Nicholas Cooley
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/SynExtend |
| git_branch: devel |
| git_last_commit: 6662838 |
| git_last_commit_date: 2025-10-17 08:59:08 -0400 (Fri, 17 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:08 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 2170/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SynExtend 1.21.2 (landing page) Nicholas Cooley
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: SynExtend |
| Version: 1.21.2 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL SynExtend |
| StartedAt: 2025-10-23 20:56:08 -0000 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 20:56:45 -0000 (Thu, 23 Oct 2025) |
| EllapsedTime: 37.2 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL SynExtend
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘SynExtend’ ...
** this is package ‘SynExtend’ version ‘1.21.2’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fPIC -g -O2 -Wall -Werror=format-security -c calcMIR2C.c -o calcMIR2C.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fPIC -g -O2 -Wall -Werror=format-security -c CDend.c -o CDend.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fPIC -g -O2 -Wall -Werror=format-security -c CShuffle.c -o CShuffle.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fPIC -g -O2 -Wall -Werror=format-security -c dendrapply.c -o dendrapply.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fPIC -g -O2 -Wall -Werror=format-security -c HitConsensus.c -o HitConsensus.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fPIC -g -O2 -Wall -Werror=format-security -c HungarianAlgo.c -o HungarianAlgo.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fPIC -g -O2 -Wall -Werror=format-security -c MoranI.c -o MoranI.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fPIC -g -O2 -Wall -Werror=format-security -c NucleotideCounts.c -o NucleotideCounts.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fPIC -g -O2 -Wall -Werror=format-security -c R_init_synextend.c -o R_init_synextend.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fPIC -g -O2 -Wall -Werror=format-security -c RandomForest.c -o RandomForest.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fPIC -g -O2 -Wall -Werror=format-security -c SEutils.c -o SEutils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fPIC -g -O2 -Wall -Werror=format-security -c XORRand.c -o XORRand.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fPIC -g -O2 -Wall -Werror=format-security -c ExoLabel/ExoLabel.c -o ExoLabel/ExoLabel.o
ExoLabel/ExoLabel.c: In function ‘R_LPOOM_cluster’:
ExoLabel/ExoLabel.c:1882:5: warning: ‘debug_weights’ may be used uninitialized [-Wmaybe-uninitialized]
1882 | SET_VECTOR_ELT(LIST_VAL, 1, debug_weights);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ExoLabel/ExoLabel.c:1777:8: note: ‘debug_weights’ was declared here
1777 | SEXP debug_weights, debug_degrees;
| ^~~~~~~~~~~~~
ExoLabel/ExoLabel.c:1883:5: warning: ‘debug_degrees’ may be used uninitialized [-Wmaybe-uninitialized]
1883 | SET_VECTOR_ELT(LIST_VAL, 2, debug_degrees);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ExoLabel/ExoLabel.c:1777:23: note: ‘debug_degrees’ was declared here
1777 | SEXP debug_weights, debug_degrees;
| ^~~~~~~~~~~~~
ExoLabel/ExoLabel.c:1884:5: warning: ‘debug_disjoint_sizes’ may be used uninitialized [-Wmaybe-uninitialized]
1884 | SET_VECTOR_ELT(LIST_VAL, 3, debug_disjoint_sizes);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ExoLabel/ExoLabel.c:1826:8: note: ‘debug_disjoint_sizes’ was declared here
1826 | SEXP debug_disjoint_sizes;
| ^~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fPIC -g -O2 -Wall -Werror=format-security -c ExoLabel/FileHandlers.c -o ExoLabel/FileHandlers.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fPIC -g -O2 -Wall -Werror=format-security -c ExoLabel/PrefixTrie.c -o ExoLabel/PrefixTrie.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fPIC -g -O2 -Wall -Werror=format-security -c ExoLabel/LoserTree.c -o ExoLabel/LoserTree.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c utilfuncs.f95 -o utilfuncs.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c tabulate_mod.f95 -o tabulate_mod.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c cart_methods.f95 -o cart_methods.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o SynExtend.so calcMIR2C.o CDend.o CShuffle.o dendrapply.o HitConsensus.o HungarianAlgo.o MoranI.o NucleotideCounts.o R_init_synextend.o RandomForest.o SEutils.o XORRand.o ExoLabel/ExoLabel.o ExoLabel/FileHandlers.o ExoLabel/PrefixTrie.o ExoLabel/LoserTree.o cart_methods.o tabulate_mod.o utilfuncs.o -fopenmp -lgfortran -lm -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-SynExtend/00new/SynExtend/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 (SynExtend)