Shubham Gupta
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/DIAlignR |
| Branch: RELEASE_3_11 |
| Last Commit: 4f8a0db |
| Last Changed Date: 2020-05-07 15:09:23 -0400 (Thu, 07 May 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:22 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE DIAlignR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 468/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DIAlignR 1.0.5 Shubham Gupta
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | [ OK ] | |
| Package: DIAlignR |
| Version: 1.0.5 |
| Command: rm -rf DIAlignR.buildbin-libdir && mkdir DIAlignR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DIAlignR_1.0.5.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DIAlignR.buildbin-libdir |
| StartedAt: 2020-10-17 06:56:49 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:57:56 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 67.3 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: DIAlignR_1.0.5.tgz |
| PackageFileSize: 2.277 MiB |
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### Running command:
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### rm -rf DIAlignR.buildbin-libdir && mkdir DIAlignR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DIAlignR_1.0.5.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DIAlignR.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DIAlignR.buildbin-libdir DIAlignR_1.0.5.tar.gz'
>>>>>>>
* installing *source* package ‘DIAlignR’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ChromatogramPeak.cpp -o ChromatogramPeak.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c DPosition.cpp -o DPosition.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c MSChromatogram.cpp -o MSChromatogram.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PeakIntegrator.cpp -o PeakIntegrator.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Rmain.cpp -o Rmain.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c affinealignment.cpp -o affinealignment.o
affinealignment.cpp:260:12: warning: enumeration value 'SS' not handled in switch [-Wswitch]
switch(TracebackPointer){
^
affinealignment.cpp:260:12: note: add missing switch cases
switch(TracebackPointer){
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c affinealignobj.cpp -o affinealignobj.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c alignment.cpp -o alignment.o
alignment.cpp:194:12: warning: 7 enumeration values not handled in switch: 'SS', 'DA', 'DB'... [-Wswitch]
switch(TracebackPointer){
^
alignment.cpp:194:12: note: add missing switch cases
switch(TracebackPointer){
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c chromSimMatrix.cpp -o chromSimMatrix.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c constrainMat.cpp -o constrainMat.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c gapPenalty.cpp -o gapPenalty.o
gapPenalty.cpp:20:11: warning: variable 'gapPenalty' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if(SimType == "correlation")
^~~~~~~~~~~~~~~~~~~~~~~~
gapPenalty.cpp:26:10: note: uninitialized use occurs here
return gapPenalty;
^~~~~~~~~~
gapPenalty.cpp:20:8: note: remove the 'if' if its condition is always true
else if(SimType == "correlation")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gapPenalty.cpp:6:20: note: initialize the variable 'gapPenalty' to silence this warning
double gapPenalty;
^
= 0.0
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c integrateArea.cpp -o integrateArea.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c interface.cpp -o interface.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c simpleFcn.cpp -o simpleFcn.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o
utils.cpp:48:9: warning: unused variable 'idx' [-Wunused-variable]
int idx = n*(1-p);
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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 DIAlignR.so ChromatogramPeak.o DPosition.o MSChromatogram.o PeakIntegrator.o RcppExports.o Rmain.o affinealignment.o affinealignobj.o alignment.o chromSimMatrix.o constrainMat.o gapPenalty.o integrateArea.o interface.o simpleFcn.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/DIAlignR.buildbin-libdir/00LOCK-DIAlignR/00new/DIAlignR/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 (DIAlignR)
>>>>>>>
>>>>>>> FIXING LINKS FOR DIAlignR.buildbin-libdir/DIAlignR/libs/DIAlignR.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "DIAlignR.buildbin-libdir/DIAlignR/libs/DIAlignR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "DIAlignR.buildbin-libdir/DIAlignR/libs/DIAlignR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "DIAlignR.buildbin-libdir/DIAlignR/libs/DIAlignR.so"