Biostrings 2.14.8
H. Pages
| Snapshot Date: 2009-12-13 23:30:35 -0800 (Sun, 13 Dec 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/Biostrings | | Last Changed Rev: 43250 / Revision: 43539 | | Last Changed Date: 2009-11-24 22:31:39 -0800 (Tue, 24 Nov 2009) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.5-bioc/meat/Biostrings.Rcheck'
* using R version 2.10.0 (2009-10-26)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.14.8'
* 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 name space can be loaded with stated dependencies ... 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 ... NOTE
prepare_Rd: InDel-class.Rd:50-51: Dropping empty section \examples
prepare_Rd: matchWCP.Rd:70-71: 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: XKeySortedDataList.Rd:30-31: Dropping empty section \details
prepare_Rd: XKeySortedDataList.Rd:40-41: Dropping empty section \examples
prepare_Rd: XKeySortedData.Rd:39-40: Dropping empty section \details
prepare_Rd: XKeySortedData.Rd:49-50: 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 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* install options are ' --no-html'
* installing *source* package ‘Biostrings’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c BAB_class.c -o BAB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c BitMatrix.c -o BitMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function ‘SparseMIndex_endIndex’:
MIndex_class.c:192: warning: unused variable ‘poffsets_order’
MIndex_class.c: In function ‘_get_cachedMIndex_elt’:
MIndex_class.c:93: warning: ‘cached_iranges.end’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c XStringSet_class.c -o XStringSet_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c XStringSet_io.c -o XStringSet_io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c XString_class.c -o XString_class.o
XString_class.c:117: warning: ‘new_RoSeqs_from_XString’ defined but not used
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function ‘align_needwunsQS’:
align_needwunsQS.c:26: warning: ‘sc’ may be used uninitialized in this function
align_needwunsQS.c:26: note: ‘sc’ was declared here
align_needwunsQS.c:39: warning: ‘lkup_val’ may be used uninitialized in this function
align_needwunsQS.c:39: note: ‘lkup_val’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c align_utils.c -o align_utils.o
align_utils.c: In function ‘PairwiseAlignedFixedSubject_align_aligned’:
align_utils.c:225: warning: ‘indelWidthSubject’ may be used uninitialized in this function
align_utils.c:225: warning: ‘indelStartSubject’ may be used uninitialized in this function
align_utils.c:225: warning: ‘indelWidthPattern’ may be used uninitialized in this function
align_utils.c:225: warning: ‘indelStartPattern’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c extract_transcripts.c -o extract_transcripts.o
extract_transcripts.c: In function ‘tlocs2rlocs’:
extract_transcripts.c:224: warning: ‘nlocs’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c find_palindromes.c -o find_palindromes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c gtestsim.c -o gtestsim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c letter_frequency.c -o letter_frequency.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c lowlevel_matching.c -o lowlevel_matching.o
lowlevel_matching.c: In function ‘_nedit_for_Proffset’:
lowlevel_matching.c:285: warning: unused variable ‘Pc’
lowlevel_matching.c:284: warning: unused variable ‘j’
lowlevel_matching.c:284: warning: unused variable ‘jmin’
lowlevel_matching.c:284: warning: unused variable ‘iplus1’
lowlevel_matching.c:284: warning: unused variable ‘i’
lowlevel_matching.c:284: warning: unused variable ‘b’
lowlevel_matching.c:284: warning: unused variable ‘B’
lowlevel_matching.c:283: warning: unused variable ‘row_length’
lowlevel_matching.c:283: warning: unused variable ‘curr_row’
lowlevel_matching.c:283: warning: unused variable ‘prev_row’
lowlevel_matching.c:283: warning: unused variable ‘max_nedit_plus1’
lowlevel_matching.c: In function ‘XStringSet_vmatch_pattern_at’:
lowlevel_matching.c:486: warning: ‘ans’ may be used uninitialized in this function
lowlevel_matching.c:485: warning: ‘ans_nrow’ may be used uninitialized in this function
lowlevel_matching.c:485: warning: ‘ans_elt’ may be used uninitialized in this function
lowlevel_matching.c: In function ‘XString_match_pattern_at’:
lowlevel_matching.c:438: warning: ‘ans’ may be used uninitialized in this function
lowlevel_matching.c:437: warning: ‘ans_elt’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_BOC.c -o match_BOC.o
match_BOC.c: In function ‘BOC_exact_search’:
match_BOC.c:331: warning: label ‘continue0’ defined but not used
