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BUILD BIN report for nem on machv2

This page was generated on 2020-10-17 11:59:03 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE nem PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1181/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nem 2.62.0
Holger Froehlich
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/nem
Branch: RELEASE_3_11
Last Commit: 12310c0
Last Changed Date: 2020-04-27 14:14:04 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  ERROR [ OK ]

Summary

Package: nem
Version: 2.62.0
Command: rm -rf nem.buildbin-libdir && mkdir nem.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh nem_2.62.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R nem.buildbin-libdir
StartedAt: 2020-10-17 07:34:31 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:34:53 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 22.0 seconds
RetCode: 0
Status:  OK 
PackageFile: nem_2.62.0.tgz
PackageFileSize: 7.357 MiB

Command output

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### Running command:
###
###   rm -rf nem.buildbin-libdir && mkdir nem.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh nem_2.62.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R nem.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=nem.buildbin-libdir nem_2.62.0.tar.gz'
>>>>>>> 

* installing *source* package ‘nem’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c MCMC.c -o MCMC.o
MCMC.c:44:45: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
                                p -= inv_nu*abs(net[s][k]-prior[s][k]);
                                            ^
MCMC.c:44:45: note: use function 'fabs' instead
                                p -= inv_nu*abs(net[s][k]-prior[s][k]);
                                            ^~~
                                            fabs
MCMC.c:72:62: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
                                        if(Psi[p][s] != 0 && abs(Psi[p][s]) <= t){ // p is a parent
                                                             ^
MCMC.c:72:62: note: use function 'fabs' instead
                                        if(Psi[p][s] != 0 && abs(Psi[p][s]) <= t){ // p is a parent
                                                             ^~~
                                                             fabs
MCMC.c:402:10: warning: unused variable 'stored' [-Wunused-variable]
    long stored = 0;
         ^
MCMC.c:403:10: warning: unused variable 'stored2' [-Wunused-variable]
    long stored2 = 0;
         ^
MCMC.c:359:35: warning: unused variable 'mutinf' [-Wunused-variable]
    double loglikMean, loglikSum, mutinf, delta, logPrior_cur_scale;  
                                  ^
5 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c netlearn.c -o netlearn.o
netlearn.c:171:13: warning: variable 'negenes' used in loop condition not modified in loop body [-Wfor-loop-analysis]
                for (i=0; negenes; i++) {
                          ^~~~~~~
netlearn.c:168:9: warning: unused variable 'lik_switch' [-Wunused-variable]
        double lik_switch;
               ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c wrapper.c -o wrapper.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o nem.so MCMC.o netlearn.o wrapper.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/nem.buildbin-libdir/00LOCK-nem/00new/nem/libs
** R
** data
** 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
Warning: Package 'nem' is deprecated and will be removed from Bioconductor
  version 3.12
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'nem' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (nem)


>>>>>>> 
>>>>>>> FIXING LINKS FOR nem.buildbin-libdir/nem/libs/nem.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "nem.buildbin-libdir/nem/libs/nem.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "nem.buildbin-libdir/nem/libs/nem.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "nem.buildbin-libdir/nem/libs/nem.so"