Jean-Philippe Fortin
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/Rbwa |
| git_branch: RELEASE_3_16 |
| git_last_commit: 079a06a |
| git_last_commit_date: 2022-11-01 11:26:35 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:15 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 Rbwa package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1607/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rbwa 1.2.0 (landing page) Jean-Philippe Fortin
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: Rbwa |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:Rbwa.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings Rbwa_1.2.0.tar.gz |
| StartedAt: 2023-04-10 23:17:41 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 23:17:59 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 18.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Rbwa.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:Rbwa.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings Rbwa_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/Rbwa.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘Rbwa/DESCRIPTION’ ... OK * this is package ‘Rbwa’ version ‘1.2.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Rbwa’ can be installed ... WARNING Found the following significant warnings: rope.c:282:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] rope.c:283:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] rope.c:291:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] rope.c:292:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] rope.c:293:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] rope.c:312:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] rope.c:313:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwashm.c:29:2: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result] bwashm.c:66:2: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result] See ‘/home/biocbuild/bbs-3.16-bioc/meat/Rbwa.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Rbwa.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.16-bioc/meat/Rbwa.Rcheck/00check.log’ for details.
Rbwa.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL Rbwa
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘Rbwa’ ...
** using staged installation
** libs
** arch -
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c kthread.c -o kthread.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c kstring.c -o kstring.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c ksw.c -o ksw.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwt.c -o bwt.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bntseq.c -o bntseq.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwa.c -o bwa.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwamem.c -o bwamem.o
gcc -I"/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c QSufSort.c -o QSufSort.o
gcc -I"/home/biocbuild/bbs-3.16-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:879:10: 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:953:15: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable]
953 | unsigned int bitsInWordMinusBitPerChar;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.16-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:282:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
282 | fread(&is_bottom, 1, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
rope.c:283:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
283 | fread(&n, 2, 1, fp);
| ^~~~~~~~~~~~~~~~~~~
rope.c:291:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
291 | fread(p[i].c, 8, 6, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~
rope.c:292:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
292 | fread(q, 2, 1, fp);
| ^~~~~~~~~~~~~~~~~~
rope.c:293:4: 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:312:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
312 | fread(&r->max_nodes, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rope.c:313:2: 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-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c rle.c -o rle.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c is.c -o is.o
gcc -I"/home/biocbuild/bbs-3.16-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-3.16-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:29:2: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result]
29 | ftruncate(shmid, BWA_CTL_SIZE);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bwashm.c:66:2: 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-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwase.c -o bwase.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwaseqio.c -o bwaseqio.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtgap.c -o bwtgap.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwtaln.c -o bwtaln.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bamlite.c -o bamlite.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c bwape.c -o bwape.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c kopen.c -o kopen.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c pemerge.c -o pemerge.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c maxk.c -o maxk.o
gcc -I"/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-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-3.16-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-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -Wall -O2 -c fastmap.c -o fastmap.o
gcc -I"/home/biocbuild/bbs-3.16-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-3.16-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)
Rbwa.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Rbwa)
>
> test_check("Rbwa")
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.04 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.02 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa index -p /tmp/Rtmp0C2Rv4/filebd42c1c6cb0b/chr12 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/fasta/chr12.fa
[main] Real time: 0.075 sec; CPU: 0.069 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 7 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa aln /tmp/Rtmp0C2Rv4/filebd42c1c6cb0b/chr12 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.003 sec; CPU: 0.003 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa aln /tmp/Rtmp0C2Rv4/filebd42c1c6cb0b/chr12 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/reads/reads1.fastq
[main] Real time: 0.002 sec; CPU: 0.002 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa aln /tmp/Rtmp0C2Rv4/filebd42c1c6cb0b/chr12 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/reads/reads2.fastq
[main] Real time: 0.001 sec; CPU: 0.002 sec
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.05 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.02 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa index -p /tmp/Rtmp0C2Rv4/chr12 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/fasta/chr12.fa
[main] Real time: 0.083 sec; CPU: 0.076 sec
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.03 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.02 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa index -p /tmp/Rtmp0C2Rv4/filebd42c61300898/chr12 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/fasta/chr12.fa
[main] Real time: 0.064 sec; CPU: 0.059 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 7 sequences (133 bp)...
