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 12:04 -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: rm -rf SynExtend.buildbin-libdir && mkdir SynExtend.buildbin-libdir && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL --build --library=SynExtend.buildbin-libdir SynExtend_1.21.1.tar.gz |
| StartedAt: 2025-06-19 10:16:30 -0400 (Thu, 19 Jun 2025) |
| EndedAt: 2025-06-19 10:18:10 -0400 (Thu, 19 Jun 2025) |
| EllapsedTime: 99.8 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: SynExtend_1.21.1.zip |
| PackageFileSize: 4.169 MiB |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf SynExtend.buildbin-libdir && mkdir SynExtend.buildbin-libdir && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL --build --library=SynExtend.buildbin-libdir SynExtend_1.21.1.tar.gz
###
##############################################################################
##############################################################################
* installing *source* package 'SynExtend' ...
** this is package 'SynExtend' version '1.21.1'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
using Fortran compiler: 'GNU Fortran (GCC) 14.2.0'
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c CDend.c -o CDend.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c CShuffle.c -o CShuffle.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c HungarianAlgo.c -o HungarianAlgo.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c LoserTree.c -o LoserTree.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c MoranI.c -o MoranI.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c NucleotideCounts.c -o NucleotideCounts.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -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 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c PrefixTrie.c -o PrefixTrie.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c R_init_synextend.c -o R_init_synextend.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c RandomForest.c -o RandomForest.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SEutils.c -o SEutils.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c XORRand.c -o XORRand.o
gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c _fortran_tabulate.f95 -o _fortran_tabulate.o
gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c _fortran_utils.f95 -o _fortran_utils.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c calcMIR2C.c -o calcMIR2C.o
gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c cart_fort.f95 -o cart_fort.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c dendrapply.c -o dendrapply.o
gcc -shared -s -static-libgcc -o SynExtend.dll tmp.def 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 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -lgfortran -lquadmath -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/meat/SynExtend.buildbin-libdir/00LOCK-SynExtend/00new/SynExtend/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'SynExtend' as SynExtend_1.21.1.zip
* DONE (SynExtend)