[Bioc-devel] Vignette building error in multiGSEA
Martin Morgan
mtmorg@n@b|oc @end|ng |rom gm@||@com
Wed Nov 4 16:53:22 CET 2020
I made sure I was using Bioc-3.13 and that my packages were valid
> BiocManager::version()
[1] '3.13'
> BiocManager::valid()
[1] TRUE
I then ran purl() and source(), eventually arriving at the error on the build system
> knitr::purl("multiGSEA.rmd")
[1] "multiGSEA.R"
> source("multiGSEA.R", echo=TRUE, max = Inf)
> knitr::kable(
+ df %>%
+ dplyr::arrange( combined_padj) %>%
+ dplyr::filter( !is.na(metabolome_padj) ) %>%
+ dplyr::select( c( pa .... [TRUNCATED]
Error: Problem with `filter()` input `..1`.
✖ object 'metabolome_padj' not found
ℹ Input `..1` is `!is.na(metabolome_padj)`.
Run `rlang::last_error()` to see where the error occurred.
In addition: Warning messages:
1: In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, :
There are ties in the preranked stats (79.1% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
2: In (function (..., deparse.level = 1) :
number of columns of result is not a multiple of vector length (arg 2312)
When I look at the column names of df, I see
> names(df)
[1] "pathway" "transcriptome_pval1" "transcriptome_pval2"
[4] "transcriptome_padj1" "transcriptome_padj2" "proteome_pval1"
[7] "proteome_pval2" "proteome_padj1" "proteome_padj2"
[10] "metabolome_pval1" "metabolome_pval2" "metabolome_padj1"
[13] "metabolome_padj2" "combined_pval" "combined_padj"
where the appended '1' and '2' suggest a merge that went in an unexpected direction?
Also like Vince I saw many hundreds of lines of ` 'select()' returned 1:many mapping between keys and columns`, which suggests to me that some code is calling `select()` or mapIds()` once for each entry, rather than once for a vector of entries. Also this
snapshotDate(): 2020-11-02
loading from cache
Martin
On 11/4/20, 8:02 AM, "Bioc-devel on behalf of Vincent Carey" <bioc-devel-bounces using r-project.org on behalf of stvjc using channing.harvard.edu> wrote:
Here's what happened when I tried to build your package as instructed in
the report page:
stvjc using stvjc-XPS-13-9300:~/BIOC_SOURCES$ R_ENVIRON_USER=~/.Renviron.bioc
Rdev CMD build multiGSEA
1/9 packages newly attached/loaded, see sessionInfo() for details.
* checking for file ‘multiGSEA/DESCRIPTION’ ... OK
* preparing ‘multiGSEA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘multiGSEA.rmd’ using rmarkdown
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
this goes on for pages. then:
select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Quitting from lines 259-267 (multiGSEA.rmd)
Error: processing vignette 'multiGSEA.rmd' failed with diagnostics:
The necessary package metabolieIDmapping is not installed.
--- failed re-building ‘multiGSEA.rmd’
SUMMARY: processing the following file failed:
‘multiGSEA.rmd’
Error: Vignette re-building failed.
Execution halted
Now is "metabolieIDmapping" a spelling error?
sessionInfo:
> library(multiGSEA)
1/70 packages newly attached/loaded, see sessionInfo() for details.
> sessionInfo()
R Under development (unstable) (2020-10-29 r79387)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS (fossa-melisa X20)
Matrix products: default
BLAS: /home/stvjc/R-dev-dist/lib/R/lib/libRblas.so
LAPACK: /home/stvjc/R-dev-dist/lib/R/lib/libRlapack.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=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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] multiGSEA_1.1.0 rmarkdown_2.5
loaded via a namespace (and not attached):
[1] Biobase_2.51.0 httr_1.4.2 bit64_4.0.5
[4] splines_4.1.0 tmvnsim_1.0-2 sn_1.6-2
[7] Rdpack_2.0 stats4_4.1.0 blob_1.2.1
[10] TFisher_0.2.0 numDeriv_2016.8-1.1 pillar_1.4.6
[13] RSQLite_2.2.1 backports_1.1.10 lattice_0.20-41
[16] glue_1.4.2 digest_0.6.27 rbibutils_1.3
[19] checkmate_2.0.0 colorspace_1.4-1 sandwich_3.0-0
[22] htmltools_0.5.0 Matrix_1.2-18 pkgconfig_2.0.3
[25] purrr_0.3.4 mvtnorm_1.1-1 scales_1.1.1
[28] BiocParallel_1.25.0 tibble_3.0.4 generics_0.0.2
[31] IRanges_2.25.0 ggplot2_3.3.2 ellipsis_0.3.1
[34] TH.data_1.0-10 BiocGenerics_0.37.0 mnormt_2.0.2
[37] survival_3.2-7 magrittr_1.5 crayon_1.3.4
[40] memoise_1.1.0 evaluate_0.14 MASS_7.3-53
[43] xml2_1.3.2 graph_1.69.0 tools_4.1.0
[46] data.table_1.13.2 gbRd_0.4-11 lifecycle_0.2.0
[49] multcomp_1.4-14 mutoss_0.1-12 S4Vectors_0.29.0
[52] munsell_0.5.0 plotrix_3.7-8 AnnotationDbi_1.53.0
[55] compiler_4.1.0 rlang_0.4.8 grid_4.1.0
[58] rappdirs_0.3.1 startup_0.15.0 multtest_2.47.0
[61] gtable_0.3.0 codetools_0.2-16 DBI_1.1.0
[64] R6_2.5.0 gridExtra_2.3 zoo_1.8-8
[67] knitr_1.30 dplyr_1.0.2 graphite_1.37.0
[70] bit_4.0.4 mathjaxr_1.0-1 fastmatch_1.1-0
[73] fgsea_1.17.0 metap_1.4 parallel_4.1.0
[76] Rcpp_1.0.5 vctrs_0.3.4 tidyselect_1.1.0
[79] xfun_0.18
>
On Wed, Nov 4, 2020 at 5:29 AM Sebastian Canzler <sebastian.canzler using ufz.de>
wrote:
> Dear BioC-Developers,
>
> after the Release of Bioconductor 3.12 I encountered a building error of
> the multiGSEA package in the devel branch (building the vignette causes
> the error, see:
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/multiGSEA/machv2-buildsrc.html
> ).
> Until now, I am not able to reproduce this error locally. Within my
> local testing environment with R 4.1 and BioC 3.13 everything runs
> smoothly.
> R CMD build finishes without errors and the vignette caused no problems
> at al.
>
> Furthermore, I didn't change anything in the package or vignette and it
> builds without error in the 3.12 version.
>
> Any advice on this issue is much appreciated.
>
> Thanks,
>
> Sebastian
>
> --
>
> Dr. Sebastian Canzler
>
> Young Investigators Group Bioinformatics & Transcriptomics
> Department of Molecular Systems Biology
>
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
> Helmholtz Centre for Environmental Research GmbH - UFZ
> Permoserstraße 15, 04318 Leipzig, Germany
> Phone +49 341 235 1353
> sebastian.canzler using ufz.de
> www.ufz.de
>
>
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