Nicholas Cooley
| Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025) |
| git_url: https://git.bioconductor.org/packages/SynExtend |
| git_branch: devel |
| git_last_commit: 66702ff |
| git_last_commit_date: 2025-05-19 12:03:56 -0400 (Mon, 19 May 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-19 12:02 -0400 (Thu, 19 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4810 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4548 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4528 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4493 |
| 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 2120/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SynExtend 1.21.1 (landing page) Nicholas Cooley
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / 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: 1.21.1 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SynExtend |
| StartedAt: 2025-06-18 15:38:14 -0400 (Wed, 18 Jun 2025) |
| EndedAt: 2025-06-18 15:38:48 -0400 (Wed, 18 Jun 2025) |
| EllapsedTime: 34.6 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SynExtend
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘SynExtend’ ...
** this is package ‘SynExtend’ version ‘1.21.1’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c CDend.c -o CDend.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c CShuffle.c -o CShuffle.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c HungarianAlgo.c -o HungarianAlgo.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c LoserTree.c -o LoserTree.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c MoranI.c -o MoranI.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c NucleotideCounts.c -o NucleotideCounts.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c OnDiskLP.c -o OnDiskLP.o
OnDiskLP.c: In function ‘R_LPOOM_cluster’:
OnDiskLP.c:2185:5: warning: ‘debug_weights’ may be used uninitialized [-Wmaybe-uninitialized]
2185 | SET_VECTOR_ELT(LIST_VAL, 1, debug_weights);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
OnDiskLP.c:2076:8: note: ‘debug_weights’ was declared here
2076 | SEXP debug_weights, debug_degrees;
| ^~~~~~~~~~~~~
OnDiskLP.c:2186:5: warning: ‘debug_degrees’ may be used uninitialized [-Wmaybe-uninitialized]
2186 | SET_VECTOR_ELT(LIST_VAL, 2, debug_degrees);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
OnDiskLP.c:2076:23: note: ‘debug_degrees’ was declared here
2076 | SEXP debug_weights, debug_degrees;
| ^~~~~~~~~~~~~
OnDiskLP.c:2187:5: warning: ‘debug_disjoint_sizes’ may be used uninitialized [-Wmaybe-uninitialized]
2187 | SET_VECTOR_ELT(LIST_VAL, 3, debug_disjoint_sizes);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
OnDiskLP.c:2125:8: note: ‘debug_disjoint_sizes’ was declared here
2125 | SEXP debug_disjoint_sizes;
| ^~~~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c PrefixTrie.c -o PrefixTrie.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c R_init_synextend.c -o R_init_synextend.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c RandomForest.c -o RandomForest.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SEutils.c -o SEutils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c XORRand.c -o XORRand.o
gfortran -fpic -g -O2 -Wall -Werror=format-security -c _fortran_tabulate.f95 -o _fortran_tabulate.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
gfortran -fpic -g -O2 -Wall -Werror=format-security -c _fortran_utils.f95 -o _fortran_utils.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c calcMIR2C.c -o calcMIR2C.o
gfortran -fpic -g -O2 -Wall -Werror=format-security -c cart_fort.f95 -o cart_fort.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c dendrapply.c -o dendrapply.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/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 -fopenmp -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/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)