Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1211/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methimpute 1.29.0 (landing page) Aaron Taudt
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the methimpute package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methimpute.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: methimpute |
Version: 1.29.0 |
Command: rm -rf methimpute.buildbin-libdir && mkdir methimpute.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh methimpute_1.29.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R methimpute.buildbin-libdir |
StartedAt: 2024-12-23 22:33:52 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 22:34:08 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 16.3 seconds |
RetCode: 0 |
Status: OK |
PackageFile: methimpute_1.29.0.tgz |
PackageFileSize: 1.537 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf methimpute.buildbin-libdir && mkdir methimpute.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh methimpute_1.29.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R methimpute.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=methimpute.buildbin-libdir methimpute_1.29.0.tar.gz' >>>>>>> * installing *source* package ‘methimpute’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c densities.cpp -o densities.o In file included from densities.cpp:1: ./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(int test, int total); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2) virtual double getLogDensityAt(int) { return(0); }; ^ ./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(double x); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double') virtual double getLogDensityAt(int) { return(0); }; ^ densities.cpp:920:91: warning: format specifies type 'int' but the argument has type 'double' [-Wformat] if (verbosity>=4) Rprintf(" lGammaR = %g, lgamma(size + obs=%d) = %g\n", lGammaR, obs_j, lgamma(size + obs_j)); ~~ ^~~~~ %f 3 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c fitHMM.cpp -o fitHMM.o In file included from fitHMM.cpp:2: In file included from ./scalehmm.h:4: ./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(int test, int total); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2) virtual double getLogDensityAt(int) { return(0); }; ^ ./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(double x); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double') virtual double getLogDensityAt(int) { return(0); }; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c fitHMM_context.cpp -o fitHMM_context.o In file included from fitHMM_context.cpp:2: In file included from ./hmm_context.h:4: ./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(int test, int total); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2) virtual double getLogDensityAt(int) { return(0); }; ^ ./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(double x); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double') virtual double getLogDensityAt(int) { return(0); }; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c hmm_context.cpp -o hmm_context.o In file included from hmm_context.cpp:1: In file included from ./hmm_context.h:4: ./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(int test, int total); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2) virtual double getLogDensityAt(int) { return(0); }; ^ ./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(double x); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double') virtual double getLogDensityAt(int) { return(0); }; ^ hmm_context.cpp:168:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] else if ((this->emissionDensities[0]->get_name() == NEGATIVE_BINOMIAL) | (this->emissionDensities[0]->get_name() == ZERO_INFLATION)) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ || hmm_context.cpp:168:12: note: cast one or both operands to int to silence this warning hmm_context.cpp:469:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] else if ((this->emissionDensities[0]->get_name() == NEGATIVE_BINOMIAL) | (this->emissionDensities[0]->get_name() == ZERO_INFLATION)) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ || hmm_context.cpp:469:12: note: cast one or both operands to int to silence this warning 4 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c methimpute_init.c -o methimpute_init.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c scalehmm.cpp -o scalehmm.o In file included from scalehmm.cpp:1: In file included from ./scalehmm.h:4: ./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(int test, int total); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2) virtual double getLogDensityAt(int) { return(0); }; ^ ./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(double x); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double') virtual double getLogDensityAt(int) { return(0); }; ^ scalehmm.cpp:411:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] else if ((this->emissionDensities[0]->get_name() == NEGATIVE_BINOMIAL) | (this->emissionDensities[0]->get_name() == ZERO_INFLATION)) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ || scalehmm.cpp:411:12: note: cast one or both operands to int to silence this warning scalehmm.cpp:593:13: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] else if ((this->emissionDensities[0]->get_name() == NEGATIVE_BINOMIAL) | (this->emissionDensities[0]->get_name() == ZERO_INFLATION)) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ || scalehmm.cpp:593:13: note: cast one or both operands to int to silence this warning scalehmm.cpp:726:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] else if ((this->emissionDensities[0]->get_name() == NEGATIVE_BINOMIAL) | (this->emissionDensities[0]->get_name() == ZERO_INFLATION)) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ || scalehmm.cpp:726:12: note: cast one or both operands to int to silence this warning 5 warnings generated. clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o methimpute.so RcppExports.o densities.o fitHMM.o fitHMM_context.o hmm_context.o methimpute_init.o scalehmm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.21-bioc/meat/methimpute.buildbin-libdir/00LOCK-methimpute/00new/methimpute/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 (methimpute) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR methimpute.buildbin-libdir/methimpute/libs/methimpute.so >>>>>>> >>>>>>> Paths before fix: methimpute.buildbin-libdir/methimpute/libs/methimpute.so: methimpute.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "methimpute.buildbin-libdir/methimpute/libs/methimpute.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "methimpute.buildbin-libdir/methimpute/libs/methimpute.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "methimpute.buildbin-libdir/methimpute/libs/methimpute.so" >>>>>>> Paths after fix: methimpute.buildbin-libdir/methimpute/libs/methimpute.so: methimpute.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)