Alexey Sergushichev
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/fgsea |
| Branch: RELEASE_3_10 |
| Last Commit: 22c00b6 |
| Last Changed Date: 2019-10-29 13:09:49 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:26:54 -0400 (Wed, 15 Apr 2020).
| Package 571/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| fgsea 1.12.0 Alexey Sergushichev
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: fgsea |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fgsea.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings fgsea_1.12.0.tar.gz |
| StartedAt: 2020-04-15 03:09:43 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:16:16 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 393.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: fgsea.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fgsea.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings fgsea_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/fgsea.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fgsea/DESCRIPTION' ... OK
* this is package 'fgsea' version '1.12.0'
* 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
* checking installed package size ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
fgsea: no visible binding for global variable 'pval'
fgsea: no visible binding for global variable 'nLeZero'
fgsea: no visible binding for global variable 'nGeZero'
fgsea: no visible binding for global variable 'leZeroMean'
fgsea: no visible binding for global variable 'geZeroMean'
fgsea: no visible binding for global variable 'nLeEs'
fgsea: no visible binding for global variable 'nGeEs'
fgseaMultilevel: no visible binding for global variable 'leZeroMean'
fgseaMultilevel: no visible binding for global variable 'geZeroMean'
fgseaMultilevel: no visible binding for global variable 'nLeEs'
fgseaMultilevel: no visible binding for global variable 'nGeEs'
fgseaMultilevel: no visible binding for global variable 'nLeZero'
fgseaMultilevel: no visible binding for global variable 'nGeZero'
fgseaMultilevel: no visible binding for global variable 'isCpGeHalf'
fgseaSimpleImpl: no visible binding for global variable 'nLeZero'
fgseaSimpleImpl: no visible binding for global variable 'nGeZero'
Undefined global functions or variables:
geZeroMean isCpGeHalf leZeroMean nGeEs nGeZero nLeEs nLeZero pval
* 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 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/fgsea/libs/i386/fgsea.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/fgsea/libs/x64/fgsea.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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. 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
reactomePathways 5.14 0.21 5.35
collapsePathways 2.83 0.17 14.70
fgseaMultilevel 0.95 0.08 19.41
fgsea 0.53 0.06 19.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
collapsePathways 3.03 0.30 15.22
fgseaMultilevel 0.94 0.05 19.69
fgsea 0.86 0.09 23.64
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/fgsea.Rcheck/00check.log'
for details.
fgsea.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/fgsea_1.12.0.tar.gz && rm -rf fgsea.buildbin-libdir && mkdir fgsea.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=fgsea.buildbin-libdir fgsea_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL fgsea_1.12.0.zip && rm fgsea_1.12.0.tar.gz fgsea_1.12.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 529k 100 529k 0 0 13.6M 0 --:--:-- --:--:-- --:--:-- 15.2M
install for i386
* installing *source* package 'fgsea' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c esCalculation.cpp -o esCalculation.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function 'Rcpp::NumericVector calcGseaStatBatchCpp(const NumericVector&, const List&, const IntegerVector&)':
fastGSEA.cpp:444:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < S.size(); ++j) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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 between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < posRanks.size(); i++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
fgseaMultilevelSupplement.cpp: In function 'void fillRandomSample(std::set<int>&, std::mt19937&, long unsigned int, unsigned int)':
fgseaMultilevelSupplement.cpp:31:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (static_cast<int>(randomSample.size()) < pathwaySize) {
^
fgseaMultilevelSupplement.cpp: In member function 'void EsRuler::duplicateSamples()':
fgseaMultilevelSupplement.cpp:56:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
^
fgseaMultilevelSupplement.cpp:66:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int sampleId = 0; 2 * sampleId < sampleSize; sampleId++) {
^
fgseaMultilevelSupplement.cpp:75:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int sampleId = 0; 2 * sampleId < sampleSize - 2; sampleId++) {
^
fgseaMultilevelSupplement.cpp: In member function 'void EsRuler::extend(double, int, double)':
fgseaMultilevelSupplement.cpp:89:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
^
fgseaMultilevelSupplement.cpp:107:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int moves = 0; moves < sampleSize * pathwaySize;) {
^
fgseaMultilevelSupplement.cpp:108:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int sample_id = 0; sample_id < sampleSize; sample_id++) {
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c fgsea_init.c -o fgsea_init.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o fgsea.dll tmp.def RcppExports.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o fgsea_init.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/fgsea.buildbin-libdir/00LOCK-fgsea/00new/fgsea/libs/i386
** 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
examplePathways html
exampleRanks html
fgsea html
fgseaLabel html
fgseaMultilevel html
fgseaSimpleImpl html
gmtPathways html
multilevelError html
multilevelImpl html
plotEnrichment html
plotGseaTable html
reactomePathways 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
install for x64
* installing *source* package 'fgsea' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c esCalculation.cpp -o esCalculation.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function 'Rcpp::NumericVector calcGseaStatBatchCpp(const NumericVector&, const List&, const IntegerVector&)':
fastGSEA.cpp:444:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < S.size(); ++j) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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 between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < posRanks.size(); i++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
fgseaMultilevelSupplement.cpp: In function 'void fillRandomSample(std::set<int>&, std::mt19937&, long unsigned int, unsigned int)':
fgseaMultilevelSupplement.cpp:31:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (static_cast<int>(randomSample.size()) < pathwaySize) {
^
fgseaMultilevelSupplement.cpp: In member function 'void EsRuler::duplicateSamples()':
fgseaMultilevelSupplement.cpp:56:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
^
fgseaMultilevelSupplement.cpp:66:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int sampleId = 0; 2 * sampleId < sampleSize; sampleId++) {
^
fgseaMultilevelSupplement.cpp:75:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int sampleId = 0; 2 * sampleId < sampleSize - 2; sampleId++) {
^
fgseaMultilevelSupplement.cpp: In member function 'void EsRuler::extend(double, int, double)':
fgseaMultilevelSupplement.cpp:89:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
^
fgseaMultilevelSupplement.cpp:107:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int moves = 0; moves < sampleSize * pathwaySize;) {
^
fgseaMultilevelSupplement.cpp:108:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int sample_id = 0; sample_id < sampleSize; sample_id++) {
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c fgsea_init.c -o fgsea_init.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o fgsea.dll tmp.def RcppExports.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o fgsea_init.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/fgsea.buildbin-libdir/fgsea/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fgsea' as fgsea_1.12.0.zip
* DONE (fgsea)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'fgsea' successfully unpacked and MD5 sums checked
|
fgsea.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
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)
Loading required package: Rcpp
>
> test_check("fgsea")
== testthat results ===========================================================
[ OK: 86 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
39.26 1.71 80.15
|
fgsea.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
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)
Loading required package: Rcpp
>
> test_check("fgsea")
== testthat results ===========================================================
[ OK: 86 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
43.40 1.12 90.68
|
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fgsea.Rcheck/examples_i386/fgsea-Ex.timings
|
fgsea.Rcheck/examples_x64/fgsea-Ex.timings
|