Alexey Sergushichev
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/fgsea |
| Branch: RELEASE_3_11 |
| Last Commit: 6389c58 |
| Last Changed Date: 2020-04-27 14:58:58 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:54:45 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE fgsea PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 596/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| fgsea 1.14.0 Alexey Sergushichev
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: fgsea |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:fgsea.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings fgsea_1.14.0.tar.gz |
| StartedAt: 2020-10-17 01:19:39 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 01:22:09 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 150.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: fgsea.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:fgsea.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings fgsea_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/fgsea.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fgsea/DESCRIPTION’ ... OK
* this is package ‘fgsea’ version ‘1.14.0’
* 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 5.1Mb
sub-directories of 1Mb or more:
extdata 1.9Mb
libs 2.7Mb
* 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
collapsePathways: no visible binding for global variable ‘pathway’
collapsePathways: no visible binding for global variable ‘ES’
fora: no visible binding for global variable ‘pval’
Undefined global functions or variables:
ES pathway 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
collapsePathways 10.063 0.405 6.045
fgseaSimple 9.778 0.667 3.417
fgseaMultilevel 8.739 0.200 4.152
mapIdsList 8.205 0.329 7.039
fgsea 8.210 0.263 4.393
* 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
‘/home/biocbuild/bbs-3.11-bioc/meat/fgsea.Rcheck/00check.log’
for details.
fgsea.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL fgsea
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘fgsea’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function ‘Rcpp::NumericVector calcGseaStatBatchCpp(const NumericVector&, const List&, const IntegerVector&)’:
fastGSEA.cpp:461:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < S.size(); ++j) {
~~^~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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 between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < posRanks.size(); i++) {
~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -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++) {
~~~~~~~~~~^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c fgsea_init.c -o fgsea_init.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o fgsea.so RcppExports.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o fgsea_init.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)
>
> test_check("fgsea")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 96 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
66.883 2.103 54.452
fgsea.Rcheck/fgsea-Ex.timings
| name | user | system | elapsed | |
| calcGseaStat | 0.032 | 0.000 | 0.032 | |
| collapsePathways | 10.063 | 0.405 | 6.045 | |
| collapsePathwaysORA | 0.195 | 0.000 | 0.188 | |
| fgsea | 8.210 | 0.263 | 4.393 | |
| fgseaLabel | 0 | 0 | 0 | |
| fgseaMultilevel | 8.739 | 0.200 | 4.152 | |
| fgseaSimple | 9.778 | 0.667 | 3.417 | |
| fora | 0.139 | 0.032 | 0.171 | |
| gmtPathways | 0.199 | 0.000 | 0.205 | |
| mapIdsList | 8.205 | 0.329 | 7.039 | |
| multilevelError | 0 | 0 | 0 | |
| plotEnrichment | 0.003 | 0.000 | 0.003 | |
| plotGseaTable | 0.448 | 0.012 | 0.460 | |
| reactomePathways | 3.079 | 0.161 | 3.887 | |
| writeGmtPathways | 0.046 | 0.000 | 0.046 | |