Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-28 17:41 -0400 (Fri, 28 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
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 669/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
epistasisGA 1.6.0 (landing page) Michael Nodzenski
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | 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. |
Package: epistasisGA |
Version: 1.6.0 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:epistasisGA.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings epistasisGA_1.6.0.tar.gz |
StartedAt: 2024-06-27 01:26:54 -0400 (Thu, 27 Jun 2024) |
EndedAt: 2024-06-27 01:30:49 -0400 (Thu, 27 Jun 2024) |
EllapsedTime: 234.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: epistasisGA.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:epistasisGA.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings epistasisGA_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/epistasisGA.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'epistasisGA/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'epistasisGA' version '1.6.0' * 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 'epistasisGA' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 ... 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 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 for x64 is not available File 'F:/biocbuild/bbs-3.19-bioc/R/library/epistasisGA/libs/x64/epistasisGA.dll': Found '_exit', possibly from '_exit' (C) 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 ... ERROR Running examples in 'epistasisGA-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: global.test > ### Title: A function to run a global test of the null hypothesis that > ### there are no SNP-disease associations across a range of chromosome > ### sizes > ### Aliases: global.test > > ### ** Examples > > > data(case) > data(dad) > data(mom) > case <- as.matrix(case) > dad <- as.matrix(dad) > mom <- as.matrix(mom) > data(snp.annotations) > set.seed(1400) > > pp.list <- preprocess.genetic.data(case[, 1:10], + father.genetic.data = dad[ , 1:10], + mother.genetic.data = mom[ , 1:10], + ld.block.vec = c(10)) Warning in socketConnection(port = port, server = TRUE, blocking = TRUE, : port 11796 cannot be opened Error in socketConnection(port = port, server = TRUE, blocking = TRUE, : cannot open the connection Calls: preprocess.genetic.data ... <Anonymous> -> <Anonymous> -> newSOCKnode -> socketConnection Execution halted * 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: 1 ERROR, 3 NOTEs See 'F:/biocbuild/bbs-3.19-bioc/meat/epistasisGA.Rcheck/00check.log' for details.
epistasisGA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL epistasisGA ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'epistasisGA' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/bigmemory/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/bigmemory/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c epistasisGA.cpp -o epistasisGA.o In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.19-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10, from epistasisGA.cpp:7: F:/biocbuild/bbs-3.19-bioc/R/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 C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/memory:78, from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27: C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here 65 | template<typename> class auto_ptr; | ^~~~~~~~ F:/biocbuild/bbs-3.19-bioc/R/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 > | ^~~~~~~~ C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here 65 | template<typename> class auto_ptr; | ^~~~~~~~ F:/biocbuild/bbs-3.19-bioc/R/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() | ^~~~~~~~ C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here 65 | template<typename> class auto_ptr; | ^~~~~~~~ F:/biocbuild/bbs-3.19-bioc/R/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() | ^~~~~~~~ C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here 65 | template<typename> class auto_ptr; | ^~~~~~~~ F:/biocbuild/bbs-3.19-bioc/R/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 ) | ^~~~~~~~ C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here 65 | template<typename> class auto_ptr; | ^~~~~~~~ F:/biocbuild/bbs-3.19-bioc/R/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 ) | ^~~~~~~~ C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here 65 | template<typename> class auto_ptr; | ^~~~~~~~ F:/biocbuild/bbs-3.19-bioc/R/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>&&)': F:/biocbuild/bbs-3.19-bioc/R/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 ); | ^~~~~~~~ C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unique_ptr.h:65:28: note: declared here 65 | template<typename> class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -shared -s -static-libgcc -o epistasisGA.dll tmp.def RcppExports.o epistasisGA.o -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-epistasisGA/00new/epistasisGA/libs/x64 ** 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 ** 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 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 3.25 0.53 3.75
epistasisGA.Rcheck/epistasisGA-Ex.timings
name | user | system | elapsed | |
GADGETS | 2.79 | 0.05 | 11.66 | |
GxE.fitness.score | 0.00 | 0.01 | 0.03 | |
GxE.test | 9.50 | 0.20 | 18.44 | |
chrom.fitness.score | 0.03 | 0.02 | 0.04 | |
combine.islands | 2.33 | 0.11 | 12.00 | |
compute.graphical.scores | 3.25 | 0.22 | 45.93 | |
epistasis.test | 7.90 | 0.75 | 18.53 | |