Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1678/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rbwa 1.10.0 (landing page) Jean-Philippe Fortin
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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: 1.10.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Rbwa |
StartedAt: 2024-12-19 15:04:48 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 15:05:22 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 34.1 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Rbwa ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘Rbwa’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c utils.c -o utils.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c kthread.c -o kthread.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c kstring.c -o kstring.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c ksw.c -o ksw.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwt.c -o bwt.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bntseq.c -o bntseq.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwa.c -o bwa.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwamem.c -o bwamem.o gcc -I"/home/biocbuild/bbs-3.20-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-3.20-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-3.20-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-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c QSufSort.c -o QSufSort.o gcc -I"/home/biocbuild/bbs-3.20-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-3.20-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-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c rle.c -o rle.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c is.c -o is.o gcc -I"/home/biocbuild/bbs-3.20-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-3.20-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-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwase.c -o bwase.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwaseqio.c -o bwaseqio.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtgap.c -o bwtgap.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtaln.c -o bwtaln.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bamlite.c -o bamlite.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwape.c -o bwape.o gcc -I"/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c pemerge.c -o pemerge.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c maxk.c -o maxk.o gcc -I"/home/biocbuild/bbs-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c fastmap.c -o fastmap.o gcc -I"/home/biocbuild/bbs-3.20-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-3.20-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)