Alexey Sergushichev
| Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/fgsea |
| git_branch: devel |
| git_last_commit: f5458a4 |
| git_last_commit_date: 2024-12-19 11:47:37 -0500 (Thu, 19 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-23 11:45 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
| 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 706/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fgsea 1.33.2 (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 22.03 LTS-SP1) / 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: 1.33.2 |
| 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_1.33.2.tar.gz |
| StartedAt: 2024-12-22 19:19:13 -0500 (Sun, 22 Dec 2024) |
| EndedAt: 2024-12-22 19:20:32 -0500 (Sun, 22 Dec 2024) |
| EllapsedTime: 78.9 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_1.33.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/fgsea.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fgsea/DESCRIPTION’ ... OK
* this is package ‘fgsea’ version ‘1.33.2’
* 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 15.0.0 (clang-1500.1.0.2.5)’
* 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 6.046 0.246 4.739
* 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-arm64/Resources/library’
* installing *source* package ‘fgsea’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ScoreCalculation.cpp -o ScoreCalculation.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ScoreRuler.cpp -o ScoreRuler.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c esCalculation.cpp -o esCalculation.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c fastGSEA.cpp -o fastGSEA.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c fgseaMultilevel.cpp -o fgseaMultilevel.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c geseca.cpp -o geseca.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c util.cpp -o util.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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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2024-12-22 19:20:27.086 R[63021:161431896] XType: Using static font registry.
[ 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
36.793 6.880 32.745
fgsea.Rcheck/fgsea-Ex.timings
| name | user | system | elapsed | |
| calcGseaStat | 0.013 | 0.002 | 0.016 | |
| collapsePathways | 4.441 | 0.221 | 2.863 | |
| collapsePathwaysORA | 0.055 | 0.005 | 0.060 | |
| fgsea | 3.686 | 0.152 | 1.906 | |
| fgseaLabel | 0.000 | 0.001 | 0.000 | |
| fgseaMultilevel | 3.603 | 0.209 | 1.849 | |
| fgseaSimple | 3.312 | 0.596 | 1.288 | |
| fora | 0.041 | 0.027 | 0.068 | |
| geseca | 1.771 | 0.298 | 1.124 | |
| gesecaSimple | 0.051 | 0.033 | 0.309 | |
| gmtPathways | 0.032 | 0.011 | 0.041 | |
| mapIdsList | 3.680 | 0.309 | 2.640 | |
| multilevelError | 0 | 0 | 0 | |
| plotEnrichment | 0.000 | 0.001 | 0.001 | |
| plotEnrichmentData | 0.149 | 0.017 | 0.167 | |
| plotGseaTable | 6.046 | 0.246 | 4.739 | |
| reactomePathways | 0.906 | 0.035 | 0.945 | |
| writeGmtPathways | 0.015 | 0.002 | 0.018 | |