Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKLMNOPQRSTU[V]WXYZ

BUILD BIN report for VegaMC on machv2

This page was generated on 2020-10-17 11:59:52 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE VegaMC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1872/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VegaMC 3.26.0
Sandro Morganella
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/VegaMC
Branch: RELEASE_3_11
Last Commit: 20f11c6
Last Changed Date: 2020-04-27 14:29:13 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: VegaMC
Version: 3.26.0
Command: rm -rf VegaMC.buildbin-libdir && mkdir VegaMC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VegaMC_3.26.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R VegaMC.buildbin-libdir
StartedAt: 2020-10-17 08:10:35 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 08:11:23 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 47.5 seconds
RetCode: 0
Status:  OK 
PackageFile: VegaMC_3.26.0.tgz
PackageFileSize: 1.791 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf VegaMC.buildbin-libdir && mkdir VegaMC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VegaMC_3.26.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R VegaMC.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=VegaMC.buildbin-libdir VegaMC_3.26.0.tar.gz'
>>>>>>> 

* installing *source* package ‘VegaMC’ ...
** 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 run_vegaMC.c -o run_vegaMC.o
run_vegaMC.c:491:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^~~~
run_vegaMC.c:526:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^~~~
run_vegaMC.c:618:18: warning: unused variable 'brkt' [-Wunused-variable]
    char *elem, *brkt;
                 ^
3 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 sort_data.c -o sort_data.o
sort_data.c:131:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^~~~
sort_data.c:180:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^~~~
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 vegaMC.c -o vegaMC.o
vegaMC.c:458:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    lambda_gradient = abs(lambda);
                      ^
vegaMC.c:458:23: note: use function 'fabsf' instead
    lambda_gradient = abs(lambda);
                      ^~~
                      fabsf
1 warning generated.
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 VegaMC.so run_vegaMC.o sort_data.o vegaMC.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/VegaMC.buildbin-libdir/00LOCK-VegaMC/00new/VegaMC/libs
** R
** 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
** 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 (VegaMC)


>>>>>>> 
>>>>>>> FIXING LINKS FOR VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.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" "VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.so"