| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:02 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 | ||||
|
To the developers/maintainers of the epistasisGA package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 618/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| epistasisGA 1.1.4 (landing page) Michael Nodzenski
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: epistasisGA |
| Version: 1.1.4 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:epistasisGA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings epistasisGA_1.1.4.tar.gz |
| StartedAt: 2023-02-07 01:02:06 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 01:08:00 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 354.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: epistasisGA.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:epistasisGA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings epistasisGA_1.1.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/epistasisGA.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘epistasisGA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epistasisGA’ version ‘1.1.4’
* 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 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 7.9Mb
sub-directories of 1Mb or more:
libs 7.4Mb
* 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 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 ... OK
* 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 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 26.742 1.322 18.551
network.plot 25.754 0.883 17.662
GxE.test 13.888 0.694 13.681
epistasis.test 10.343 0.848 9.593
global.test 8.340 1.817 8.807
* 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 ...
‘E_GADGETS.Rmd’ using ‘UTF-8’... OK
‘GADGETS.Rmd’ using ‘UTF-8’... OK
‘Including_Maternal_SNPs.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/epistasisGA.Rcheck/00check.log’
for details.
epistasisGA.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL epistasisGA
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘epistasisGA’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/bigmemory/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/bigmemory/include' -I/usr/local/include -fPIC -g -O2 -Wall -c epistasisGA.cpp -o epistasisGA.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
from epistasisGA.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.17-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 /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-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /home/biocbuild/bbs-3.17-bioc/R/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-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
250 | 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-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /home/biocbuild/bbs-3.17-bioc/R/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-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
507 | 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-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /home/biocbuild/bbs-3.17-bioc/R/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-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
520 | 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-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /home/biocbuild/bbs-3.17-bioc/R/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-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
603 | 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-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /home/biocbuild/bbs-3.17-bioc/R/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-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
612 | 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-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /home/biocbuild/bbs-3.17-bioc/R/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-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.17-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>&&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
614 | 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-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /home/biocbuild/bbs-3.17-bioc/R/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++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o epistasisGA.so RcppExports.o epistasisGA.o -llapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> library(testthat)
> library(epistasisGA)
>
> test_check("epistasisGA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
>
> proc.time()
user system elapsed
3.880 0.186 4.107
epistasisGA.Rcheck/epistasisGA-Ex.timings
| name | user | system | elapsed | |
| GADGETS | 3.338 | 0.294 | 3.340 | |
| GxE.fitness.score | 0.020 | 0.000 | 0.021 | |
| GxE.test | 13.888 | 0.694 | 13.681 | |
| chrom.fitness.score | 0.020 | 0.000 | 0.019 | |
| combine.islands | 2.333 | 0.412 | 2.419 | |
| compute.graphical.scores | 26.742 | 1.322 | 18.551 | |
| epistasis.test | 10.343 | 0.848 | 9.593 | |
| global.test | 8.340 | 1.817 | 8.807 | |
| network.plot | 25.754 | 0.883 | 17.662 | |
| permute.dataset | 2.309 | 0.495 | 2.428 | |
| preprocess.genetic.data | 2.262 | 0.528 | 2.352 | |
| run.gadgets | 2.387 | 0.413 | 2.407 | |