Jean-Philippe Fortin
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/Rbwa |
| git_branch: RELEASE_3_20 |
| git_last_commit: 82c4a0b |
| git_last_commit_date: 2024-10-29 11:09:03 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Rbwa |
| Version: 1.10.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Rbwa.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Rbwa_1.10.0.tar.gz |
| StartedAt: 2024-11-20 11:27:27 -0000 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 11:27:51 -0000 (Wed, 20 Nov 2024) |
| EllapsedTime: 24.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Rbwa.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:Rbwa.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Rbwa_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Rbwa.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rbwa/DESCRIPTION’ ... OK
* this is package ‘Rbwa’ version ‘1.10.0’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
* checking code 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/Rbwa.Rcheck/00check.log’
for details.
Rbwa.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL Rbwa
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘Rbwa’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c utils.c -o utils.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c kthread.c -o kthread.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c kstring.c -o kstring.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c ksw.c -o ksw.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwt.c -o bwt.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bntseq.c -o bntseq.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwa.c -o bwa.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwamem.c -o bwamem.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwamem_pair.c -o bwamem_pair.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwamem_extra.c -o bwamem_extra.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c malloc_wrap.c -o malloc_wrap.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c QSufSort.c -o QSufSort.o
gcc -I"/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c rope.c -o rope.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c rle.c -o rle.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c is.c -o is.o
gcc -I"/home/biocbuild/R/R-4.4.1/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
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwashm.c -o bwashm.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwase.c -o bwase.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwaseqio.c -o bwaseqio.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtgap.c -o bwtgap.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtaln.c -o bwtaln.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bamlite.c -o bamlite.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwape.c -o bwape.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c kopen.c -o kopen.o
In file included from /home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/string.h:633,
from kopen.c:6:
In function 'cmd2argv',
inlined from 'kopen' at kopen.c:306:13:
kopen.c:248:9: warning: '__builtin_strncpy' specified bound between 18446744071562067969 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
248 | strncpy(argv[0], cmd + beg, end - beg);
| ^~~~~~~
kopen.c:247:32: warning: argument 1 range [18446744071562067970, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
247 | argv[0] = str = (char*)calloc(end - beg + 1, 1);
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/bits/string2.h:1296:
/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/stdlib.h: In function 'kopen':
/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/stdlib.h:467:14: note: in a call to allocation function 'calloc' declared here
467 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c pemerge.c -o pemerge.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c maxk.c -o maxk.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtsw2_core.c -o bwtsw2_core.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtsw2_main.c -o bwtsw2_main.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtsw2_aux.c -o bwtsw2_aux.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwt_lite.c -o bwt_lite.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtsw2_chain.c -o bwtsw2_chain.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c fastmap.c -o fastmap.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtsw2_pair.c -o bwtsw2_pair.o
gcc -I"/home/biocbuild/R/R-4.4.1/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/R/R-4.4.1/site-library/Rbwa/bwa index -p /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b7b464bf8/chr12 /home/biocbuild/R/R-4.4.1/site-library/Rbwa/fasta/chr12.fa
[main] Real time: 0.085 sec; CPU: 0.059 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/R/R-4.4.1/site-library/Rbwa/bwa aln /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b7b464bf8/chr12 /home/biocbuild/R/R-4.4.1/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.004 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/R/R-4.4.1/site-library/Rbwa/bwa aln /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b7b464bf8/chr12 /home/biocbuild/R/R-4.4.1/site-library/Rbwa/reads/reads1.fastq
[main] Real time: 0.003 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/R/R-4.4.1/site-library/Rbwa/bwa aln /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b7b464bf8/chr12 /home/biocbuild/R/R-4.4.1/site-library/Rbwa/reads/reads2.fastq
