| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:29 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 665/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fgsea 1.25.0 (landing page) Alexey Sergushichev
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: fgsea |
| Version: 1.25.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fgsea.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings fgsea_1.25.0.tar.gz |
| StartedAt: 2022-12-28 23:47:20 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 23:55:55 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 515.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: fgsea.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fgsea.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings fgsea_1.25.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/fgsea.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'fgsea/DESCRIPTION' ... OK
* this is package 'fgsea' version '1.25.0'
* 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 whether package 'fgsea' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
data 1.1Mb
extdata 3.9Mb
libs 1.1Mb
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/fgsea/libs/x64/fgsea.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotGseaTable 7.13 0.16 18.29
collapsePathways 4.39 0.07 12.38
mapIdsList 4.07 0.28 13.05
fgsea 1.17 0.07 11.26
fgseaMultilevel 1.02 0.06 10.96
fgseaSimple 0.73 0.08 16.04
geseca 0.51 0.06 13.31
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/fgsea.Rcheck/00check.log'
for details.
fgsea.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL fgsea
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'fgsea' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ScoreCalculation.cpp -o ScoreCalculation.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ScoreRuler.cpp -o ScoreRuler.o
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:20,
from util.h:5,
from ScoreRuler.cpp:2:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
F:/biocbuild/bbs-3.17-bioc/R/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>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c esCalculation.cpp -o esCalculation.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fastGSEA.cpp -o fastGSEA.o
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:20,
from util.h:5,
from fastGSEA.cpp:13:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
F:/biocbuild/bbs-3.17-bioc/R/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>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
fastGSEA.cpp: In function 'Rcpp::NumericVector calcGseaStatBatchCpp(const Rcpp::NumericVector&, const Rcpp::List&, const Rcpp::IntegerVector&)':
fastGSEA.cpp:446:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
446 | for (int j = 0; j < S.size(); ++j) {
| ~~^~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fgseaMultilevel.cpp -o fgseaMultilevel.o
fgseaMultilevel.cpp: In function 'Rcpp::DataFrame fgseaMultilevelCpp(const Rcpp::NumericVector&, const Rcpp::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 long unsigned int'} [-Wsign-compare]
10 | for (int i = 0; i < posRanks.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:20,
from util.h:5,
from fgseaMultilevelSupplement.cpp:3:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
F:/biocbuild/bbs-3.17-bioc/R/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>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
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, SampleChunks&, double, std::mt19937&)':
fgseaMultilevelSupplement.cpp:260:14: warning: unused variable 'fl' [-Wunused-variable]
260 | bool fl = false;
| ^~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.o
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:20,
from util.h:5,
from util.cpp:1:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
F:/biocbuild/bbs-3.17-bioc/R/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>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
g++ -shared -s -static-libgcc -o fgsea.dll tmp.def RcppExports.o ScoreCalculation.o ScoreRuler.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o geseca.o util.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-fgsea/00new/fgsea/libs/x64
** 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
** 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) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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.
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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
47.20 2.79 335.46
fgsea.Rcheck/fgsea-Ex.timings
| name | user | system | elapsed | |
| calcGseaStat | 0.03 | 0.00 | 0.03 | |
| collapsePathways | 4.39 | 0.07 | 12.38 | |
| collapsePathwaysORA | 0.11 | 0.00 | 0.11 | |
| fgsea | 1.17 | 0.07 | 11.26 | |
| fgseaLabel | 0 | 0 | 0 | |
| fgseaMultilevel | 1.02 | 0.06 | 10.96 | |
| fgseaSimple | 0.73 | 0.08 | 16.04 | |
| fora | 0.08 | 0.00 | 0.08 | |
| geseca | 0.51 | 0.06 | 13.31 | |
| gesecaSimple | 0.25 | 0.03 | 4.22 | |
| gmtPathways | 0.14 | 0.00 | 0.14 | |
| mapIdsList | 4.07 | 0.28 | 13.05 | |
| multilevelError | 0 | 0 | 0 | |
| plotEnrichment | 0.01 | 0.00 | 0.02 | |
| plotGseaTable | 7.13 | 0.16 | 18.29 | |
| reactomePathways | 1.31 | 0.14 | 1.46 | |
| writeGmtPathways | 0.02 | 0.01 | 0.03 | |