Steffen Neumann
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/Rdisop |
| git_branch: RELEASE_3_13 |
| git_last_commit: 2f422e0 |
| git_last_commit_date: 2021-05-19 11:39:52 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:49 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the Rdisop package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rdisop.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. |
| Package 1530/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rdisop 1.52.0 (landing page) Steffen Neumann
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Rdisop |
| Version: 1.52.0 |
| Command: rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rdisop_1.52.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rdisop.buildbin-libdir |
| StartedAt: 2021-10-15 03:40:30 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 03:41:41 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 70.6 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Rdisop_1.52.0.tgz |
| PackageFileSize: 352.5 KiB |
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### Running command:
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### rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rdisop_1.52.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rdisop.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rdisop.buildbin-libdir Rdisop_1.52.0.tar.gz'
>>>>>>>
* installing *source* package ‘Rdisop’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c disop.cpp -o disop.o
disop.cpp:106:8: warning: unused variable 'parityeven' [-Wunused-variable]
bool parityeven = !parityodd;
^
disop.cpp:191:6: warning: unused variable 'number_molecules_shown' [-Wunused-variable]
int number_molecules_shown = 100;
^
In file included from disop.cpp:28:
./imslib/src/ims/decomp/decomputils.h:92:53: warning: unused typedef 'weight_type' [-Wunused-local-typedef]
typedef typename DecompositionWeights::weight_type weight_type;
^
disop.cpp:174:42: warning: unused typedef 'decomposition_type' [-Wunused-local-typedef]
typedef decompositions_t::value_type decomposition_type;
^
disop.cpp:169:39: warning: unused typedef 'mass_type' [-Wunused-local-typedef]
typedef distribution_t::mass_type mass_type;
^
disop.cpp:171:47: warning: unused typedef 'nominal_mass_type' [-Wunused-local-typedef]
typedef distribution_t::nominal_mass_type nominal_mass_type;
^
disop.cpp:377:40: warning: unused typedef 'mass_type' [-Wunused-local-typedef]
typedef distribution_t::mass_type mass_type;
^
disop.cpp:626:43: warning: unused typedef 'scorer_type' [-Wunused-local-typedef]
typedef DistributionProbabilityScorer scorer_type;
^
disop.cpp:709:32: warning: unused typedef 'elements_type' [-Wunused-local-typedef]
typedef alphabet_t::container elements_type;
^
disop.cpp:814:33: warning: unused typedef 'elements_type' [-Wunused-local-typedef]
typedef alphabet_t::container elements_type;
^
10 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: warning: '&&' within '||' [-Wlogical-op-parentheses]
for (; letter_pos < last_pos &&
~~~~~~~~~~~~~~~~~~~~~~^~
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: note: place parentheses around the '&&' expression to silence this warning
for (; letter_pos < last_pos &&
^
(
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:9:
./imslib/src/ims/decomp/decomputils.h:92:53: warning: unused typedef 'weight_type' [-Wunused-local-typedef]
typedef typename DecompositionWeights::weight_type weight_type;
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
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 Rdisop.so disop.o imslib/src/ims/element.o imslib/src/ims/composedelement.o imslib/src/ims/isotopedistribution.o imslib/src/ims/alphabet.o imslib/src/ims/weights.o imslib/src/ims/distributedalphabet.o imslib/src/ims/transformation.o imslib/src/ims/isotopespecies.o imslib/src/ims/base/parser/alphabettextparser.o imslib/src/ims/base/parser/distributedalphabettextparser.o imslib/src/ims/base/parser/massestextparser.o imslib/src/ims/base/parser/moleculesequenceparser.o imslib/src/ims/base/parser/standardmoleculesequenceparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o imslib/src/ims/calib/linepairstabber.o imslib/src/ims/calib/matchmatrix.o imslib/src/ims/calib/linearpointsetmatcher.o imslib/src/ims/decomp/realmassdecomposer.o imslib/src/ims/utils/distribution.o imslib/src/ims/distributionprobabilityscorer.o imslib/src/ims/characteralphabet.o imslib/src/ims/nitrogenrulefilter.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.13-bioc/meat/Rdisop.buildbin-libdir/00LOCK-Rdisop/00new/Rdisop/libs
** R
** 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 (Rdisop)
>>>>>>>
>>>>>>> FIXING LINKS FOR Rdisop.buildbin-libdir/Rdisop/libs/Rdisop.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" "Rdisop.buildbin-libdir/Rdisop/libs/Rdisop.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "Rdisop.buildbin-libdir/Rdisop/libs/Rdisop.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "Rdisop.buildbin-libdir/Rdisop/libs/Rdisop.so"