| Back to Rapid builds (Linux only) of a subset of BioC 3.23 Report updated every 6 hours |
This page was generated on 2026-01-02 03:53 -0500 (Fri, 02 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-18 r89199) -- "Unsuffered Consequences" | 926 |
| 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 87/230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| fgsea 1.37.4 (landing page) Alexey Sergushichev
| teran2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||
|
To the developers/maintainers of the fgsea package: - 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: 1.37.4 |
| Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:fgsea.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings fgsea_1.37.4.tar.gz |
| StartedAt: 2026-01-02 02:12:49 -0500 (Fri, 02 Jan 2026) |
| EndedAt: 2026-01-02 02:26:37 -0500 (Fri, 02 Jan 2026) |
| EllapsedTime: 827.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: fgsea.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:fgsea.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings fgsea_1.37.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/fgsea.Rcheck’
* using R Under development (unstable) (2025-12-18 r89199)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘fgsea/DESCRIPTION’ ... OK
* this is package ‘fgsea’ version ‘1.37.4’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Alexey Sergushichev <alsergbox@gmail.com>’
License components with restrictions and base license permitting such:
MIT + file LICENCE
File 'LICENCE':
YEAR: 2016-2019
COPYRIGHT HOLDER: Alexey Sergushichev
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Unknown, possibly misspelled, fields in DESCRIPTION:
‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’
Package CITATION file contains call(s) to old-style citEntry(). Please
use bibentry() instead.
The Description field should not start with the package name,
'This package' or similar.
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
installed size is 9.9Mb
sub-directories of 1Mb or more:
data 1.1Mb
extdata 3.9Mb
libs 4.6Mb
* 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 loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘addGesecaScores’
* 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
‘GetAssayData’
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’
plotCoregulationProfileImage: no visible global function definition for
‘DefaultAssay’
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 GetAssayData 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 ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NOTE
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotGseaTable 14.430 0.532 12.102
fgseaSimple 7.105 1.286 2.079
collapsePathways 7.501 0.397 5.283
mapIdsList 5.894 0.522 4.459
fgsea 5.895 0.333 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/fgsea.Rcheck/00check.log’
for details.
fgsea.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL fgsea
###
##############################################################################
##############################################################################
* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘fgsea’ ...
** this is package ‘fgsea’ version ‘1.37.4’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ScoreCalculation.cpp -o ScoreCalculation.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ScoreRuler.cpp -o ScoreRuler.o
ScoreRuler.cpp: In member function ‘void ScoreRuler::extend(double, int, double)’:
ScoreRuler.cpp:76:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
76 | for (moves = 0; moves < sampleSize * genesetSize;) {
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c esCalculation.cpp -o esCalculation.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function ‘Rcpp::NumericVector calcGseaStatBatchCpp(const Rcpp::NumericVector&, const Rcpp::List&, const Rcpp::IntegerVector&)’:
fastGSEA.cpp:449:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
449 | for (int j = 0; j < S.size(); ++j) {
| ~~^~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fgseaMultilevel.cpp -o fgseaMultilevel.o
fgseaMultilevel.cpp: In function ‘Rcpp::DataFrame fgseaMultilevelCpp(const Rcpp::NumericVector&, SEXPREC* const&, int, int, int, double, bool, double, bool)’:
fgseaMultilevel.cpp:15:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15 | for (int i = 0; i < posRanks.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
fgseaMultilevelSupplement.cpp: In member function ‘bool EsRuler::resampleGenesets(random_engine_t&)’:
fgseaMultilevelSupplement.cpp:64:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
64 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
| ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:76:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
76 | for (int sampleId = 0; sampleId < sampleSize; sampleId++){
| ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:84:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
84 | while (startFrom < sampleSize && get<0>(stats[startFrom]) == get<0>(stats[0])) {
| ~~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
89 | if (startFrom == sampleSize) {
| ~~~~~~~~~~^~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:101:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
101 | for (int i = startFrom; i < sampleSize; ++i) {
| ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
116 | for (int i = startFrom; i < sampleSize; ++i) {
| ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function ‘void EsRuler::extend(double, int, double)’:
fgseaMultilevelSupplement.cpp:144:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
144 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
| ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:180:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
180 | for (int j = 0; j < sampleSize; ++j) {
| ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:187:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
187 | for (int i = 0; i < sampleSize; ++i) {
| ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:206:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