match_BOC.c:268: warning: unused variable ‘noffsets’
match_BOC.c:268: warning: unused variable ‘offsets’
match_BOC.c:268: warning: unused variable ‘j’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_BOC2.c -o match_BOC2.o
match_BOC2.c: In function ‘BOC2_exact_search’:
match_BOC2.c:288: warning: label ‘continue0’ defined but not used
match_BOC2.c:234: warning: unused variable ‘noffsets’
match_BOC2.c:234: warning: unused variable ‘offsets’
match_BOC2.c:234: warning: unused variable ‘j’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_WCP.c -o match_WCP.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
match_pattern_boyermoore.c: In function ‘_match_pattern_boyermoore’:
match_pattern_boyermoore.c:401: warning: ‘c’ may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: ‘j1’ may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: ‘i2’ may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: ‘i1’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_pattern_indels.c -o match_pattern_indels.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_pdict.c -o match_pdict.o
match_pdict.c: In function ‘XStringSet_vmatch_pdict’:
match_pdict.c:320: warning: ‘ans’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_pdict_ACtree.c -o match_pdict_ACtree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c:593: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function ‘build_Twobit’:
match_pdict_Twobit.c:125: warning: ‘twobit_sign2pos’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function ‘match_ppheadtail0’:
match_pdict_utils.c:836: warning: unused variable ‘ncol’
match_pdict_utils.c: In function ‘_match_pdict_all_flanks’:
match_pdict_utils.c:989: warning: unused variable ‘subtotal_NFC’
match_pdict_utils.c:989: warning: unused variable ‘total_NFC’
match_pdict_utils.c:988: warning: unused variable ‘NFC’
match_pdict_utils.c:988: warning: unused variable ‘nloci’
match_pdict_utils.c:988: warning: unused variable ‘ndup’
match_pdict_utils.c: At top level:
match_pdict_utils.c:464: warning: ‘match_headtail_by_loc’ defined but not used
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c matchprobes.c -o matchprobes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c replace_letter_at.c -o replace_letter_at.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c strutils.c -o strutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c utils.c -o utils.o
utils.c: In function ‘_get_twobit_signature_at’:
utils.c:240: warning: ‘twobit_sign’ may be used uninitialized in this function
utils.c: In function ‘_get_twobit_signature’:
utils.c:226: warning: ‘twobit_sign’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c xscat.c -o xscat.o
xscat.c: In function ‘XStringSet_xscat’:
xscat.c:86: warning: ‘ans_length’ may be used uninitialized in this function
xscat.c:63: warning: ‘ans_xsbaseclassname’ may be used uninitialized in this function
xscat.c: In function ‘XString_xscat’:
xscat.c:36: warning: ‘ans_classname’ may be used uninitialized in this function
xscat.c:36: warning: ‘ans_length’ may be used uninitialized in this function
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 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_ACtree.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 utils.o xscat.o -L/home/biocbuild/bbs-2.5-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from package:base :
Map,
cbind,
mapply,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rbind,
rep.int,
table
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "XString" no definition for class: “AsIs”
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "XStringSet" no definition for class: “AsIs”
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "XStringSet" no definition for class: “probetable”
Creating a new generic function for "setequal" in "Biostrings"
Creating a new generic function for "is.unsorted" in "Biostrings"
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "BStringViews" no definition for class: “file”
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "consensusString" no definition for class: “BStringViews”
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "consensusString" no definition for class: “DNAStringViews”
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "consensusString" no definition for class: “RNAStringViews”
Creating a new generic function for "ls" in "Biostrings"
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "PDict" no definition for class: “AsIs”
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "PDict" no definition for class: “probetable”
** help
*** installing help indices
** building package indices ...
* DONE (Biostrings)