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BioC 3.5: BUILD BIN report for diffHic on veracruz2

This page was generated on 2017-08-16 13:33:12 -0400 (Wed, 16 Aug 2017).

Package 347/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffHic 1.8.1
Aaron Lun
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/diffHic
Last Changed Rev: 129582 / Revision: 131943
Last Changed Date: 2017-05-14 11:36:56 -0400 (Sun, 14 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: diffHic
Version: 1.8.1
Command: rm -rf diffHic.buildbin-libdir && mkdir diffHic.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh diffHic_1.8.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R diffHic.buildbin-libdir
StartedAt: 2017-08-16 10:01:54 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 10:02:31 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 36.8 seconds
RetCode: 0
Status:  OK 
PackageFile: diffHic_1.8.1.tgz
PackageFileSize: 1.945 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf diffHic.buildbin-libdir && mkdir diffHic.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh diffHic_1.8.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R diffHic.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=diffHic.buildbin-libdir diffHic_1.8.1.tar.gz'
>>>>>>> 

* installing *source* package ‘diffHic’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c binner.cpp -o binner.o
binner.cpp:36:84: warning: field 'ischanged' will be initialized after field 'curcounts' [-Wreorder]
binner::binner(SEXP all, SEXP bin, int f, int l) : fbin(f), lbin(l), nbins(l-f+1), ischanged(NULL), curcounts(NULL) {
                                                                                   ^
In file included from binner.cpp:1:
./read_count.h:42:36: warning: private field 'lib' is not used [-Wunused-private-field]
        int curab, curtb, curlib, curdex, lib;
                                          ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c check_input.cpp -o check_input.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c cluster_2d.cpp -o cluster_2d.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_background.cpp -o count_background.o
count_background.cpp:249:10: warning: unused variable 'backaverage' [-Wunused-variable]
                double backaverage, maxaverage;
                       ^
count_background.cpp:249:23: warning: unused variable 'maxaverage' [-Wunused-variable]
                double backaverage, maxaverage;
                                    ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_connect.cpp -o count_connect.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_patch.cpp -o count_patch.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c directionality.cpp -o directionality.o
directionality.cpp:45:9: warning: unused variable 'current_average' [-Wunused-variable]
        double current_average;
               ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c iterative_correction.cpp -o iterative_correction.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c neighbors.cpp -o neighbors.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c pair_stats.cpp -o pair_stats.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c quadrant_bg.cpp -o quadrant_bg.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c report_hic_pairs.cpp -o report_hic_pairs.o
report_hic_pairs.cpp:575:6: warning: private field 'bin_width' is not used [-Wunused-private-field]
        int bin_width;
            ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c trended_filter.cpp -o trended_filter.o
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 diffHic.so binner.o check_input.o cluster_2d.o count_background.o count_connect.o count_patch.o directionality.o init.o iterative_correction.o neighbors.o pair_stats.o quadrant_bg.o report_hic_pairs.o trended_filter.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-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
installing to /Users/biocbuild/bbs-3.5-bioc/meat/diffHic.buildbin-libdir/diffHic/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (diffHic)


>>>>>>> 
>>>>>>> FIXING LINKS FOR diffHic.buildbin-libdir/diffHic/libs//diffHic.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" "diffHic.buildbin-libdir/diffHic/libs//diffHic.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "diffHic.buildbin-libdir/diffHic/libs//diffHic.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" "diffHic.buildbin-libdir/diffHic/libs//diffHic.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "diffHic.buildbin-libdir/diffHic/libs//diffHic.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "diffHic.buildbin-libdir/diffHic/libs//diffHic.so"