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This page was generated on 2024-03-27 11:38:51 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
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 2164/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TransView 1.47.0  (landing page)
Julius Muller
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/TransView
git_branch: devel
git_last_commit: e5622ac
git_last_commit_date: 2023-10-24 09:51:41 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

BUILD BIN results for TransView on palomino3


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.

raw results


Summary

Package: TransView
Version: 1.47.0
Command: rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=TransView.buildbin-libdir TransView_1.47.0.tar.gz
StartedAt: 2024-03-27 09:19:40 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 09:20:24 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 43.9 seconds
RetCode: 0
Status:   OK  
PackageFile: TransView_1.47.0.zip
PackageFileSize: 6.076 MiB

Command output

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### Running command:
###
###   rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=TransView.buildbin-libdir TransView_1.47.0.tar.gz
###
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* installing *source* package 'TransView' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-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 F:/biocbuild/bbs-3.19-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 -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-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
** 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 'TransView' as TransView_1.47.0.zip
* DONE (TransView)