Julius Muller
| Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/TransView |
| git_branch: devel |
| git_last_commit: b526566 |
| git_last_commit_date: 2025-07-24 08:36:41 -0400 (Thu, 24 Jul 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-09 12:08 -0400 (Sat, 09 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| 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 2210/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Julius Muller
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the TransView package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TransView.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: TransView |
| Version: 1.53.1 |
| Command: rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL --build --library=TransView.buildbin-libdir TransView_1.53.1.tar.gz |
| StartedAt: 2025-08-09 10:26:12 -0400 (Sat, 09 Aug 2025) |
| EndedAt: 2025-08-09 10:27:35 -0400 (Sat, 09 Aug 2025) |
| EllapsedTime: 83.4 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: TransView_1.53.1.zip |
| PackageFileSize: 6.564 MiB |
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### Running command:
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### rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL --build --library=TransView.buildbin-libdir TransView_1.53.1.tar.gz
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* installing *source* package 'TransView' ...
** this is package 'TransView' version '1.53.1'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c R_init_TransView.c -o R_init_TransView.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c bam_plbuf.c -o bam_plbuf.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c bin_density.c -o bin_density.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c construct_dc.c -o construct_dc.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c parse_sam.c -o parse_sam.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c slice_dc.c -o slice_dc.o
slice_dc.c: In function 'slice_dc':
slice_dc.c:184:33: warning: 'slicep' may be used uninitialized [-Wmaybe-uninitialized]
184 | expand(slicep,new_vecp,rebuildc,wsize);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
slice_dc.c:101:22: note: 'slicep' was declared here
101 | int *slicep= INTEGER_POINTER(slice);
| ^~~~~~
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c visuals.c -o visuals.o
gcc -shared -s -static-libgcc -o TransView.dll tmp.def R_init_TransView.o bam_plbuf.o bin_density.o construct_dc.o parse_sam.o slice_dc.o visuals.o F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lnghttp2 -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -lz -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/meat/TransView.buildbin-libdir/00LOCK-TransView/00new/TransView/libs/x64
** R
** 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
Warning in fun(libname, pkgname) :
Package 'TransView' is deprecated and will be removed from Bioconductor
version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
Package 'TransView' is deprecated and will be removed from Bioconductor
version 3.23
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'TransView' as TransView_1.53.1.zip
* DONE (TransView)