Jean-Philippe Fortin
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/Rbwa |
| git_branch: devel |
| git_last_commit: 441c698 |
| git_last_commit_date: 2024-10-29 11:09:03 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1666/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rbwa 1.11.0 (landing page) Jean-Philippe Fortin
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the Rbwa package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rbwa.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: Rbwa |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Rbwa |
| StartedAt: 2024-12-23 15:02:10 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 15:02:38 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 27.8 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Rbwa
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘Rbwa’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c kthread.c -o kthread.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c kstring.c -o kstring.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c ksw.c -o ksw.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwt.c -o bwt.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bntseq.c -o bntseq.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwa.c -o bwa.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwamem.c -o bwamem.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwamem_pair.c -o bwamem_pair.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwamem_extra.c -o bwamem_extra.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c malloc_wrap.c -o malloc_wrap.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c QSufSort.c -o QSufSort.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function ‘BWTIncBuildRelativeRank’:
bwt_gen.c:879:17: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable]
879 | bgint_t oldInverseSa0RelativeRank = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
bwt_gen.c: In function ‘BWTIncMergeBwt’:
bwt_gen.c:953:22: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable]
953 | unsigned int bitsInWordMinusBitPerChar;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c rope.c -o rope.o
rope.c: In function ‘rope_restore_node’:
rope.c:282:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
282 | fread(&is_bottom, 1, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
rope.c:283:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
283 | fread(&n, 2, 1, fp);
| ^~~~~~~~~~~~~~~~~~~
rope.c:291:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
291 | fread(p[i].c, 8, 6, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~
rope.c:292:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
292 | fread(q, 2, 1, fp);
| ^~~~~~~~~~~~~~~~~~
rope.c:293:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
293 | fread(q + 1, 1, *q, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~
rope.c: In function ‘rope_restore’:
rope.c:312:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
312 | fread(&r->max_nodes, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rope.c:313:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
313 | fread(&r->block_len, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c rle.c -o rle.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c is.c -o is.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtindex.c -o bwtindex.o
ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
ar: `u' modifier ignored since `D' is the default (see `U')
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwashm.c -o bwashm.o
bwashm.c: In function ‘bwa_shm_stage’:
bwashm.c:29:9: warning: ignoring return value of ‘ftruncate’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
29 | ftruncate(shmid, BWA_CTL_SIZE);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bwashm.c:66:9: warning: ignoring return value of ‘ftruncate’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
66 | ftruncate(shmid, idx->l_mem);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwase.c -o bwase.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwaseqio.c -o bwaseqio.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtgap.c -o bwtgap.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtaln.c -o bwtaln.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bamlite.c -o bamlite.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwape.c -o bwape.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c kopen.c -o kopen.o
In file included from /usr/include/string.h:548,
from kopen.c:6:
In function ‘strncpy’,
inlined from ‘cmd2argv’ at kopen.c:248:2,
inlined from ‘kopen’ at kopen.c:306:13:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin___strncpy_chk’ specified bound between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
95 | return __builtin___strncpy_chk (__dest, __src, __len,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
96 | __glibc_objsize (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘cmd2argv’,
inlined from ‘kopen’ at kopen.c:306:13:
kopen.c:247:32: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
247 | argv[0] = str = (char*)calloc(end - beg + 1, 1);
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from kopen.c:7:
/usr/include/stdlib.h: In function ‘kopen’:
/usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here
675 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c pemerge.c -o pemerge.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c maxk.c -o maxk.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtsw2_core.c -o bwtsw2_core.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtsw2_main.c -o bwtsw2_main.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtsw2_aux.c -o bwtsw2_aux.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwt_lite.c -o bwt_lite.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtsw2_chain.c -o bwtsw2_chain.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c fastmap.c -o fastmap.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtsw2_pair.c -o bwtsw2_pair.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c main.c -o main.o
gcc -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt
mkdir -p ../inst
cp bwa ../inst/bwa
rm -f gmon.out *.o a.out bwa *~ *.a
rm -f bwa
** 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
* DONE (Rbwa)