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This page was generated on 2024-04-17 11:37:19 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 1943/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ShortRead 1.60.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/ShortRead
git_branch: RELEASE_3_18
git_last_commit: 4304db4
git_last_commit_date: 2023-10-24 09:39:49 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

INSTALL results for ShortRead on palomino4


To the developers/maintainers of the ShortRead package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ShortRead.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: ShortRead
Version: 1.60.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL ShortRead
StartedAt: 2024-04-15 16:08:28 -0400 (Mon, 15 Apr 2024)
EndedAt: 2024-04-15 16:10:05 -0400 (Mon, 15 Apr 2024)
EllapsedTime: 96.6 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL ShortRead
###
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* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'ShortRead' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c alphabet.c -o alphabet.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c count.c -o count.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c io.c -o io.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c io_bowtie.c -o io_bowtie.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c io_soap.c -o io_soap.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c readBfaToc.cc -o readBfaToc.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_maq_map.cc -o read_maq_map.o
In file included from read_maq_map.cc:13:
maqmap_m.h: In function 'maqmap_T<max_readlen>* maqmap_read_header(bioc_gzFile) [with int max_readlen = 128]':
maqmap_m.h:102:18: warning: pointer 'mm' used after 'void free(void*)' [-Wuse-after-free]
  102 |             error("MAQ format '%d' not supported", mm->format);
In function 'void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 128]',
    inlined from 'void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 128]' at maqmap_m.h:74:35,
    inlined from 'maqmap_T<max_readlen>* maqmap_read_header(bioc_gzFile) [with int max_readlen = 128]' at maqmap_m.h:101:30:
maqmap_m.h:84:14: note: call to 'void free(void*)' here
   84 |     std::free(mm);
      |     ~~~~~~~~~^~~~
maqmap_m.h: In function 'maqmap_T<max_readlen>* maqmap_read_header(bioc_gzFile) [with int max_readlen = 64]':
maqmap_m.h:102:18: warning: pointer 'mm' used after 'void free(void*)' [-Wuse-after-free]
  102 |             error("MAQ format '%d' not supported", mm->format);
In function 'void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 64]',
    inlined from 'void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 64]' at maqmap_m.h:74:35,
    inlined from 'maqmap_T<max_readlen>* maqmap_read_header(bioc_gzFile) [with int max_readlen = 64]' at maqmap_m.h:101:30:
maqmap_m.h:84:14: note: call to 'void free(void*)' here
   84 |     std::free(mm);
      |     ~~~~~~~~~^~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sampler.c -o sampler.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c trim.c -o trim.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c util.c -o util.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c xsnap.c -o xsnap.o
g++ -std=gnu++17 -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -LF:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-ShortRead/00new/ShortRead/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 (ShortRead)