Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:52:20 -0400 (Wed, 16 Oct 2019).
Package 739/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
h5vc 2.18.0 Paul Theodor Pyl
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] |
Package: h5vc |
Version: 2.18.0 |
Command: rm -rf h5vc.buildbin-libdir && mkdir h5vc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh h5vc_2.18.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R h5vc.buildbin-libdir |
StartedAt: 2019-10-16 08:44:36 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 08:45:17 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 41.2 seconds |
RetCode: 0 |
Status: OK |
PackageFile: h5vc_2.18.0.tgz |
PackageFileSize: 1.837 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf h5vc.buildbin-libdir && mkdir h5vc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh h5vc_2.18.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R h5vc.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=h5vc.buildbin-libdir h5vc_2.18.0.tar.gz' >>>>>>> * installing *source* package ‘h5vc’ ... ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c bam.c -o bam.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c sam.c -o sam.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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:140:6: 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++ -std=gnu++11 -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 bam.o bam_plbuf.o sam.o tallyBAM.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/usrlib/libhts.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.9-bioc/meat/h5vc.buildbin-libdir/00LOCK-h5vc/00new/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 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 (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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/Resources/lib/libquadmath.0.dylib" "h5vc.buildbin-libdir/h5vc/libs//h5vc.so"