[main] Real time: 0.003 sec; CPU: 0.002 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... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/R/R-4.4.1/site-library/Rbwa/bwa index -p /home/biocbuild/tmp/Rtmp3cGWxX/chr12 /home/biocbuild/R/R-4.4.1/site-library/Rbwa/fasta/chr12.fa
[main] Real time: 0.086 sec; CPU: 0.060 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... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/R/R-4.4.1/site-library/Rbwa/bwa index -p /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b83fc4bc/chr12 /home/biocbuild/R/R-4.4.1/site-library/Rbwa/fasta/chr12.fa
[main] Real time: 0.082 sec; CPU: 0.061 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 0.001 CPU sec, 0.000 real sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/R/R-4.4.1/site-library/Rbwa/bwa mem /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b83fc4bc/chr12 /home/biocbuild/R/R-4.4.1/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.005 sec; CPU: 0.003 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/R/R-4.4.1/site-library/Rbwa/bwa mem /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b83fc4bc/chr12 /home/biocbuild/R/R-4.4.1/site-library/Rbwa/reads/reads1.fastq /home/biocbuild/R/R-4.4.1/site-library/Rbwa/reads/reads2.fastq
[main] Real time: 0.004 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... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/R/R-4.4.1/site-library/Rbwa/bwa index -p /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b16d2d32e/chr12 /home/biocbuild/R/R-4.4.1/site-library/Rbwa/fasta/chr12.fa
[main] Real time: 0.083 sec; CPU: 0.061 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/R/R-4.4.1/site-library/Rbwa/bwa aln /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b16d2d32e/chr12 /home/biocbuild/R/R-4.4.1/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.004 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/R/R-4.4.1/site-library/Rbwa/bwa aln /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b16d2d32e/chr12 /home/biocbuild/R/R-4.4.1/site-library/Rbwa/reads/reads1.fastq
[main] Real time: 0.003 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/R/R-4.4.1/site-library/Rbwa/bwa aln /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b16d2d32e/chr12 /home/biocbuild/R/R-4.4.1/site-library/Rbwa/reads/reads2.fastq
[main] Real time: 0.003 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/R/R-4.4.1/site-library/Rbwa/bwa samse /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b16d2d32e/chr12 /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b16d2d32e/output.sai /home/biocbuild/R/R-4.4.1/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.004 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/R/R-4.4.1/site-library/Rbwa/bwa sampe /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b16d2d32e/chr12 /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b16d2d32e/output1.sai /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b16d2d32e/output2.sai /home/biocbuild/R/R-4.4.1/site-library/Rbwa/reads/reads1.fastq /home/biocbuild/R/R-4.4.1/site-library/Rbwa/reads/reads2.fastq
[main] Real time: 0.003 sec; CPU: 0.002 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... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /home/biocbuild/R/R-4.4.1/site-library/Rbwa/bwa index -p /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b1af26eea/chr12 /home/biocbuild/R/R-4.4.1/site-library/Rbwa/fasta/chr12.fa
[main] Real time: 0.096 sec; CPU: 0.064 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/R/R-4.4.1/site-library/Rbwa/bwa aln /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b1af26eea/chr12 /home/biocbuild/R/R-4.4.1/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.003 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/R/R-4.4.1/site-library/Rbwa/bwa aln /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b1af26eea/chr12 /home/biocbuild/R/R-4.4.1/site-library/Rbwa/reads/reads1.fastq
[main] Real time: 0.003 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/R/R-4.4.1/site-library/Rbwa/bwa aln /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b1af26eea/chr12 /home/biocbuild/R/R-4.4.1/site-library/Rbwa/reads/reads2.fastq
[main] Real time: 0.003 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/R/R-4.4.1/site-library/Rbwa/bwa samse /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b1af26eea/chr12 /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b1af26eea/output.sai /home/biocbuild/R/R-4.4.1/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.003 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/R/R-4.4.1/site-library/Rbwa/bwa sampe /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b1af26eea/chr12 /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b1af26eea/output1.sai /home/biocbuild/tmp/Rtmp3cGWxX/file1d827b1af26eea/output2.sai /home/biocbuild/R/R-4.4.1/site-library/Rbwa/reads/reads1.fastq /home/biocbuild/R/R-4.4.1/site-library/Rbwa/reads/reads2.fastq
[main] Real time: 0.003 sec; CPU: 0.002 sec
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 39 ]
>
> proc.time()
user system elapsed
1.636 0.241 1.952
Rbwa.Rcheck/Rbwa-Ex.timings
| name | user | system | elapsed | |
| bwa_aln | 0.059 | 0.010 | 0.102 | |
| bwa_build_index | 0.053 | 0.008 | 0.086 | |
| bwa_mem | 0.065 | 0.004 | 0.101 | |
| bwa_sam | 0.062 | 0.011 | 0.105 | |
| xa2multi | 0.074 | 0.014 | 0.121 | |