Alexey Sergushichev
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/fgsea |
| git_branch: RELEASE_3_16 |
| git_last_commit: ac74ccd |
| git_last_commit_date: 2022-11-01 11:13:59 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:04 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the fgsea package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 675/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fgsea 1.24.0 (landing page) Alexey Sergushichev
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: fgsea |
| Version: 1.24.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:fgsea.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings fgsea_1.24.0.tar.gz |
| StartedAt: 2023-04-10 20:41:55 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 20:47:13 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 318.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: fgsea.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:fgsea.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings fgsea_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/fgsea.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘fgsea/DESCRIPTION’ ... OK
* this is package ‘fgsea’ version ‘1.24.0’
* 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
* checking installed package size ... NOTE
installed size is 10.3Mb
sub-directories of 1Mb or more:
data 1.1Mb
extdata 3.9Mb
libs 5.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 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'
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 ‘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’
plotGesecaTable: no visible global function definition for ‘modifyList’
plotGesecaTable: no visible binding for global variable ‘pathway’
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:
. ES condition denomProb expressionValue gene gsScore id log2err
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 22.940 1.348 20.592
mapIdsList 12.058 0.854 9.583
collapsePathways 10.685 0.420 7.247
fgsea 7.354 0.571 3.743
fgseaSimple 6.605 1.165 2.688
fgseaMultilevel 7.246 0.523 3.517
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘fgsea-tutorial.Rmd’ using ‘UTF-8’... OK
‘geseca-tutorial.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.16-bioc/meat/fgsea.Rcheck/00check.log’
for details.
fgsea.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL fgsea
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘fgsea’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c ScoreCalculation.cpp -o ScoreCalculation.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c ScoreRuler.cpp -o ScoreRuler.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/lexical_cast.hpp:30,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/constants/constants.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/special_functions/digamma.hpp:20,
from util.h:5,
from ScoreRuler.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
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++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c esCalculation.cpp -o esCalculation.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c fastGSEA.cpp -o fastGSEA.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/lexical_cast.hpp:30,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/constants/constants.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/special_functions/digamma.hpp:20,
from util.h:5,
from fastGSEA.cpp:13:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
fastGSEA.cpp: In function ‘Rcpp::NumericVector calcGseaStatBatchCpp(const NumericVector&, const List&, const IntegerVector&)’:
fastGSEA.cpp:446:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
446 | for (int j = 0; j < S.size(); ++j) {
| ~~^~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c fgseaMultilevel.cpp -o fgseaMultilevel.o
fgseaMultilevel.cpp: In function ‘Rcpp::DataFrame fgseaMultilevelCpp(const NumericVector&, const NumericVector&, int, int, int, double, bool)’:
fgseaMultilevel.cpp:10:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
10 | for (int i = 0; i < posRanks.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/lexical_cast.hpp:30,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/constants/constants.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/special_functions/digamma.hpp:20,
from util.h:5,
from fgseaMultilevelSupplement.cpp:3:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
fgseaMultilevelSupplement.cpp: In member function ‘void EsRuler::duplicateSamples()’:
fgseaMultilevelSupplement.cpp:40:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
40 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
| ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:50:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
50 | for (int sampleId = 0; 2 * sampleId < sampleSize; sampleId++) {
| ~~~~~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:59:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
59 | for (int sampleId = 0; 2 * sampleId < sampleSize - 2; sampleId++) {
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function ‘void EsRuler::extend(double, int, double)’:
fgseaMultilevelSupplement.cpp:73:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
73 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
| ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:77:16: warning: unused variable ‘currentES’ [-Wunused-variable]
77 | double currentES = calcES(ranks, currentSamples[sampleId]);
| ^~~~~~~~~
fgseaMultilevelSupplement.cpp:90:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
90 | for (int j = 0; j < sampleSize; ++j) {
| ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:97:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
97 | for (int i = 0; i < sampleSize; ++i) {
| ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:112:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
112 | for (int moves = 0; moves < sampleSize * pathwaySize;) {
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:113:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
113 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
| ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:118:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
118 | for (int i = 0; i < sampleSize; ++i) {
| ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function ‘int EsRuler::perturbate(const std::vector<double>&, int, EsRuler::SampleChunks&, double, std::mt19937&)’:
fgseaMultilevelSupplement.cpp:260:14: warning: unused variable ‘fl’ [-Wunused-variable]
260 | bool fl = false;
| ^~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c geseca.cpp -o geseca.o
geseca.cpp: In function ‘Rcpp::List gesecaCpp(const NumericMatrix&, const 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++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c util.cpp -o util.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/lexical_cast.hpp:30,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/constants/constants.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/special_functions/digamma.hpp:20,
from util.h:5,
from util.cpp:1:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -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 -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/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 version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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> # 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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[ FAIL 0 | WARN 1 | SKIP 1 | PASS 125 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (1)
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 125 ]
>
> proc.time()
user system elapsed
107.809 17.401 90.679
fgsea.Rcheck/fgsea-Ex.timings
| name | user | system | elapsed | |
| calcGseaStat | 0.036 | 0.000 | 0.035 | |
| collapsePathways | 10.685 | 0.420 | 7.247 | |
| collapsePathwaysORA | 0.121 | 0.004 | 0.117 | |
| fgsea | 7.354 | 0.571 | 3.743 | |
| fgseaLabel | 0 | 0 | 0 | |
| fgseaMultilevel | 7.246 | 0.523 | 3.517 | |
| fgseaSimple | 6.605 | 1.165 | 2.688 | |
| fora | 0.639 | 0.207 | 0.108 | |
| geseca | 3.439 | 0.712 | 3.092 | |
| gesecaSimple | 1.806 | 0.228 | 1.274 | |
| gmtPathways | 0.874 | 0.260 | 0.066 | |
| mapIdsList | 12.058 | 0.854 | 9.583 | |
| multilevelError | 0 | 0 | 0 | |
| plotEnrichment | 0.003 | 0.000 | 0.003 | |
| plotGseaTable | 22.940 | 1.348 | 20.592 | |
| reactomePathways | 3.011 | 0.192 | 3.202 | |
| writeGmtPathways | 0.06 | 0.00 | 0.06 | |