Biostrings 2.24.0
H. Pages
| Snapshot Date: 2012-03-31 17:01:49 -0700 (Sat, 31 Mar 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/Biostrings | | Last Changed Rev: 64678 / Revision: 64719 | | Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | WARNINGS | |
| puck5 | Linux (Ubuntu 12.04) / 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 |
* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Biostrings.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.24.0'
* 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 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
.needwunsQS: warning in matrix(0, nr = n1 + 1, nc = n2 + 1): partial
argument match of 'nr' to 'nrow'
.needwunsQS: warning in matrix(0, nr = n1 + 1, nc = n2 + 1): partial
argument match of 'nc' to 'ncol'
g.test: warning in pchisq(STATISTIC, PARAMETER, lower = FALSE): partial
argument match of 'lower' to 'lower.tail'
* 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 ... WARNING
'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 compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: 'readFASTA' is deprecated.
Warning: 'writeFASTA' is deprecated.
Warning: 'writeFASTA' is deprecated.
Warning: 'writeFASTA' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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/hpages/test-puck5/bbs-2.10-bioc/meat/Biostrings.Rcheck/00check.log'
for details.
* installing *source* package 'Biostrings' ...
** libs
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c BAB_class.c -o BAB_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c BitMatrix.c -o BitMatrix.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c MIndex_class.c -o MIndex_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c XStringSet_class.c -o XStringSet_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c XStringSet_io.c -o XStringSet_io.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c XString_class.c -o XString_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c align_needwunsQS.c -o align_needwunsQS.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c align_utils.c -o align_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c find_palindromes.c -o find_palindromes.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c gtestsim.c -o gtestsim.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c io_utils.c -o io_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c letter_frequency.c -o letter_frequency.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c lowlevel_matching.c -o lowlevel_matching.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c match_BOC.c -o match_BOC.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c match_BOC2.c -o match_BOC2.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c match_pattern_indels.c -o match_pattern_indels.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c match_pdict.c -o match_pdict.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c match_pdict_Twobit.c -o match_pdict_Twobit.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c match_pdict_utils.c -o match_pdict_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c matchprobes.c -o matchprobes.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c replace_letter_at.c -o replace_letter_at.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c strutils.c -o strutils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c translate.c -o translate.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c utils.c -o utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -c xscat.c -o xscat.o
gcc -std=gnu99 -shared -L/usr/local/lib -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/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-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)