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BioC 3.2: BUILD BIN report for destiny on oaxaca

This page was generated on 2015-10-27 17:42:36 -0400 (Tue, 27 Oct 2015).

Package 270/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
destiny 1.0.0
Philipp Angerer
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/destiny
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  ERROR  skipped  skipped 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: destiny
Version: 1.0.0
Command: rm -rf destiny.buildbin-libdir && mkdir destiny.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh destiny_1.0.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R destiny.buildbin-libdir
StartedAt: 2015-10-27 09:44:28 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 09:45:06 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 38.6 seconds
RetCode: 0
Status:  OK 
PackageFile: destiny_1.0.0.tgz
PackageFileSize: 762.4 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf destiny.buildbin-libdir && mkdir destiny.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh destiny_1.0.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R destiny.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=destiny.buildbin-libdir destiny_1.0.0.tar.gz'
>>>>>>> 

* installing *source* package ‘destiny’ ...
** libs
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include"  -g -fPIC  -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include"  -g -fPIC  -Wall -mtune=core2 -g -O2 -c censoring.cpp -o censoring.o
censoring.cpp:60:15: warning: variable 'm0' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        } else if (!one_uncertain && one_missing) {
                                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:71:20: note: uninitialized use occurs here
                                * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
                                               ^˜
censoring.cpp:60:11: note: remove the 'if' if its condition is always true
                        } else if (!one_uncertain && one_missing) {
                               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:60:15: warning: variable 'm0' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
                        } else if (!one_uncertain && one_missing) {
                                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:71:20: note: uninitialized use occurs here
                                * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
                                               ^˜
censoring.cpp:60:15: note: remove the '&&' if its condition is always true
                        } else if (!one_uncertain && one_missing) {
                                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:55:13: note: initialize the variable 'm0' to silence this warning
                        double m0, m1;
                                 ^
                                  = 0.0
censoring.cpp:60:15: warning: variable 'm1' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        } else if (!one_uncertain && one_missing) {
                                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:71:48: note: uninitialized use occurs here
                                * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
                                                                           ^˜
censoring.cpp:60:11: note: remove the 'if' if its condition is always true
                        } else if (!one_uncertain && one_missing) {
                               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:60:15: warning: variable 'm1' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
                        } else if (!one_uncertain && one_missing) {
                                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:71:48: note: uninitialized use occurs here
                                * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
                                                                           ^˜
censoring.cpp:60:15: note: remove the '&&' if its condition is always true
                        } else if (!one_uncertain && one_missing) {
                                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:55:17: note: initialize the variable 'm1' to silence this warning
                        double m0, m1;
                                     ^
                                      = 0.0
censoring.cpp:60:15: warning: variable 'use_d' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        } else if (!one_uncertain && one_missing) {
                                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:66:21: note: uninitialized use occurs here
                        const double v = use_d ? d : c;
                                         ^˜˜˜˜
censoring.cpp:60:11: note: remove the 'if' if its condition is always true
                        } else if (!one_uncertain && one_missing) {
                               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:60:15: warning: variable 'use_d' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
                        } else if (!one_uncertain && one_missing) {
                                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:66:21: note: uninitialized use occurs here
                        const double v = use_d ? d : c;
                                         ^˜˜˜˜
censoring.cpp:60:15: note: remove the '&&' if its condition is always true
                        } else if (!one_uncertain && one_missing) {
                                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:18:12: note: initialize the variable 'use_d' to silence this warning
        bool use_d;
                  ^
                   = false
6 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include"  -g -fPIC  -Wall -mtune=core2 -g -O2 -c no_censoring.cpp -o no_censoring.o
no_censoring.cpp:24:3: warning: variable 'v2sqr_sum' is uninitialized when used here [-Wuninitialized]
                v2sqr_sum += v2[i] * v2[i];
                ^˜˜˜˜˜˜˜˜
no_censoring.cpp:16:51: note: initialize the variable 'v2sqr_sum' to silence this warning
        double v1sum, v2sum, v12sum, v1sqr_sum, v2sqr_sum;
                                                         ^
                                                          = 0.0
1 warning generated.
clang++ -std=c++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 destiny.so RcppExports.o censoring.o no_censoring.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/destiny.buildbin-libdir/destiny/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘destiny’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
* DONE (destiny)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgcc_s.1.dylib" "destiny.buildbin-libdir/destiny/libs//destiny.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.3.dylib" "destiny.buildbin-libdir/destiny/libs//destiny.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.5.2.dylib" "destiny.buildbin-libdir/destiny/libs//destiny.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "destiny.buildbin-libdir/destiny/libs//destiny.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libquadmath.0.dylib" "destiny.buildbin-libdir/destiny/libs//destiny.so"