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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Rbwa.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Rbwa_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rbwa.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ... WARNING
Found the following significant warnings:
  rope.c:282:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  rope.c:283:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  rope.c:291:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  rope.c:292:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  rope.c:293:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  rope.c:312:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  rope.c:313:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  bwashm.c:29:9: warning: ignoring return value of ‘ftruncate’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  bwashm.c:66:9: warning: ignoring return value of ‘ftruncate’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-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 ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rbwa.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Rbwa
###
##############################################################################
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* installing to library ‘/media/volume/teran2_disk/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)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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] 0.03 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... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa index -p /tmp/RtmpiPugBX/file27d636593e4dc3/chr12 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/fasta/chr12.fa
[main] Real time: 0.103 sec; CPU: 0.041 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: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa aln /tmp/RtmpiPugBX/file27d636593e4dc3/chr12 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.007 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: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa aln /tmp/RtmpiPugBX/file27d636593e4dc3/chr12 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/reads/reads1.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: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa aln /tmp/RtmpiPugBX/file27d636593e4dc3/chr12 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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] 0.03 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... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa index -p /tmp/RtmpiPugBX/chr12 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/fasta/chr12.fa
[main] Real time: 0.103 sec; CPU: 0.041 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... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa index -p /tmp/RtmpiPugBX/file27d6361fd205e0/chr12 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/fasta/chr12.fa
[main] Real time: 0.112 sec; CPU: 0.040 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, 0.004 real sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa mem /tmp/RtmpiPugBX/file27d6361fd205e0/chr12 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.011 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 0.000 CPU sec, 0.005 real sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa mem /tmp/RtmpiPugBX/file27d6361fd205e0/chr12 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/reads/reads1.fastq /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/reads/reads2.fastq
[main] Real time: 0.014 sec; CPU: 0.002 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... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa index -p /tmp/RtmpiPugBX/file27d636d3a1774/chr12 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/fasta/chr12.fa
[main] Real time: 0.101 sec; CPU: 0.040 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: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa aln /tmp/RtmpiPugBX/file27d636d3a1774/chr12 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/fastq/sequences.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: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa aln /tmp/RtmpiPugBX/file27d636d3a1774/chr12 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/reads/reads1.fastq
[main] Real time: 0.006 sec; CPU: 0.001 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: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa aln /tmp/RtmpiPugBX/file27d636d3a1774/chr12 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/reads/reads2.fastq
[main] Real time: 0.005 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: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa samse /tmp/RtmpiPugBX/file27d636d3a1774/chr12 /tmp/RtmpiPugBX/file27d636d3a1774/output.sai /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.007 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: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa sampe /tmp/RtmpiPugBX/file27d636d3a1774/chr12 /tmp/RtmpiPugBX/file27d636d3a1774/output1.sai /tmp/RtmpiPugBX/file27d636d3a1774/output2.sai /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/reads/reads1.fastq /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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] 0.03 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... 0.01 sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa index -p /tmp/RtmpiPugBX/file27d6367bcfa115/chr12 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/fasta/chr12.fa
[main] Real time: 0.080 sec; CPU: 0.041 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: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa aln /tmp/RtmpiPugBX/file27d6367bcfa115/chr12 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.002 sec; CPU: 0.001 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: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa aln /tmp/RtmpiPugBX/file27d6367bcfa115/chr12 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/reads/reads1.fastq
[main] Real time: 0.004 sec; CPU: 0.001 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: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa aln /tmp/RtmpiPugBX/file27d6367bcfa115/chr12 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/reads/reads2.fastq
[main] Real time: 0.002 sec; CPU: 0.001 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: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa samse /tmp/RtmpiPugBX/file27d6367bcfa115/chr12 /tmp/RtmpiPugBX/file27d6367bcfa115/output.sai /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/fastq/sequences.fastq
[main] Real time: 0.006 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: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/bwa sampe /tmp/RtmpiPugBX/file27d6367bcfa115/chr12 /tmp/RtmpiPugBX/file27d6367bcfa115/output1.sai /tmp/RtmpiPugBX/file27d6367bcfa115/output2.sai /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/reads/reads1.fastq /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rbwa/reads/reads2.fastq
[main] Real time: 0.004 sec; CPU: 0.001 sec
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
  0.808   0.162   1.802