| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:52 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the ShortRead package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1861/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ShortRead 1.56.1 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ShortRead |
| Version: 1.56.1 |
| Command: rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --build --library=ShortRead.buildbin-libdir ShortRead_1.56.1.tar.gz |
| StartedAt: 2023-04-11 08:47:22 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 08:48:48 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 85.4 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: ShortRead_1.56.1.zip |
| PackageFileSize: 5.402 MiB |
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### Running command:
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### rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --build --library=ShortRead.buildbin-libdir ShortRead_1.56.1.tar.gz
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* installing *source* package 'ShortRead' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c alphabet.c -o alphabet.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c count.c -o count.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io_bowtie.c -o io_bowtie.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io_soap.c -o io_soap.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readBfaToc.cc -o readBfaToc.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_maq_map.cc -o read_maq_map.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sampler.c -o sampler.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c trim.c -o trim.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c util.c -o util.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c xsnap.c -o xsnap.o
g++ -std=gnu++14 -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-3.16-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-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_1.56.1.zip
* DONE (ShortRead)