Julius Muller
| Snapshot Date: 2024-11-24 13:40 -0500 (Sun, 24 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/TransView |
| git_branch: devel |
| git_last_commit: c3729dd |
| git_last_commit_date: 2024-10-29 09:43:11 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-25 11:39 -0500 (Mon, 25 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4349 |
| 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 2167/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TransView 1.51.0 (landing page) Julius Muller
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
|
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: 1.51.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL TransView |
| StartedAt: 2024-11-24 15:49:27 -0500 (Sun, 24 Nov 2024) |
| EndedAt: 2024-11-24 15:50:32 -0500 (Sun, 24 Nov 2024) |
| EllapsedTime: 65.2 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL TransView
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'TransView' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_TransView.c -o R_init_TransView.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam_plbuf.c -o bam_plbuf.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bin_density.c -o bin_density.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c construct_dc.c -o construct_dc.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c parse_sam.c -o parse_sam.o
parse_sam.c: In function 'quality_check':
parse_sam.c:161:75: warning: format '%d' expects argument of type 'int', but argument 2 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
161 | warning("Read length neither found in core.isize=%d, core.l_qseq=%d or cigar=%d!\n",temp_read->core.isize,temp_read->core.l_qseq,bam1_cigar(temp_read));
| ~^ ~~~~~~~~~~~~~~~~~~~~~
| | |
| int hts_pos_t {aka long long int}
| %lld
parse_sam.c:161:103: warning: format '%d' expects argument of type 'int', but argument 4 has type 'uint32_t *' {aka 'unsigned int *'} [-Wformat=]
161 | warning("Read length neither found in core.isize=%d, core.l_qseq=%d or cigar=%d!\n",temp_read->core.isize,temp_read->core.l_qseq,bam1_cigar(temp_read));
| ~^
| |
| int
| %n
parse_sam.c: In function 'print_readinfo':
parse_sam.c:202:22: warning: format '%d' expects argument of type 'int', but argument 2 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
202 | printf("Pos %d\n",current_read->core.pos);
| ~^ ~~~~~~~~~~~~~~~~~~~~~~
| | |
| int hts_pos_t {aka long long int}
| %lld
parse_sam.c:203:33: warning: format '%d' expects argument of type 'int', but argument 3 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
203 | printf("Len %d -> END: %d\n",rm->read_length,rm->read_length+current_read->core.pos);
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| int hts_pos_t {aka long long int}
| %lld
parse_sam.c: In function 'seq_density':
parse_sam.c:314:61: warning: format '%d' expects argument of type 'int', but argument 3 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
314 | warning("BUFFER only %d\n But POS: %d cur_seq_len: %d EXTEND: %d -> %d \n GLOBAL %d\n",
| ~^
| |
| int
| %lld
315 | BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND,
| ~~~~~~~~~~~~~~~~~~~~~~
| |
| hts_pos_t {aka long long int}
parse_sam.c:314:94: warning: format '%d' expects argument of type 'int', but argument 6 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
314 | warning("BUFFER only %d\n But POS: %d cur_seq_len: %d EXTEND: %d -> %d \n GLOBAL %d\n",
| ~^
| |
| int
| %lld
315 | BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND,
316 | current_read->core.pos+rm.read_length+user_args->EXTEND,abs_gen_end);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| hts_pos_t {aka long long int}
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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 E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TransView)