Alexey Sergushichev
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/fgsea |
| git_branch: master |
| git_last_commit: 51f3941 |
| git_last_commit_date: 2022-03-03 04:59:05 -0400 (Thu, 03 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:30 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 643/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fgsea 1.21.2 (landing page) Alexey Sergushichev
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: fgsea |
| Version: 1.21.2 |
| Command: rm -rf fgsea.buildbin-libdir && mkdir fgsea.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=fgsea.buildbin-libdir fgsea_1.21.2.tar.gz |
| StartedAt: 2022-03-17 21:08:10 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 21:09:09 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 58.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: fgsea_1.21.2.zip |
| PackageFileSize: 1.646 MiB |
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### Running command:
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### rm -rf fgsea.buildbin-libdir && mkdir fgsea.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=fgsea.buildbin-libdir fgsea_1.21.2.tar.gz
###
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* installing *source* package 'fgsea' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c esCalculation.cpp -o esCalculation.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c fastGSEA.cpp -o fastGSEA.o
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 long unsigned int'} [-Wsign-compare]
for (int j = 0; j < S.size(); ++j) {
~~^~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c fgseaMultilevel.cpp -o fgseaMultilevel.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:20,
from fgseaMultilevelSupplement.h:9,
from fgseaMultilevel.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
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 long unsigned int'} [-Wsign-compare]
for (int i = 0; i < posRanks.size(); i++) {
~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:20,
from fgseaMultilevelSupplement.h:9,
from fgseaMultilevelSupplement.cpp:1:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
fgseaMultilevelSupplement.cpp: In member function 'void EsRuler::duplicateSamples()':
fgseaMultilevelSupplement.cpp:44:37: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:54:41: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
for (int sampleId = 0; 2 * sampleId < sampleSize; sampleId++) {
~~~~~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:63:41: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
for (int sampleId = 0; 2 * sampleId < sampleSize - 2; sampleId++) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function 'void EsRuler::extend(double, int, double)':
fgseaMultilevelSupplement.cpp:77:37: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:81:16: warning: unused variable 'currentES' [-Wunused-variable]
double currentES = calcES(ranks, currentSamples[sampleId]);
^~~~~~~~~
fgseaMultilevelSupplement.cpp:94:31: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
for (int j = 0; j < sampleSize; ++j) {
~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:101:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
for (int i = 0; i < sampleSize; ++i) {
~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:116:35: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
for (int moves = 0; moves < sampleSize * pathwaySize;) {
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:117:45: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:122:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
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:264:14: warning: unused variable 'fl' [-Wunused-variable]
bool fl = false;
^~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c util.cpp -o util.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o fgsea.dll tmp.def RcppExports.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o util.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/meat/fgsea.buildbin-libdir/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
converting help for package 'fgsea'
finding HTML links ... done
calcGseaStat html
calcGseaStatBatchCpp html
collapsePathways html
collapsePathwaysORA html
examplePathways html
exampleRanks html
fgsea html
fgseaLabel html
fgseaMultilevel html
fgseaSimple html
fgseaSimpleImpl html
fora html
gmtPathways html
mapIdsList html
multilevelError html
multilevelImpl html
plotEnrichment html
plotGseaTable html
reactomePathways html
writeGmtPathways html
** 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
* MD5 sums
packaged installation of 'fgsea' as fgsea_1.21.2.zip
* DONE (fgsea)