Package: Biostrings

Version: 2.18.4

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings Biostrings_2.18.4.tar.gz

StartedAt: 2011-04-07 05:12:36 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 05:21:32 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 536.0 seconds

RetCode: 0

Status:  OK

CheckDir: Biostrings.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/Biostrings.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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 ‘2.18.4’
* 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 ... NOTE
prepare_Rd: InDel-class.Rd:50-51: Dropping empty section \examples
prepare_Rd: WCP.Rd:32-33: Dropping empty section \details
prepare_Rd: WCP.Rd:42-43: Dropping empty section \examples
prepare_Rd: XKeySortedData.Rd:39-40: Dropping empty section \details
prepare_Rd: XKeySortedData.Rd:49-50: Dropping empty section \examples
prepare_Rd: XKeySortedDataList.Rd:30-31: Dropping empty section \details
prepare_Rd: XKeySortedDataList.Rd:40-41: Dropping empty section \examples
prepare_Rd: matchWCP.Rd:70-71: Dropping empty section \examples
* 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' calls not declared from:
  BSgenome.Hsapiens.UCSC.hg18 hgu133aprobe
* 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) and $(LAPACK_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-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c BAB_class.c -o BAB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c BitMatrix.c -o BitMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c MIndex_class.c -o MIndex_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-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-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c XStringSet_class.c -o XStringSet_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c XStringSet_io.c -o XStringSet_io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c XString_class.c -o XString_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c align_needwunsQS.c -o align_needwunsQS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c align_utils.c -o align_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c extract_transcripts.c -o extract_transcripts.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c find_palindromes.c -o find_palindromes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c gtestsim.c -o gtestsim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c io_utils.c -o io_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c letter_frequency.c -o letter_frequency.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c lowlevel_matching.c -o lowlevel_matching.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_BOC.c -o match_BOC.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_BOC2.c -o match_BOC2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_WCP.c -o match_WCP.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-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-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-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-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-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-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_pdict.c -o match_pdict.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-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-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-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-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-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-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c matchprobes.c -o matchprobes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-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-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c strutils.c -o strutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c translate.c -o translate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/IRanges/include"   -fpic  -g -O2 -c utils.c -o utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-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-2.7-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.7-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, mapply, order, paste, pmax, pmax.int, pmin,
    pmin.int, rbind, rep.int, table

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	0.096	0.004	0.098
DNAString-class	0.004	0.000	0.002
FASTA-io-legacy	12.877	0.512	13.599
GENETIC_CODE	0.004	0.000	0.004
HNF4alpha	0.06	0.00	0.06
IUPAC_CODE_MAP	0.012	0.000	0.009
MIndex-class	0	0	0
MaskedXString-class	0.404	0.024	1.503
MultipleAlignment-class	2.892	0.020	2.909
PDict-class	5.696	0.040	5.735
PairwiseAlignedXStringSet-class	0.24	0.00	0.24
QualityScaledXStringSet-class	0.032	0.000	0.033
RNAString-class	0.008	0.000	0.010
XString-class	0.012	0.000	0.010
XStringQuality-class	0.112	0.000	0.110
XStringSet-class	9.797	0.092	9.894
XStringSet-io	5.504	0.056	5.559
XStringSetList-class	0.076	0.000	0.075
XStringViews-class	0.228	0.008	0.234
XStringViews-constructors	0.040	0.000	0.039
align-utils	0.076	0.000	0.076
basecontent	0.004	0.000	0.004
chartr	0.588	0.020	0.612
complementSeq	0.040	0.000	0.039
detail	0.972	0.024	1.159
dinucleotideFrequencyTest	0.028	0.000	0.029
extractTranscripts	0.236	0.036	0.289
findPalindromes	5.081	0.036	5.217
gregexpr2	0.000	0.000	0.002
injectHardMask	0.064	0.004	0.068
letter	0.012	0.000	0.015
letterFrequency	2.588	0.048	2.636
longestConsecutive	0	0	0
lowlevel-matching	1.008	0.028	1.035
maskMotif	1.556	0.040	1.650
match-utils	0.036	0.000	0.036
matchLRPatterns	0.536	0.012	0.591
matchPDict-exact	254.508	1.024	255.666
matchPDict-inexact	44.727	0.284	45.378
matchPWM	2.128	0.016	2.142
matchPattern	2.928	0.056	3.002
matchProbePair	1.108	0.008	1.113
matchprobes	0.764	0.004	0.769
misc	0.012	0.004	0.015
needwunsQS	0	0	0
nucleotideFrequency	1.152	0.012	1.164
pairwiseAlignment	1.308	0.016	1.333
phiX174Phage	0.916	0.008	0.924
pid	0.532	0.000	0.533
replaceLetterAt	1.164	0.088	1.253
reverse	2.105	0.056	2.157
reverseSeq	0.040	0.000	0.038
stringDist	8.248	0.008	8.332
substitution_matrices	0.772	0.004	0.777
toComplex	0.000	0.000	0.002
translate	1.392	0.000	1.393
trimLRPatterns	0.244	0.004	0.250
xscat	3.516	0.016	3.533
yeastSEQCHR1	0.004	0.000	0.004