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 803/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneticsPed 1.69.0 (landing page) David Henderson
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
To the developers/maintainers of the GeneticsPed package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneticsPed.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: GeneticsPed |
Version: 1.69.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneticsPed |
StartedAt: 2024-12-23 15:02:31 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 15:02:37 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 6.1 seconds |
RetCode: 1 |
Status: ERROR |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneticsPed ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘GeneticsPed’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ainverse.cc -o ainverse.o In file included from ainverse.cc:9: In file included from ./../include/ainverse.h:20: ./../include/pedtemplate.h:18:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ <command line>:2:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c eibd.cc -o eibd.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c ggmatmult.f -o ggmatmult.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c gpi.f -o gpi.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c inbreed.cc -o inbreed.o In file included from inbreed.cc:10: In file included from ./../include/inbreed.h:18: ./../include/pedtemplate.h:18:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ <command line>:2:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c inverseAdditive.cc -o inverseAdditive.o inverseAdditive.cc:1:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ <command line>:2:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c meuwissen.cc -o meuwissen.o meuwissen.cc:1:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ <command line>:2:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c pedSort.cc -o pedSort.o pedSort.cc:1:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ <command line>:2:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c pedtemplate.cc -o pedtemplate.o In file included from pedtemplate.cc:15: ./../include/pedtemplate.h:18:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ <command line>:2:9: note: previous definition is here #define R_NO_REMAP 1 ^ pedtemplate.cc:373:21: warning: format specifies type 'int' but the argument has type 'decltype(__x.base() - __y.base())' (aka 'long') [-Wformat] Rprintf("%d\t", p - pedigree.begin()); ~~ ^~~~~~~~~~~~~~~~~~~~ %ld 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c register.cc -o register.o In file included from register.cc:8: In file included from ./../include/meuwissen.h:7: In file included from ./../include/../include/inbreed.h:18: ./../include/pedtemplate.h:18:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ <command line>:2:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sargolzaei.c -o sargolzaei.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c sortped.cc -o sortped.o In file included from sortped.cc:1: ./../include/sortped.h:5:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ <command line>:2:9: note: previous definition is here #define R_NO_REMAP 1 ^ sortped.cc:55:5: error: use of undeclared identifier 'error' error("Problems in pedigree. Stopping inbreeding calculations\n"); ^ 1 warning and 1 error generated. make: *** [sortped.o] Error 1 ERROR: compilation failed for package ‘GeneticsPed’ * removing ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/GeneticsPed’