| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:23 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (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 1943/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ShortRead 1.60.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.60.0 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL ShortRead |
| StartedAt: 2024-04-15 15:20:12 -0400 (Mon, 15 Apr 2024) |
| EndedAt: 2024-04-15 15:21:04 -0400 (Mon, 15 Apr 2024) |
| EllapsedTime: 51.8 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL ShortRead
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘ShortRead’ ...
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 8
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c alphabet.c -o alphabet.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c count.c -o count.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c io.c -o io.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c io_bowtie.c -o io_bowtie.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c io_soap.c -o io_soap.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -Wall -c readBfaToc.cc -o readBfaToc.o
readBfaToc.cc: In function ‘SEXPREC* readBfaToc(SEXP)’:
readBfaToc.cc:35:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
35 | (void) fread( seq_name, sizeof(char), name_len, fp );
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readBfaToc.cc:36:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
36 | (void) fread( &seq_ori_len, sizeof(int), 1, fp );
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readBfaToc.cc:37:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
37 | (void) fread( &seq_len, sizeof(int), 1, fp );
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -Wall -c read_maq_map.cc -o read_maq_map.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c sampler.c -o sampler.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c trim.c -o trim.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c util.c -o util.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c xsnap.c -o xsnap.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o ShortRead.so 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 -fopenmp -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-ShortRead/00new/ShortRead/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ShortRead)