| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 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" | 4554 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 1967/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ShortRead 1.67.1 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. |
| Package: ShortRead |
| Version: 1.67.1 |
| Command: rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL --build --library=ShortRead.buildbin-libdir ShortRead_1.67.1.tar.gz |
| StartedAt: 2025-08-15 11:19:19 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 11:23:25 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 245.7 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: ShortRead_1.67.1.zip |
| PackageFileSize: 5.595 MiB |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL --build --library=ShortRead.buildbin-libdir ShortRead_1.67.1.tar.gz
###
##############################################################################
##############################################################################
* installing *source* package 'ShortRead' ...
** this is package 'ShortRead' version '1.67.1'
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -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 Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -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 IRanges_stubs.c -o IRanges_stubs.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -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_ShortRead.c -o R_init_ShortRead.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -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 S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -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 XVector_stubs.c -o XVector_stubs.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -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 alphabet.c -o alphabet.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -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 count.c -o count.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -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 io.c -o io.o
io.c: In function 'read_prb_as_character':
io.c:227:38: warning: format '%f' expects argument of type 'double', but argument 2 has type 'const char *' [-Wformat=]
227 | error("could not read file '%f'", translateChar(STRING_ELT(fname, 0)));
| ~^
| |
| double
| %s
io.c: In function '_read_solexa_export_file':
io.c:658:49: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=]
658 | error("invalid 'strand' field '%s', %s:%d",
| ~^
| |
| char *
| %d
659 | *elt[13], fname, lineno);
| ~~~~~~~~
| |
| int
io.c:676:48: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=]
676 | error("invalid 'filtering' field '%s', %s:%d",
| ~^
| |
| char *
| %d
677 | *elt[21], fname, lineno);
| ~~~~~~~~
| |
| int
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -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 io_bowtie.c -o io_bowtie.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -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 io_soap.c -o io_soap.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include' -I"C:/rtools45/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-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include' -I"C:/rtools45/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(gzFile) [with int max_readlen = 128]':
maqmap_m.h:102:21: warning: pointer 'mm' used after 'void free(void*)' [-Wuse-after-free]
102 | Rf_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(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(gzFile) [with int max_readlen = 64]':
maqmap_m.h:102:21: warning: pointer 'mm' used after 'void free(void*)' [-Wuse-after-free]
102 | Rf_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(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-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -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 sampler.c -o sampler.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -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 trim.c -o trim.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -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 util.c -o util.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -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 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 -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/ShortRead.buildbin-libdir/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
* MD5 sums
packaged installation of 'ShortRead' as ShortRead_1.67.1.zip
* DONE (ShortRead)