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This page was generated on 2023-06-06 11:00:42 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
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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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1879/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ShortRead 1.59.0 (landing page) Bioconductor Package Maintainer
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
| Package: ShortRead |
| Version: 1.59.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL ShortRead |
| StartedAt: 2023-06-05 08:32:37 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 08:33:46 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 69.5 seconds |
| RetCode: 0 |
| Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL ShortRead ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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 (GCC) 10.3.1’ using C++ compiler: ‘g++ (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c R_init_ShortRead.c -o R_init_ShortRead.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c alphabet.c -o alphabet.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c count.c -o count.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c io.c -o io.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c io_bowtie.c -o io_bowtie.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c io_soap.c -o io_soap.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/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 -c readBfaToc.cc -o readBfaToc.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/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 -c read_maq_map.cc -o read_maq_map.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c sampler.c -o sampler.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c trim.c -o trim.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c util.c -o util.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c xsnap.c -o xsnap.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/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/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/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)