| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:28 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 chopsticks package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chopsticks.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 330/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chopsticks 1.67.0 (landing page) Hin-Tak Leung
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: chopsticks |
| Version: 1.67.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL chopsticks |
| StartedAt: 2023-05-08 22:01:01 -0000 (Mon, 08 May 2023) |
| EndedAt: 2023-05-08 22:01:22 -0000 (Mon, 08 May 2023) |
| EllapsedTime: 20.9 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL chopsticks
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘chopsticks’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c adler32.c -o adler32.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c bind.c -o bind.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c compress.c -o compress.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c crc32.c -o crc32.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c deflate.c -o deflate.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c force_hom.c -o force_hom.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c glm_test.c -o glm_test.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c glm_test_R.c -o glm_test_R.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c gzio.c -o gzio.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c hash_index.c -o hash_index.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ibs.c -o ibs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c in.c -o in.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c infback.c -o infback.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c inffast.c -o inffast.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c inflate.c -o inflate.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c inftrees.c -o inftrees.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c input.c -o input.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c inputNew.c -o inputNew.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c input_unsorted.c -o input_unsorted.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ld_graphic_eps.c -o ld_graphic_eps.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ld_with.c -o ld_with.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c mla.c -o mla.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c outdata.c -o outdata.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c pairwise_linkage.c -o pairwise_linkage.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c read_chiamo.c -o read_chiamo.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c read_hapmap.c -o read_hapmap.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c read_pedfile.c -o read_pedfile.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c read_signals.c -o read_signals.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c readped.c -o readped.o
readped.c: In function ‘readped’:
readped.c:233:33: warning: ‘%d’ directive output may be truncated writing between 1 and 11 bytes into a region of size between 0 and 80 [-Wformat-truncation=]
233 | snprintf(fmid, MAX_ID, "%s%c%d", fid, sepchar, memi);
| ^~
In file included from /usr/include/stdio.h:894,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include/R.h:44,
from readped.c:1:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output between 3 and 93 bytes into a destination of size 81
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c sdfpw.c -o sdfpw.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c single_snp_tests.c -o single_snp_tests.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c snp_summary.c -o snp_summary.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c snpmpy.c -o snpmpy.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c solve_cubic.c -o solve_cubic.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c solve_quadratic.c -o solve_quadratic.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c structure.c -o structure.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c trees.c -o trees.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c uncompr.c -o uncompr.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c zutil.c -o zutil.o
gcc -shared -L/usr/local/lib -o chopsticks.so adler32.o bind.o compress.o crc32.o deflate.o force_hom.o glm_test.o glm_test_R.o gzio.o hash_index.o ibs.o in.o infback.o inffast.o inflate.o inftrees.o input.o inputNew.o input_unsorted.o ld_graphic_eps.o ld_with.o mla.o outdata.o pairwise_linkage.o read_chiamo.o read_hapmap.o read_pedfile.o read_signals.o readped.o sdfpw.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o solve_quadratic.o structure.o trees.o uncompr.o zutil.o
installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-chopsticks/00new/chopsticks/libs
** R
** data
** 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 (chopsticks)