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BioC 3.5: BUILD BIN report for deepSNV on toluca2

This page was generated on 2017-04-23 14:36:16 -0400 (Sun, 23 Apr 2017).

Package 326/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deepSNV 1.21.4
Moritz Gerstung
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/deepSNV
Last Changed Rev: 127759 / Revision: 129046
Last Changed Date: 2017-03-27 12:51:27 -0400 (Mon, 27 Mar 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS [ OK ]
veracruz2 OS X 10.11.6 El Capitan / x86_64  ERROR  ERROR  skipped  skipped 

Summary

Package: deepSNV
Version: 1.21.4
Command: rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh deepSNV_1.21.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R deepSNV.buildbin-libdir
StartedAt: 2017-04-23 11:53:42 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 11:54:12 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 30.3 seconds
RetCode: 0
Status:  OK 
PackageFile: deepSNV_1.21.4.tgz
PackageFileSize: 2.609 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh deepSNV_1.21.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R deepSNV.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=deepSNV.buildbin-libdir deepSNV_1.21.4.tar.gz'
>>>>>>> 

* installing *source* package ‘deepSNV’ ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking malloc.h usability... no
checking malloc.h presence... no
checking for malloc.h... no
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for off_t... yes
checking for size_t... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c bam2R.cpp -o bam2R.o
bam2R.cpp:69:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
bam2R.cpp:79:6: warning: unused variable 'c' [-Wunused-variable]
        int c = 0;
            ^
bam2R.cpp:76:13: warning: unused variable 'iter' [-Wunused-variable]
        hts_itr_t *iter = NULL;
                   ^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c betabinom.c -o betabinom.o
betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable]
        int i, log=0;
               ^
1 warning generated.
clang++ -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 deepSNV.so bam2R.o betabinom.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/lib/libhts.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/biocbuild/bbs-3.5-bioc/meat/deepSNV.buildbin-libdir/deepSNV/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (deepSNV)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "deepSNV.buildbin-libdir/deepSNV/libs//deepSNV.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "deepSNV.buildbin-libdir/deepSNV/libs//deepSNV.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "deepSNV.buildbin-libdir/deepSNV/libs//deepSNV.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "deepSNV.buildbin-libdir/deepSNV/libs//deepSNV.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "deepSNV.buildbin-libdir/deepSNV/libs//deepSNV.so"