206 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
| ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:212:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
212 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
| ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:217:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
217 | for (int i = 0; i < sampleSize; ++i) {
| ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function ‘std::tuple<double, bool, double> EsRuler::getPvalue(double, double, bool)’:
fgseaMultilevelSupplement.cpp:246:15: warning: unused variable ‘n’ [-Wunused-variable]
246 | int const n = (int) ranks.size();
| ^
fgseaMultilevelSupplement.cpp:247:15: warning: unused variable ‘k’ [-Wunused-variable]
247 | int const k = pathwaySize;
| ^
fgseaMultilevelSupplement.cpp: In member function ‘EsRuler::PerturbateResult EsRuler::perturbate_until(const std::vector<long int>&, int, SampleChunks&, gsea_t, random_engine_t&, const std::function<bool(int, int)>&)’:
fgseaMultilevelSupplement.cpp:435:14: warning: unused variable ‘fl’ [-Wunused-variable]
435 | bool fl = false;
| ^~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c geseca.cpp -o geseca.o
geseca.cpp: In function ‘Rcpp::List gesecaCpp(const Rcpp::NumericMatrix&, const Rcpp::NumericVector&, unsigned int, unsigned int, int, double)’:
geseca.cpp:9:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
9 | for (unsigned i = 0; i < E.nrow(); i++){
| ~~^~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c util.cpp -o util.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o fgsea.so RcppExports.o ScoreCalculation.o ScoreRuler.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o geseca.o util.o
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-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) (2025-12-18 r89199) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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")
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|= | 1%
|
|== | 3%
|
|=== | 4%
|
|==== | 5%
|
|===== | 7%
|
|====== | 8%
|
|======= | 10%
|
|======== | 11%
|
|========= | 12%
|
|========== | 14%
|
|=========== | 15%
|
|============ | 16%
|
|============ | 18%
|
|============= | 19%
|
|============== | 21%
|
|=============== | 22%
|
|================ | 23%
|
|================= | 25%
|
|================== | 26%
|
|=================== | 27%
|
|==================== | 29%
|
|===================== | 30%
|
|====================== | 32%
|
|======================= | 33%
|
|======================== | 34%
|
|========================= | 36%
|
|========================== | 37%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================= | 41%
|
|============================== | 42%
|
|=============================== | 44%
|
|================================ | 45%
|
|================================= | 47%
|
|================================== | 48%
|
|=================================== | 49%
|
|=================================== | 51%
|
|==================================== | 52%
|
|===================================== | 53%
|
|====================================== | 55%
|
|======================================= | 56%
|
|======================================== | 58%
|
|========================================= | 59%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================ | 63%
|
|============================================= | 64%
|
|============================================== | 66%
|
|=============================================== | 67%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 71%
|
|=================================================== | 73%
|
|==================================================== | 74%
|
|===================================================== | 75%
|
|====================================================== | 77%
|
|======================================================= | 78%
|
|======================================================== | 79%
|
|========================================================= | 81%
|
|========================================================== | 82%
|
|========================================================== | 84%
|
|=========================================================== | 85%
|
|============================================================ | 86%
|
|============================================================= | 88%
|
|============================================================== | 89%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================= | 93%
|
|================================================================== | 95%
|
|=================================================================== | 96%
|
|==================================================================== | 97%
|
|===================================================================== | 99%
|
|======================================================================| 100%
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 148 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_gsea_analysis.R:80:5'
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 148 ]
>
> proc.time()
user system elapsed
68.783 15.123 67.653
fgsea.Rcheck/fgsea-Ex.timings
| name | user | system | elapsed | |
| calcGseaStat | 0.013 | 0.001 | 0.013 | |
| collapsePathways | 7.501 | 0.397 | 5.283 | |
| collapsePathwaysORA | 0.136 | 0.002 | 0.126 | |
| fgsea | 5.895 | 0.333 | 3.099 | |
| fgseaLabel | 0 | 0 | 0 | |
| fgseaMultilevel | 3.478 | 0.251 | 2.910 | |
| fgseaSimple | 7.105 | 1.286 | 2.079 | |
| fora | 0.526 | 0.214 | 0.117 | |
| geseca | 1.716 | 0.562 | 1.883 | |
| gesecaSimple | 0.958 | 0.118 | 0.820 | |
| gmtPathways | 0.576 | 0.228 | 0.054 | |
| mapIdsList | 5.894 | 0.522 | 4.459 | |
| multilevelError | 0 | 0 | 0 | |
| plotEnrichment | 0.003 | 0.001 | 0.001 | |
| plotEnrichmentData | 0.363 | 0.027 | 0.389 | |
| plotGseaTable | 14.430 | 0.532 | 12.102 | |
| reactomePathways | 1.820 | 0.094 | 1.914 | |
| writeGmtPathways | 0.023 | 0.002 | 0.024 | |