| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-01 11:35:52 -0400 (Wed, 01 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
| 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 |  | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:epistasisGA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings epistasisGA_1.6.0.tar.gz |
| StartedAt: 2024-05-01 05:14:09 -0400 (Wed, 01 May 2024) |
| EndedAt: 2024-05-01 05:19:40 -0400 (Wed, 01 May 2024) |
| EllapsedTime: 330.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: epistasisGA.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:epistasisGA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings epistasisGA_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/epistasisGA.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘epistasisGA’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 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
network.plot 31.351 2.472 22.768
compute.graphical.scores 23.419 1.255 16.005
global.test 15.529 2.975 20.034
epistasis.test 9.852 0.949 9.136
GxE.test 9.949 0.593 9.594
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/epistasisGA.Rcheck/00check.log’
for details.
epistasisGA.Rcheck/00install.out
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###
### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL epistasisGA
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘epistasisGA’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/bigmemory/include' -I/usr/local/include -fpic -g -O2 -Wall -c epistasisGA.cpp -o epistasisGA.o
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.19-bioc/R/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 /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from epistasisGA.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.19-bioc/R/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 >
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from epistasisGA.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.19-bioc/R/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()
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from epistasisGA.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.19-bioc/R/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()
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from epistasisGA.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.19-bioc/R/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 )
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from epistasisGA.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.19-bioc/R/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 )
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from epistasisGA.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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 );
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from epistasisGA.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o epistasisGA.so RcppExports.o epistasisGA.o -llapack -L/home/biocbuild/bbs-3.19-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
3.185 0.322 3.502
epistasisGA.Rcheck/epistasisGA-Ex.timings
| name | user | system | elapsed | |
| GADGETS | 2.753 | 0.295 | 2.665 | |
| GxE.fitness.score | 0.008 | 0.001 | 0.010 | |
| GxE.test | 9.949 | 0.593 | 9.594 | |
| chrom.fitness.score | 0.018 | 0.000 | 0.018 | |
| combine.islands | 2.656 | 0.468 | 2.687 | |
| compute.graphical.scores | 23.419 | 1.255 | 16.005 | |
| epistasis.test | 9.852 | 0.949 | 9.136 | |
| global.test | 15.529 | 2.975 | 20.034 | |
| network.plot | 31.351 | 2.472 | 22.768 | |
| permute.dataset | 2.762 | 0.444 | 2.782 | |
| preprocess.genetic.data | 3.705 | 0.701 | 3.752 | |
| run.gadgets | 2.934 | 0.630 | 3.072 | |