Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 |
Package 665/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
epistasisGA 1.8.0 (landing page) Michael Nodzenski
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the epistasisGA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epistasisGA.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: epistasisGA |
Version: 1.8.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:epistasisGA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings epistasisGA_1.8.0.tar.gz |
StartedAt: 2024-11-20 07:38:57 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 07:42:10 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 192.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: epistasisGA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:epistasisGA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings epistasisGA_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/epistasisGA.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘epistasisGA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘epistasisGA’ version ‘1.8.0’ * 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 ‘epistasisGA’ can be installed ... OK * used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ * checking installed package size ... NOTE installed size is 8.3Mb sub-directories of 1Mb or more: libs 7.9Mb * 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 ... NOTE Problems with news in ‘NEWS.md’: No news entries found. * checking code 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 ... OK * checking Rd files ... NOTE checkRd: (-1) GADGETS.Rd:158: Lost braces 158 | the cluster. See code{run.gadgets} for additional details.} | ^ * 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... 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 compute.graphical.scores 30.735 1.664 30.277 network.plot 29.280 1.649 20.232 GxE.test 21.248 0.688 11.706 epistasis.test 11.259 1.020 10.237 global.test 8.629 1.962 8.668 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/epistasisGA.Rcheck/00check.log’ for details.
epistasisGA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL epistasisGA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘epistasisGA’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/bigmemory/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/bigmemory/include' -I/usr/local/include -fPIC -g -O2 -Wall -c epistasisGA.cpp -o epistasisGA.o In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.4.1/site-library/bigmemory/include/bigmemory/BigMatrix.h:10, from epistasisGA.cpp:7: /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/memory:78, from /home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include/armadillo:38, from /home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58, from /home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from epistasisGA.cpp:1: /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template<typename> class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template<typename> class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template<typename> class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template<typename> class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template<typename> class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template<typename> class auto_ptr; | ^~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)': /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here 59 | template<typename> class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o epistasisGA.so RcppExports.o epistasisGA.o -lopenblas -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-epistasisGA/00new/epistasisGA/libs ** R ** data ** 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 (epistasisGA)
epistasisGA.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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. > library(testthat) > library(epistasisGA) > > test_check("epistasisGA") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 3.495 0.458 3.874
epistasisGA.Rcheck/epistasisGA-Ex.timings
name | user | system | elapsed | |
GADGETS | 3.560 | 0.393 | 3.521 | |
GxE.fitness.score | 0.009 | 0.002 | 0.009 | |
GxE.test | 21.248 | 0.688 | 11.706 | |
chrom.fitness.score | 0.039 | 0.000 | 0.019 | |
combine.islands | 2.509 | 0.457 | 2.454 | |
compute.graphical.scores | 30.735 | 1.664 | 30.277 | |
epistasis.test | 11.259 | 1.020 | 10.237 | |
global.test | 8.629 | 1.962 | 8.668 | |
network.plot | 29.280 | 1.649 | 20.232 | |
permute.dataset | 2.424 | 0.619 | 2.593 | |
preprocess.genetic.data | 2.406 | 0.641 | 2.519 | |
run.gadgets | 2.541 | 0.469 | 2.516 | |