM, "Bioc-devel on behalf of Ludwig Geistlinger" <bioc-devel-bounces using r-project.org on behalf of Ludwig.Geistlinger using sph.cuny.edu><mailto:bioc-devel-bounces using r-project.orgonbehalfofLudwig.Geistlinger@sph.cuny.edu> wrote:
Hi,
According to
http://bioconductor.org/checkResults/devel/bioc-LATEST/index.html
all SPB machines run different snapshots of R-devel with the most recent one (2019-01-22 r76000,
already >1 month outdated) installed on celaya2.
I observe two things:
1. My package builds on celaya2, but fails to build on the other SPB machines running older R-devel snapshots.
http://bioconductor.org/checkResults/devel/bioc-LATEST/CNVRanger/
2. Further, I can't reproduce the SPB built error using a recent R-devel snapshot (2019-02-24 r76155) through the bioconductor/devel_base2 docker container.
Can you please advise on how to best proceed from my side? Just wait for the SPB R-devel being updated?
> sessionInfo()
R Under development (unstable) (2019-02-24 r76155)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)
Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] TCGAutils_1.3.19
[2] BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99
[3] BSgenome.Btaurus.UCSC.bosTau6_1.4.0
[4] BSgenome_1.51.0
[5] rtracklayer_1.43.1
[6] Biostrings_2.51.2
[7] XVector_0.23.0
[8] regioneR_1.15.2
[9] BiocStyle_2.11.0
[10] CNVRanger_0.99.7
[11] curatedTCGAData_1.5.8
[12] edgeR_3.25.3
[13] limma_3.39.12
[14] RaggedExperiment_1.7.4
[15] MultiAssayExperiment_1.9.15
[16] SummarizedExperiment_1.13.0
[17] DelayedArray_0.9.8
[18] BiocParallel_1.17.16
[19] matrixStats_0.54.0
[20] ensembldb_2.7.9
[21] AnnotationFilter_1.7.0
[22] GenomicFeatures_1.35.7
[23] AnnotationDbi_1.45.0
[24] Biobase_2.43.1
[25] GenomicRanges_1.35.1
[26] GenomeInfoDb_1.19.2
[27] IRanges_2.17.4
[28] S4Vectors_0.21.10
[29] AnnotationHub_2.15.7
[30] BiocGenerics_0.29.1
loaded via a namespace (and not attached):
[1] ProtGenerics_1.15.0 bitops_1.0-6
[3] bit64_0.9-7 progress_1.2.0
[5] httr_1.4.0 GenomicDataCommons_1.7.3
[7] tools_3.6.0 R6_2.4.0
[9] DBI_1.0.0 lazyeval_0.2.1
[11] tidyselect_0.2.5 prettyunits_1.0.2
[13] bit_1.1-14 curl_3.3
[15] compiler_3.6.0 rvest_0.3.2
[17] xml2_1.2.0 readr_1.3.1
[19] rappdirs_0.3.1 stringr_1.4.0
[21] digest_0.6.18 Rsamtools_1.99.2
[23] rmarkdown_1.11 pkgconfig_2.0.2
[25] htmltools_0.3.6 rlang_0.3.1
[27] rstudioapi_0.9.0 RSQLite_2.1.1
[29] shiny_1.2.0 jsonlite_1.6
[31] dplyr_0.8.0.1 RCurl_1.95-4.11
[33] magrittr_1.5 GenomeInfoDbData_1.2.0
[35] Matrix_1.2-15 Rcpp_1.0.0
[37] stringi_1.3.1 yaml_2.2.0
[39] zlibbioc_1.29.0 grid_3.6.0
[41] blob_1.1.1 promises_1.0.1
[43] ExperimentHub_1.9.1 crayon_1.3.4
[45] lattice_0.20-38 hms_0.4.2
[47] locfit_1.5-9.1 knitr_1.21
[49] pillar_1.3.1 biomaRt_2.39.2
[51] XML_3.98-1.17 glue_1.3.0
[53] evaluate_0.13 BiocManager_1.30.4
[55] httpuv_1.4.5.1 purrr_0.3.0
[57] assertthat_0.2.0 xfun_0.5
[59] mime_0.6 xtable_1.8-3
[61] later_0.8.0 tibble_2.0.1
[63] GenomicAlignments_1.19.1 memoise_1.1.0
[65] interactiveDisplayBase_1.21.0
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