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BioC 3.0: BUILD BIN report for PING on perceval

This page was generated on 2015-04-10 09:56:46 -0700 (Fri, 10 Apr 2015).

Package 663/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PING 2.10.0
Renan Sauteraud
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/PING
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK [ OK ]
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: PING
Version: 2.10.0
Command: rm -rf PING.buildbin-libdir && mkdir PING.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PING_2.10.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R PING.buildbin-libdir
StartedAt: 2015-04-10 08:32:36 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 08:33:34 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 58.4 seconds
RetCode: 0
Status:  OK 
PackageFile: PING_2.10.0.tgz
PackageFileSize: 5.329 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PING.buildbin-libdir && mkdir PING.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PING_2.10.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R PING.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=PING.buildbin-libdir PING_2.10.0.tar.gz'
>>>>>>> 

* installing *source* package ‘PING’ ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c init.c -o init.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ping.c -o ping.o
ping.c: In function ‘fitModelAllk’:
ping.c:145: warning: suggest parentheses around comparison in operand of &
ping.c: In function ‘iterEM’:
ping.c:659: warning: unused variable ‘mu’
ping.c: In function ‘ECM1’:
ping.c:912: warning: suggest parentheses around comparison in operand of &
ping.c:1072: warning: suggest parentheses around comparison in operand of &
ping.c:760: warning: unused variable ‘k’
ping.c: In function ‘ECM1PE’:
ping.c:1320: warning: suggest parentheses around comparison in operand of &
ping.c:1473: warning: suggest parentheses around comparison in operand of &
ping.c:1108: warning: unused variable ‘k’
ping.c: In function ‘ECM2’:
ping.c:1536: warning: unused variable ‘ee’
ping.c:1536: warning: unused variable ‘ggR’
ping.c:1536: warning: unused variable ‘ggF’
ping.c:1536: warning: unused variable ‘aaR’
ping.c:1536: warning: unused variable ‘aaF’
ping.c:1536: warning: unused variable ‘etaDiff’
ping.c:1527: warning: unused variable ‘k’
ping.c: In function ‘ECM2PE’:
ping.c:1743: warning: unused variable ‘ee’
ping.c:1743: warning: unused variable ‘ggR’
ping.c:1743: warning: unused variable ‘ggF’
ping.c:1743: warning: unused variable ‘aaR’
ping.c:1743: warning: unused variable ‘aaF’
ping.c:1743: warning: unused variable ‘etaDiff’
ping.c:1734: warning: unused variable ‘k’
ping.c: In function ‘getInfMat’:
ping.c:2590: warning: unused variable ‘PhiRw’
ping.c:2590: warning: unused variable ‘PhiFw’
ping.c: In function ‘getInfMatPE’:
ping.c:3040: warning: unused variable ‘PhiFRw’
ping.c: In function ‘mergePeak’:
ping.c:3301: warning: unused variable ‘j’
ping.c:3301: warning: unused variable ‘i’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -L/usr/local/lib -o PING.so init.o ping.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/PING.buildbin-libdir/PING/libs
** R
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: levels, as.factor, elementMetadata, elementMetadata<-
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: levels, as.factor, elementMetadata, elementMetadata<-
* DONE (PING)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgcc_s.1.dylib" "PING.buildbin-libdir/PING/libs//PING.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.2.dylib" "PING.buildbin-libdir/PING/libs//PING.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.5.2.dylib" "PING.buildbin-libdir/PING/libs//PING.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "PING.buildbin-libdir/PING/libs//PING.so"