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Package 77/631HostnameOS / ArchBUILDCHECKBUILD BIN
Biostrings 2.27.8
H. Pages
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biostrings
Last Changed Rev: 72405 / Revision: 72575
Last Changed Date: 2013-01-09 11:41:44 -0800 (Wed, 09 Jan 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: Biostrings
Version: 2.27.8
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Biostrings_2.27.8.tar.gz
StartedAt: 2013-01-16 01:01:26 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 01:11:37 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 611.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Biostrings.Rcheck
Warnings: 2

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘2.27.8’
* 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 for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Biostrings’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00_pkg_src/Biostrings/man/MaskedXString-class.Rd’:
  ‘[IRanges]{Ranges-utils}’

Missing link or links in documentation object ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00_pkg_src/Biostrings/man/MultipleAlignment-class.Rd’:
  ‘[IRanges:Ranges-utils]{narrow}’

Missing link or links in documentation object ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00_pkg_src/Biostrings/man/XStringViews-class.Rd’:
  ‘[IRanges:IRanges-setops]{gaps}’

See the information in section ‘Cross-references’ of the ‘Writing R
Extensions’ manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘twoWayAlphabetFrequency’
Undocumented S4 methods:
  generic 'splitAsListReturnedClass' and siglist 'AAStringSet'
  generic 'splitAsListReturnedClass' and siglist 'BStringSet'
  generic 'splitAsListReturnedClass' and siglist 'DNAStringSet'
  generic 'splitAsListReturnedClass' and siglist 'RNAStringSet'
  generic 'twoWayAlphabetFrequency' and siglist 'XString,XString'
  generic 'twoWayAlphabetFrequency' and siglist 'XString,XStringSet'
  generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XString'
  generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XStringSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
matchPDict-exact   275.850  1.152 277.164
matchPDict-inexact  58.999  0.508  59.519
PDict-class         12.101  0.180  12.283
XStringSet-class    10.073  0.168  10.279
XStringSet-io        9.293  0.064   9.360
stringDist           7.541  0.000   7.546
findPalindromes      5.208  0.048   5.300
* 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

WARNING: There were 2 warnings.
NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00check.log’
for details.

Biostrings.Rcheck/00install.out:

* installing *source* package ‘Biostrings’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c BAB_class.c -o BAB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c BitMatrix.c -o BitMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c MIndex_class.c -o MIndex_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c XStringSet_class.c -o XStringSet_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c XStringSet_io.c -o XStringSet_io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c XString_class.c -o XString_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c align_needwunsQS.c -o align_needwunsQS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c align_utils.c -o align_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c find_palindromes.c -o find_palindromes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c gtestsim.c -o gtestsim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c io_utils.c -o io_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c letter_frequency.c -o letter_frequency.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c lowlevel_matching.c -o lowlevel_matching.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c match_BOC.c -o match_BOC.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c match_BOC2.c -o match_BOC2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c match_pdict.c -o match_pdict.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c matchprobes.c -o matchprobes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c strutils.c -o strutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c translate.c -o translate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -c utils.c -o utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-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_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-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-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
** installing vignettes
   ‘Biostrings2Classes.Rnw’ 
   ‘MultipleAlignments.Rnw’ 
   ‘PairwiseAlignments.Rnw’ 
   ‘matchprobes.Rnw’ 
** testing if installed package can be loaded

* DONE (Biostrings)

Biostrings.Rcheck/Biostrings-Ex.timings:

nameusersystemelapsed
AAString-class0.020.000.02
AMINO_ACID_CODE0.0200.0000.017
AlignedXStringSet-class0.3560.0040.363
DNAString-class0.0120.0000.014
GENETIC_CODE0.0160.0000.017
HNF4alpha0.0600.0000.058
IUPAC_CODE_MAP0.020.000.02
MIndex-class0.0080.0000.008
MaskedXString-class0.3600.0120.398
MultipleAlignment-class2.8920.0042.893
PDict-class12.101 0.18012.283
PairwiseAlignments-class0.6800.0240.704
PairwiseAlignments-io3.3880.1443.530
QualityScaledXStringSet-class0.0320.0000.032
RNAString-class0.0160.0000.017
XString-class0.0280.0000.028
XStringQuality-class0.1640.0000.164
XStringSet-class10.073 0.16810.279
XStringSet-comparison4.7520.1604.915
XStringSet-io9.2930.0649.360
XStringSetList-class0.3320.0080.340
XStringViews-class0.3560.0120.368
align-utils0.0640.0040.067
chartr0.6880.0480.759
detail1.4760.0361.528
dinucleotideFrequencyTest0.0360.0040.040
findPalindromes5.2080.0485.300
getSeq0.0800.0160.095
gregexpr20.0080.0000.006
injectHardMask0.0640.0040.070
letter0.6440.0320.676
letterFrequency1.9720.0522.028
longestConsecutive0.0040.0000.004
lowlevel-matching0.9440.0040.946
maskMotif1.7640.0921.881
match-utils0.0480.0000.049
matchLRPatterns0.5120.0560.604
matchPDict-exact275.850 1.152277.164
matchPDict-inexact58.999 0.50859.519
matchPWM2.3050.0042.311
matchPattern3.4520.0283.507
matchProbePair1.1240.0161.142
matchprobes0.3440.0200.369
misc0.0240.0000.025
needwunsQS0.0040.0000.006
nucleotideFrequency0.9120.0120.921
pairwiseAlignment1.2360.0001.236
phiX174Phage0.8640.0000.866
pid0.5800.0000.581
replaceLetterAt0.9040.0040.913
reverseComplement1.7720.0641.839
stringDist7.5410.0007.546
substitution_matrices0.7760.0080.784
toComplex0.0080.0000.010
translate1.6760.0161.692
trimLRPatterns0.1440.0000.142
xscat2.6960.0042.701
yeastSEQCHR10.0080.0000.007