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Package 59/419HostnameOS / ArchBUILDCHECKBUILD BIN
Biostrings 2.18.4
H. Pages
Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/Biostrings
Last Changed Rev: 53339 / Revision: 54588
Last Changed Date: 2011-03-01 14:56:14 -0800 (Tue, 01 Mar 2011)
lamb2 Linux (openSUSE 11.2) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 

Summary

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

Command output

* 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

Biostrings.Rcheck/00install.out:

* 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)

Biostrings.Rcheck/Biostrings-Ex.timings:

nameusersystemelapsed
AAString-class0.0040.0000.007
AMINO_ACID_CODE0.0000.0000.002
AlignedXStringSet-class0.0960.0040.098
DNAString-class0.0040.0000.002
FASTA-io-legacy12.877 0.51213.599
GENETIC_CODE0.0040.0000.004
HNF4alpha0.060.000.06
IUPAC_CODE_MAP0.0120.0000.009
MIndex-class000
MaskedXString-class0.4040.0241.503
MultipleAlignment-class2.8920.0202.909
PDict-class5.6960.0405.735
PairwiseAlignedXStringSet-class0.240.000.24
QualityScaledXStringSet-class0.0320.0000.033
RNAString-class0.0080.0000.010
XString-class0.0120.0000.010
XStringQuality-class0.1120.0000.110
XStringSet-class9.7970.0929.894
XStringSet-io5.5040.0565.559
XStringSetList-class0.0760.0000.075
XStringViews-class0.2280.0080.234
XStringViews-constructors0.0400.0000.039
align-utils0.0760.0000.076
basecontent0.0040.0000.004
chartr0.5880.0200.612
complementSeq0.0400.0000.039
detail0.9720.0241.159
dinucleotideFrequencyTest0.0280.0000.029
extractTranscripts0.2360.0360.289
findPalindromes5.0810.0365.217
gregexpr20.0000.0000.002
injectHardMask0.0640.0040.068
letter0.0120.0000.015
letterFrequency2.5880.0482.636
longestConsecutive000
lowlevel-matching1.0080.0281.035
maskMotif1.5560.0401.650
match-utils0.0360.0000.036
matchLRPatterns0.5360.0120.591
matchPDict-exact254.508 1.024255.666
matchPDict-inexact44.727 0.28445.378
matchPWM2.1280.0162.142
matchPattern2.9280.0563.002
matchProbePair1.1080.0081.113
matchprobes0.7640.0040.769
misc0.0120.0040.015
needwunsQS000
nucleotideFrequency1.1520.0121.164
pairwiseAlignment1.3080.0161.333
phiX174Phage0.9160.0080.924
pid0.5320.0000.533
replaceLetterAt1.1640.0881.253
reverse2.1050.0562.157
reverseSeq0.0400.0000.038
stringDist8.2480.0088.332
substitution_matrices0.7720.0040.777
toComplex0.0000.0000.002
translate1.3920.0001.393
trimLRPatterns0.2440.0040.250
xscat3.5160.0163.533
yeastSEQCHR10.0040.0000.004