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BUILD BIN report for h5vc on merida1

This page was generated on 2019-04-16 11:57:16 -0400 (Tue, 16 Apr 2019).

Package 705/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
h5vc 2.16.0
Paul Theodor Pyl
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/h5vc
Branch: RELEASE_3_8
Last Commit: fd6bd12
Last Changed Date: 2018-10-30 11:41:52 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: h5vc
Version: 2.16.0
Command: rm -rf h5vc.buildbin-libdir && mkdir h5vc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh h5vc_2.16.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R h5vc.buildbin-libdir
StartedAt: 2019-04-16 04:11:27 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 04:12:10 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 42.6 seconds
RetCode: 0
Status:  OK 
PackageFile: h5vc_2.16.0.tgz
PackageFileSize: 1.042 MiB

Command output

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###
### Running command:
###
###   rm -rf h5vc.buildbin-libdir && mkdir h5vc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh h5vc_2.16.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R h5vc.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=h5vc.buildbin-libdir h5vc_2.16.0.tar.gz'
>>>>>>> 

* installing *source* package ‘h5vc’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c tallyBAM.cpp -o tallyBAM.o
tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable]
  int len = nttable->end - nttable->beg;
      ^
tallyBAM.cpp:60:18: warning: variable 'c' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        }else if(p->indel > 0){
                 ^˜˜˜˜˜˜˜˜˜˜˜
tallyBAM.cpp:64:16: note: uninitialized use occurs here
        str += c;
               ^
tallyBAM.cpp:60:15: note: remove the 'if' if its condition is always true
        }else if(p->indel > 0){
              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tallyBAM.cpp:55:15: note: initialize the variable 'c' to silence this warning
        char c;
              ^
               = '\0'
tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable]
  int len = nttable->end - nttable->beg;
      ^
tallyBAM.cpp:141:6: warning: unused variable 'c' [-Wunused-variable]
        int c = 0;
            ^
tallyBAM.cpp:43:12: warning: unused function 'pileup_func_old' [-Wunused-function]
static int pileup_func_old(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
           ^
5 warnings 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 h5vc.so tallyBAM.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
installing to /Users/biocbuild/bbs-3.8-bioc/meat/h5vc.buildbin-libdir/h5vc/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
* DONE (h5vc)


>>>>>>> 
>>>>>>> FIXING LINKS FOR h5vc.buildbin-libdir/h5vc/libs//h5vc.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "h5vc.buildbin-libdir/h5vc/libs//h5vc.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "h5vc.buildbin-libdir/h5vc/libs//h5vc.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "h5vc.buildbin-libdir/h5vc/libs//h5vc.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "h5vc.buildbin-libdir/h5vc/libs//h5vc.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "h5vc.buildbin-libdir/h5vc/libs//h5vc.so"