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This page was generated on 2021-10-15 15:06:47 -0400 (Fri, 15 Oct 2021).

BUILD BIN results for plier on machv2

To the developers/maintainers of the plier package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/plier.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1402/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plier 1.62.0  (landing page)
Crispin Miller
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/plier
git_branch: RELEASE_3_13
git_last_commit: 405f847
git_last_commit_date: 2021-05-19 11:35:20 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: plier
Version: 1.62.0
Command: rm -rf plier.buildbin-libdir && mkdir plier.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh plier_1.62.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R plier.buildbin-libdir
StartedAt: 2021-10-15 03:29:34 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 03:30:43 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 69.2 seconds
RetCode: 0
Status:   OK  
PackageFile: plier_1.62.0.tgz
PackageFileSize: 43.69 KiB

Command output

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###
### Running command:
###
###   rm -rf plier.buildbin-libdir && mkdir plier.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh plier_1.62.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R plier.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=plier.buildbin-libdir plier_1.62.0.tar.gz'
>>>>>>> 

* installing *source* package ‘plier’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c affyplier.cpp -o affyplier.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c plier_impl.cpp -o plier_impl.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c plieralg.cpp -o plieralg.o
plieralg.cpp:49:12: warning: unused variable 'g_ErrorCode' [-Wunused-variable]
static int g_ErrorCode=NoError;
           ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rwrapper.cpp -o rwrapper.o
rwrapper.cpp:192:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
    delete pm_ptr;  
    ^
          []
rwrapper.cpp:151:23: note: allocated with 'new[]' here
    double **pm_ptr = new double *[*num_exp];
                      ^
rwrapper.cpp:193:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
    delete mm_ptr;
    ^
          []
rwrapper.cpp:152:23: note: allocated with 'new[]' here
    double **mm_ptr = new double *[*num_exp];
                      ^
rwrapper.cpp:194:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
    delete rpct;
    ^
          []
rwrapper.cpp:159:21: note: allocated with 'new[]' here
    long    *rpct = new long [*num_exp]; /* the API expects a long array that it wants to delete itself (replicate). We have an int array that R owns so we need to create the long one here, but let the API handle the clean up. Which is nice. */
                    ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 plier.so affyplier.o plier_impl.o plieralg.o rwrapper.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.13-bioc/meat/plier.buildbin-libdir/00LOCK-plier/00new/plier/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (plier)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgcc_s.1.dylib" "plier.buildbin-libdir/plier/libs/plier.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "plier.buildbin-libdir/plier/libs/plier.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "plier.buildbin-libdir/plier/libs/plier.so"