Package: Biostrings

Version: 2.22.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings Biostrings_2.22.0.tar.gz

StartedAt: 2012-03-23 23:28:53 -0700 (Fri, 23 Mar 2012)

EndedAt: 2012-03-23 23:38:25 -0700 (Fri, 23 Mar 2012)

EllapsedTime: 572.6 seconds

RetCode: 0

Status:  OK

CheckDir: Biostrings.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/Biostrings.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biostrings/DESCRIPTION’ ... OK
* this is package ‘Biostrings’ version ‘2.22.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘Rmpi’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘Biostrings’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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 ... NOTE
.checkFormat: no visible binding for global variable ‘filepath’
* 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 ... NOTE
‘library’ or ‘require’ call not declared from: ‘BSgenome.Hsapiens.UCSC.hg18’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/Biostrings.Rcheck/Biostrings/libs/Biostrings.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘Biostrings’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c BAB_class.c -o BAB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c BitMatrix.c -o BitMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c MIndex_class.c -o MIndex_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c XStringSet_class.c -o XStringSet_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c XStringSet_io.c -o XStringSet_io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c XString_class.c -o XString_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c align_needwunsQS.c -o align_needwunsQS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c align_utils.c -o align_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c find_palindromes.c -o find_palindromes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c gtestsim.c -o gtestsim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c io_utils.c -o io_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c letter_frequency.c -o letter_frequency.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c lowlevel_matching.c -o lowlevel_matching.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_BOC.c -o match_BOC.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_BOC2.c -o match_BOC2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_WCP.c -o match_WCP.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_pattern_indels.c -o match_pattern_indels.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_pdict.c -o match_pdict.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_pdict_Twobit.c -o match_pdict_Twobit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_pdict_utils.c -o match_pdict_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c matchprobes.c -o matchprobes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c replace_letter_at.c -o replace_letter_at.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c strutils.c -o strutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c translate.c -o translate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c utils.c -o utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c xscat.c -o xscat.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o SparseList_utils.o XStringSet_class.o XStringSet_io.o XString_class.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o io_utils.o letter_frequency.o lowlevel_matching.o match_BOC.o match_BOC2.o match_PWM.o match_WCP.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replace_letter_at.o strutils.o translate.o utils.o xscat.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/Biostrings.Rcheck/Biostrings/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘setequal’ from package ‘base’ in package ‘Biostrings’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’
Creating a new generic function for ‘offset’ in package ‘Biostrings’
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘Alignments.Rnw’ 
   ‘Biostrings2Classes.Rnw’ 
   ‘MultipleAlignments.Rnw’ 
   ‘matchprobes.Rnw’ 
** testing if installed package can be loaded

* DONE (Biostrings)

name	user	system	elapsed
AAString-class	0.008	0.000	0.006
AMINO_ACID_CODE	0.004	0.000	0.002
AlignedXStringSet-class	0.244	0.004	0.251
DNAString-class	0.004	0.000	0.003
FASTA-io-legacy	13.785	0.516	14.434
GENETIC_CODE	0.004	0.000	0.004
HNF4alpha	0.052	0.000	0.049
IUPAC_CODE_MAP	0.008	0.000	0.008
MIndex-class	0.000	0.000	0.001
MaskedXString-class	0.388	0.004	0.871
MultipleAlignment-class	2.512	0.008	2.582
PDict-class	7.036	0.096	7.317
PairwiseAlignedXStringSet-class	0.204	0.008	0.214
QualityScaledXStringSet-class	0.028	0.004	0.031
RNAString-class	0.008	0.000	0.010
XString-class	0.008	0.000	0.009
XStringQuality-class	0.06	0.00	0.06
XStringSet-class	7.257	0.164	7.534
XStringSet-io	8.268	0.048	8.543
XStringSetList-class	0.096	0.000	0.095
XStringViews-class	0.308	0.008	0.316
XStringViews-constructor	0.032	0.000	0.030
align-utils	0.048	0.004	0.051
chartr	1.128	0.008	1.169
detail	1.188	0.052	1.283
dinucleotideFrequencyTest	0.020	0.004	0.027
findPalindromes	5.217	0.044	5.666
getSeq	0.044	0.012	0.055
gregexpr2	0.004	0.000	0.003
injectHardMask	0.060	0.000	0.058
letter	0.008	0.008	0.016
letterFrequency	1.620	0.080	1.885
longestConsecutive	0.000	0.000	0.001
lowlevel-matching	0.604	0.008	0.699
maskMotif	2.352	0.064	2.495
match-utils	0.028	0.004	0.031
matchLRPatterns	0.548	0.020	0.625
matchPDict-exact	271.213	1.168	275.297
matchPDict-inexact	59.860	0.360	60.792
matchPWM	2.024	0.012	2.038
matchPattern	3.268	0.060	3.338
matchProbePair	1.088	0.004	1.096
matchprobes	0.412	0.004	0.416
misc	0.016	0.000	0.018
needwunsQS	0	0	0
nucleotideFrequency	0.916	0.016	0.974
pairwiseAlignment	1.304	0.060	1.398
phiX174Phage	1.020	0.020	1.091
pid	0.504	0.136	0.654
replaceLetterAt	0.892	0.004	0.899
reverseComplement	1.849	0.116	1.968
stringDist	7.560	0.008	7.574
substitution_matrices	0.808	0.008	0.820
toComplex	0.004	0.000	0.003
translate	1.652	0.008	1.673
trimLRPatterns	0.128	0.000	0.125
xscat	2.516	0.024	2.545
yeastSEQCHR1	0.004	0.000	0.006