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Package 67/467HostnameOS / ArchBUILDCHECKBUILD BIN
Biostrings 2.20.4
H. Pages
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/Biostrings
Last Changed Rev: 58404 / Revision: 59457
Last Changed Date: 2011-09-26 17:01:44 -0700 (Mon, 26 Sep 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: Biostrings
Version: 2.20.4
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings Biostrings_2.20.4.tar.gz
StartedAt: 2011-10-20 11:58:10 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 12:07:55 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 585.4 seconds
RetCode: 0
Status:  OK 
CheckDir: Biostrings.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/Biostrings.Rcheck’
* using R version 2.13.2 (2011-09-30)
* 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 ‘2.20.4’
* 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 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 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

Biostrings.Rcheck/00install.out:

* installing *source* package ‘Biostrings’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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 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
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-class0.0080.0000.007
AMINO_ACID_CODE0.0040.0000.003
AlignedXStringSet-class0.0920.0080.099
DNAString-class0.0040.0000.003
FASTA-io-legacy13.973 0.50815.040
GENETIC_CODE0.0040.0040.006
HNF4alpha0.0640.0000.081
IUPAC_CODE_MAP0.0080.0000.010
MIndex-class000
MaskedXString-class0.6960.0080.892
MultipleAlignment-class2.7440.0042.750
PDict-class6.9320.0727.065
PairwiseAlignedXStringSet-class0.2920.0000.290
QualityScaledXStringSet-class0.0360.0000.036
RNAString-class0.0120.0000.011
XString-class0.0120.0000.011
XStringQuality-class0.0760.0000.073
XStringSet-class7.6930.2807.976
XStringSet-io7.3360.0447.382
XStringSetList-class0.0840.0000.085
XStringViews-class0.2520.0040.255
XStringViews-constructor0.0440.0040.047
align-utils0.1240.0000.123
basecontent0.0040.0000.004
chartr0.5880.0200.608
complementSeq0.3360.0000.364
detail0.8760.0360.983
dinucleotideFrequencyTest0.0320.0000.033
findPalindromes5.1010.0365.216
gregexpr20.0040.0000.003
injectHardMask0.0880.0200.107
letter0.020.000.02
letterFrequency2.2160.0522.348
longestConsecutive000
lowlevel-matching1.0840.0081.116
maskMotif1.7480.0201.803
match-utils0.0400.0000.041
matchLRPatterns0.5160.0200.592
matchPDict-exact278.069 1.336281.743
matchPDict-inexact58.064 0.25658.782
matchPWM2.0440.0042.068
matchPattern2.9960.0443.073
matchProbePair1.0880.0041.099
matchprobes0.7450.0120.900
misc0.0200.0000.017
needwunsQS0.0000.0000.001
nucleotideFrequency1.4240.0241.463
pairwiseAlignment1.3840.0001.385
phiX174Phage0.9680.0281.045
pid0.5600.0200.581
replaceLetterAt1.2640.0881.364
reverse2.3520.0362.390
reverseSeq0.0440.0000.044
stringDist7.6040.0207.956
substitution_matrices1.0250.0041.030
toComplex0.0000.0000.002
translate1.4520.0041.457
trimLRPatterns0.2240.0040.228
xscat3.5760.0203.683
yeastSEQCHR10.0000.0040.005