Nicholas Cooley
| Snapshot Date: 2025-01-23 13:40 -0500 (Thu, 23 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/SynExtend |
| git_branch: devel |
| git_last_commit: c217db1 |
| git_last_commit_date: 2025-01-22 13:43:00 -0500 (Wed, 22 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-24 11:43 -0500 (Fri, 24 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4609 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4393 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 3839 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 3835 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| 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 2100/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SynExtend 1.19.4 (landing page) Nicholas Cooley
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | 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 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the SynExtend package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SynExtend.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: SynExtend |
| Version: 1.19.4 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SynExtend |
| StartedAt: 2025-01-23 15:08:19 -0500 (Thu, 23 Jan 2025) |
| EndedAt: 2025-01-23 15:08:21 -0500 (Thu, 23 Jan 2025) |
| EllapsedTime: 2.7 seconds |
| RetCode: 1 |
| Status: ERROR |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SynExtend
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘SynExtend’ ...
** this is package ‘SynExtend’ version ‘1.19.4’
** 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 SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CDend.c -o CDend.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CShuffle.c -o CShuffle.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c HungarianAlgo.c -o HungarianAlgo.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LoserTree.c -o LoserTree.o
LoserTree.c:246:10: warning: unused variable 'num_read' [-Wunused-variable]
size_t num_read;
^
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 MoranI.c -o MoranI.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c NucleotideCounts.c -o NucleotideCounts.o
NucleotideCounts.c:267:7: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = INTEGER(NTHREADS)[0];
^
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 OnDiskLP.c -o OnDiskLP.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PrefixTrie.c -o PrefixTrie.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_synextend.c -o R_init_synextend.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RandomForest.c -o RandomForest.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SEutils.c -o SEutils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XORRand.c -o XORRand.o
XORRand.c:67:7: warning: unused variable 'threads' [-Wunused-variable]
int threads = INTEGER(NTHREADS)[0];
^
1 warning generated.
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c _fortran_tabulate.f95 -o _fortran_tabulate.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c _fortran_utils.f95 -o _fortran_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c calcMIR2C.c -o calcMIR2C.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c cart_fort.f95 -o cart_fort.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dendrapply.c -o dendrapply.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SynExtend.so CDend.o CShuffle.o HungarianAlgo.o LoserTree.o MoranI.o NucleotideCounts.o OnDiskLP.o PrefixTrie.o R_init_synextend.o RandomForest.o SEutils.o XORRand.o _fortran_tabulate.o _fortran_utils.o calcMIR2C.o cart_fort.o dendrapply.o -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: search path '/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0' not found
ld: library 'emutls_w' not found
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [SynExtend.so] Error 1
ERROR: compilation failed for package ‘SynExtend’
* removing ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/SynExtend’