[M::mem_process_seqs] Processed 7 reads in 0.000 CPU sec, 0.000 real sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa mem /tmp/Rtmp0C2Rv4/filebd42c61300898/chr12 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.002 sec; CPU: 0.002 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 8 sequences (808 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 8 reads in 0.001 CPU sec, 0.001 real sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa mem /tmp/Rtmp0C2Rv4/filebd42c61300898/chr12 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/reads/reads1.fastq /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/reads/reads2.fastq
[main] Real time: 0.002 sec; CPU: 0.003 sec
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.04 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.02 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa index -p /tmp/Rtmp0C2Rv4/filebd42cf54e5d2/chr12 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/fasta/chr12.fa
[main] Real time: 0.064 sec; CPU: 0.056 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 7 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa aln /tmp/Rtmp0C2Rv4/filebd42cf54e5d2/chr12 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.001 sec; CPU: 0.002 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa aln /tmp/Rtmp0C2Rv4/filebd42cf54e5d2/chr12 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/reads/reads1.fastq
[main] Real time: 0.002 sec; CPU: 0.003 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa aln /tmp/Rtmp0C2Rv4/filebd42cf54e5d2/chr12 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/reads/reads2.fastq
[main] Real time: 0.002 sec; CPU: 0.002 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 7 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa samse /tmp/Rtmp0C2Rv4/filebd42cf54e5d2/chr12 /tmp/Rtmp0C2Rv4/filebd42cf54e5d2/output.sai /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.002 sec; CPU: 0.002 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] fail to infer insert size: too few good pairs
[bwa_sai2sam_pe_core] time elapses: 0.00 sec
[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_sai2sam_pe_core] time elapses: 0.00 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec
[bwa_sai2sam_pe_core] print alignments... 0.00 sec
[bwa_sai2sam_pe_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa sampe /tmp/Rtmp0C2Rv4/filebd42cf54e5d2/chr12 /tmp/Rtmp0C2Rv4/filebd42cf54e5d2/output1.sai /tmp/Rtmp0C2Rv4/filebd42cf54e5d2/output2.sai /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/reads/reads1.fastq /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/reads/reads2.fastq
[main] Real time: 0.001 sec; CPU: 0.002 sec
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.05 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.03 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa index -p /tmp/Rtmp0C2Rv4/filebd42c580d9894/chr12 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/fasta/chr12.fa
[main] Real time: 0.084 sec; CPU: 0.079 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 7 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa aln /tmp/Rtmp0C2Rv4/filebd42c580d9894/chr12 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.001 sec; CPU: 0.002 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa aln /tmp/Rtmp0C2Rv4/filebd42c580d9894/chr12 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/reads/reads1.fastq
[main] Real time: 0.002 sec; CPU: 0.003 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa aln /tmp/Rtmp0C2Rv4/filebd42c580d9894/chr12 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/reads/reads2.fastq
[main] Real time: 0.002 sec; CPU: 0.002 sec
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 7 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa samse /tmp/Rtmp0C2Rv4/filebd42c580d9894/chr12 /tmp/Rtmp0C2Rv4/filebd42c580d9894/output.sai /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.002 sec; CPU: 0.003 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] fail to infer insert size: too few good pairs
[bwa_sai2sam_pe_core] time elapses: 0.00 sec
[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_sai2sam_pe_core] time elapses: 0.00 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec
[bwa_sai2sam_pe_core] print alignments... 0.00 sec
[bwa_sai2sam_pe_core] 4 sequences have been processed.
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/bwa sampe /tmp/Rtmp0C2Rv4/filebd42c580d9894/chr12 /tmp/Rtmp0C2Rv4/filebd42c580d9894/output1.sai /tmp/Rtmp0C2Rv4/filebd42c580d9894/output2.sai /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/reads/reads1.fastq /home/biocbuild/bbs-3.16-bioc/R/site-library/Rbwa/reads/reads2.fastq
[main] Real time: 0.001 sec; CPU: 0.002 sec
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 39 ]
>
> proc.time()
user system elapsed
1.375 0.131 1.537
Rbwa.Rcheck/Rbwa-Ex.timings
| name | user | system | elapsed | |
| bwa_aln | 0.069 | 0.006 | 0.083 | |
| bwa_build_index | 0.062 | 0.002 | 0.070 | |
| bwa_mem | 0.065 | 0.005 | 0.076 | |
| bwa_sam | 0.070 | 0.006 | 0.084 | |
| xa2multi | 0.097 | 0.007 | 0.111 | |