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 f?r Umweltforschung GmbH - UFZ
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstra?e 15, 04318 Leipzig, Germany
Phone +49 341 235 1353
sebastian.canzler at ufz.de
www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzende des Aufsichtsrats/Chairwoman of the Supervisory Board: MinDirig'in Oda Keppler
Wissenschaftlicher Gesch?ftsf?hrer/Scientific Managing Director:
Prof. Dr. Georg Teutsch
Administrative Gesch?ftsf?hrerin/Administrative Managing Director:
Dr. Sabine K?nig
Here's what happened when I tried to build your package as instructed in
the report page:
stvjc at 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.
On Wed, Nov 4, 2020 at 5:29 AM Sebastian Canzler <sebastian.canzler at 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 f?r Umweltforschung GmbH - UFZ
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstra?e 15, 04318 Leipzig, Germany
Phone +49 341 235 1353
sebastian.canzler at ufz.de
www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzende des Aufsichtsrats/Chairwoman of the Supervisory Board:
MinDirig'in Oda Keppler
Wissenschaftlicher Gesch?ftsf?hrer/Scientific Managing Director:
Prof. Dr. Georg Teutsch
Administrative Gesch?ftsf?hrerin/Administrative Managing Director:
Dr. Sabine K?nig
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
? 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 at r-project.org on behalf of stvjc at channing.harvard.edu> wrote:
Here's what happened when I tried to build your package as instructed in
the report page:
stvjc at 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 at 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 f?r Umweltforschung GmbH - UFZ
> Helmholtz Centre for Environmental Research GmbH - UFZ
> Permoserstra?e 15, 04318 Leipzig, Germany
> Phone +49 341 235 1353
> sebastian.canzler at ufz.de
> www.ufz.de
>
>
> Sitz der Gesellschaft/Registered Office: Leipzig
> Registergericht/Registration Office: Amtsgericht Leipzig
> Handelsregister Nr./Trade Register Nr.: B 4703
> Vorsitzende des Aufsichtsrats/Chairwoman of the Supervisory Board:
> MinDirig'in Oda Keppler
> Wissenschaftlicher Gesch?ftsf?hrer/Scientific Managing Director:
> Prof. Dr. Georg Teutsch
> Administrative Gesch?ftsf?hrerin/Administrative Managing Director:
> Dr. Sabine K?nig
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
The information in this e-mail is intended only for the ...{{dropped:18}}
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