Alexey Sergushichev
| Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/fgsea |
| git_branch: RELEASE_3_21 |
| git_last_commit: e0a2456 |
| git_last_commit_date: 2025-04-15 11:03:11 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:16 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 727/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fgsea 1.34.0 (landing page) Alexey Sergushichev
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the fgsea package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fgsea.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: fgsea |
| Version: 1.34.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fgsea.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fgsea_1.34.0.tar.gz |
| StartedAt: 2025-04-21 20:44:13 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 20:47:55 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 221.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: fgsea.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fgsea.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fgsea_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/fgsea.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fgsea/DESCRIPTION’ ... OK
* this is package ‘fgsea’ version ‘1.34.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘fgsea’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... INFO
installed size is 5.6Mb
sub-directories of 1Mb or more:
data 1.1Mb
extdata 3.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
setUpBPPARAM: warning in MulticoreParam(workers = nproc, progress =
TRUE): partial argument match of 'progress' to 'progressbar'
addGesecaScores: no visible global function definition for
‘DefaultAssay’
addGesecaScores: no visible global function definition for ‘GetAssay’
collapsePathways: no visible binding for global variable ‘pathway’
collapsePathways: no visible binding for global variable ‘ES’
collapsePathwaysGeseca: no visible binding for global variable
‘pvalCond’
collapsePathwaysGeseca: no visible binding for global variable
‘pathway’
collapsePathwaysGeseca: no visible binding for global variable
‘reciprocalPvalCond’
collapsePathwaysGeseca: no visible binding for global variable ‘pScore’
collapsePathwaysGeseca: no visible binding for global variable ‘pval’
fgseaMultilevel: no visible binding for global variable ‘modeFraction’
fgseaMultilevel: no visible binding for global variable ‘denomProb’
fora: no visible binding for global variable ‘es’
fora: no visible binding for global variable ‘k’
fora: no visible binding for global variable ‘m’
fora: no visible binding for global variable ‘pval’
geseca: no visible binding for global variable ‘gsScore’
geseca: no visible binding for global variable ‘log2err’
geseca: no visible binding for global variable ‘nGeScore’
geseca: no visible binding for global variable ‘pctVar’
geseca: no visible binding for global variable ‘size’
geseca: no visible binding for global variable ‘pathway’
geseca: no visible global function definition for ‘.’
geseca: no visible binding for global variable ‘pval’
geseca: no visible binding for global variable ‘padj’
gesecaSimple: no visible binding for global variable ‘pctVar’
gesecaSimple: no visible binding for global variable ‘size’
gesecaSimple: no visible binding for global variable ‘pval’
gesecaSimpleImpl: no visible binding for global variable ‘pval’
gesecaSimpleImpl: no visible binding for global variable ‘nGeScore’
gesecaSimpleImpl: no visible binding for global variable ‘padj’
gesecaSimpleImpl: no visible binding for global variable ‘size’
plotCoregulationProfile: no visible binding for global variable ‘id’
plotCoregulationProfile: no visible binding for global variable ‘gene’
plotCoregulationProfile: no visible binding for global variable
‘expressionValue’
plotCoregulationProfile: no visible binding for global variable ‘x’
plotCoregulationProfile: no visible binding for global variable ‘y’
plotCoregulationProfile: no visible binding for global variable
‘condition’
plotCoregulationProfileReduction: no visible global function definition
for ‘DefaultAssay’
plotCoregulationProfileSpatial: no visible global function definition
for ‘DefaultAssay’
plotGesecaTable: no visible global function definition for ‘modifyList’
plotGesecaTable: no visible binding for global variable ‘pathway’
plotGesecaTable: no visible binding for global variable ‘value’
plotGesecaTable : <anonymous>: no visible binding for global variable
‘pathway’
plotGesecaTable : <anonymous>: no visible binding for global variable
‘value’
plotGseaTable: no visible global function definition for ‘modifyList’
Undefined global functions or variables:
. DefaultAssay ES GetAssay condition denomProb es expressionValue
gene gsScore id k log2err m modeFraction modifyList nGeScore pScore
padj pathway pctVar pval pvalCond reciprocalPvalCond size value x y
Consider adding
importFrom("utils", "modifyList")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotGseaTable 15.806 0.624 13.584
collapsePathways 13.216 0.741 9.059
fgseaSimple 9.217 1.893 3.563
mapIdsList 8.426 0.626 6.929
fgsea 7.132 0.447 4.032
fgseaMultilevel 6.865 0.411 3.696
geseca 4.797 0.965 3.099
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/fgsea.Rcheck/00check.log’
for details.
fgsea.Rcheck/00install.out
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL fgsea
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘fgsea’ ...
** this is package ‘fgsea’ version ‘1.34.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ScoreCalculation.cpp -o ScoreCalculation.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ScoreRuler.cpp -o ScoreRuler.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c esCalculation.cpp -o esCalculation.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastGSEA.cpp -o fastGSEA.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fgseaMultilevel.cpp -o fgseaMultilevel.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
fgseaMultilevelSupplement.cpp:77:16: warning: unused variable 'currentES' [-Wunused-variable]
double currentES = calcES(ranks, currentSamples[sampleId]);
^
fgseaMultilevelSupplement.cpp:270:14: warning: unused variable 'fl' [-Wunused-variable]
bool fl = false;
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c geseca.cpp -o geseca.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c util.cpp -o util.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o fgsea.so RcppExports.o ScoreCalculation.o ScoreRuler.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o geseca.o util.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-fgsea/00new/fgsea/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (fgsea)
fgsea.Rcheck/tests/testthat.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(fgsea)
>
> test_check("fgsea")
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2025-04-21 20:47:40.525 R[71984:727352192] XType: com.apple.fonts is not accessible.
2025-04-21 20:47:40.525 R[71984:727352192] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 2 | SKIP 2 | PASS 141 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_gsea_analysis.R:80:5'
• On Mac (1): 'test_gsea_stat.R:98:5'
[ FAIL 0 | WARN 2 | SKIP 2 | PASS 141 ]
>
> proc.time()
user system elapsed
97.985 20.177 91.909
fgsea.Rcheck/fgsea-Ex.timings
| name | user | system | elapsed | |
| calcGseaStat | 0.037 | 0.009 | 0.045 | |
| collapsePathways | 13.216 | 0.741 | 9.059 | |
| collapsePathwaysORA | 0.194 | 0.011 | 0.207 | |
| fgsea | 7.132 | 0.447 | 4.032 | |
| fgseaLabel | 0.001 | 0.000 | 0.000 | |
| fgseaMultilevel | 6.865 | 0.411 | 3.696 | |
| fgseaSimple | 9.217 | 1.893 | 3.563 | |
| fora | 0.132 | 0.027 | 0.160 | |
| geseca | 4.797 | 0.965 | 3.099 | |
| gesecaSimple | 0.894 | 0.404 | 1.276 | |
| gmtPathways | 0.107 | 0.014 | 0.125 | |
| mapIdsList | 8.426 | 0.626 | 6.929 | |
| multilevelError | 0 | 0 | 0 | |
| plotEnrichment | 0.001 | 0.002 | 0.014 | |
| plotEnrichmentData | 0.455 | 0.040 | 0.502 | |
| plotGseaTable | 15.806 | 0.624 | 13.584 | |
| reactomePathways | 2.224 | 0.138 | 2.416 | |
| writeGmtPathways | 0.045 | 0.003 | 0.048 | |