Package: Biostrings

Version: 2.19.11

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings Biostrings_2.19.11.tar.gz

StartedAt: 2011-02-24 18:19:13 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 18:32:12 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 778.9 seconds

RetCode: 0

Status:  OK

CheckDir: Biostrings.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/Biostrings.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘2.19.11’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘Biostrings’ can be installed ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘Biostrings’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c BAB_class.c -o BAB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c BitMatrix.c -o BitMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c MIndex_class.c -o MIndex_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-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-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c XStringSet_class.c -o XStringSet_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c XStringSet_io.c -o XStringSet_io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c XString_class.c -o XString_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c align_needwunsQS.c -o align_needwunsQS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c align_utils.c -o align_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c extract_transcripts.c -o extract_transcripts.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c find_palindromes.c -o find_palindromes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c gtestsim.c -o gtestsim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c io_utils.c -o io_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c letter_frequency.c -o letter_frequency.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c lowlevel_matching.c -o lowlevel_matching.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_BOC.c -o match_BOC.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_BOC2.c -o match_BOC2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_WCP.c -o match_WCP.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-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-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-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-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-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-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_pdict.c -o match_pdict.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-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-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-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-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-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-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c matchprobes.c -o matchprobes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-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-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c strutils.c -o strutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c translate.c -o translate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c utils.c -o utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-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 extract_transcripts.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-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/Biostrings.Rcheck/Biostrings/libs
** R
** data
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Creating a new generic function for "setequal" in "Biostrings"
Creating a new generic function for "ls" in "Biostrings"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (Biostrings)

name	user	system	elapsed
AAString-class	0.004	0.000	0.007
AMINO_ACID_CODE	0.000	0.000	0.002
AlignedXStringSet-class	0.252	0.000	0.253
DNAString-class	0.000	0.000	0.002
FASTA-io-legacy	13.229	0.732	14.648
GENETIC_CODE	0.004	0.000	0.004
HNF4alpha	0.052	0.004	0.057
IUPAC_CODE_MAP	0.012	0.000	0.009
MIndex-class	0	0	0
MaskedXString-class	0.504	0.020	0.740
MultipleAlignment-class	2.792	0.016	2.881
PDict-class	5.676	0.068	5.797
PairwiseAlignedXStringSet-class	0.224	0.008	0.230
QualityScaledXStringSet-class	0.032	0.000	0.033
RNAString-class	0.012	0.000	0.010
XString-class	0.008	0.004	0.010
XStringQuality-class	0.104	0.000	0.106
XStringSet-class	9.613	0.196	10.075
XStringSet-io	6.244	0.084	6.365
XStringSetList-class	0.080	0.000	0.079
XStringViews-class	0.260	0.000	0.281
XStringViews-constructor	0.044	0.000	0.045
align-utils	0.088	0.004	0.092
basecontent	0.004	0.000	0.004
chartr	0.596	0.028	0.648
complementSeq	0.048	0.004	0.054
detail	0.952	0.040	1.180
dinucleotideFrequencyTest	0.032	0.000	0.030
extractTranscripts	0.252	0.020	0.271
findPalindromes	5.161	0.016	5.292
gregexpr2	0.004	0.000	0.003
injectHardMask	0.080	0.004	0.083
letter	0.016	0.000	0.018
letterFrequency	2.676	0.072	2.751
longestConsecutive	0	0	0
lowlevel-matching	1.068	0.008	1.093
maskMotif	1.652	0.036	1.788
match-utils	0.036	0.000	0.039
matchLRPatterns	0.572	0.020	0.643
matchPDict-exact	253.580	2.008	317.525
matchPDict-inexact	50.003	0.860	173.365
matchPWM	2.152	0.016	2.330
matchPattern	3.048	0.052	4.937
matchProbePair	1.120	0.012	2.186
matchprobes	0.780	0.008	2.014
misc	0.016	0.000	0.016
needwunsQS	0	0	0
nucleotideFrequency	1.420	0.044	5.214
pairwiseAlignment	1.325	0.004	2.246
phiX174Phage	0.924	0.016	2.189
pid	0.536	0.000	2.046
replaceLetterAt	1.252	0.028	1.289
reverse	2.128	0.120	3.868
reverseSeq	0.036	0.000	0.038
stringDist	8.256	0.012	8.349
substitution_matrices	0.812	0.000	1.030
toComplex	0.004	0.000	0.002
translate	1.533	0.004	1.615
trimLRPatterns	0.224	0.004	0.228
xscat	3.056	0.068	3.293
yeastSEQCHR1	0.004	0.000	0.004