Biostrings 2.12.10
H. Pages
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/Biostrings | | Last Changed Rev: 42117 / Revision: 42512 | | Last Changed Date: 2009-10-01 17:49:29 -0700 (Thu, 01 Oct 2009) |
| wilson1 | 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 'E:/biocbld/bbs-2.4-bioc/meat/Biostrings.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.12.10'
* 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 ... WARNING
Found the following significant warnings:
xscat.c:86: warning: 'ans_length' is used uninitialized in this function
xscat.c:36: warning: 'ans_classname' is used uninitialized in this function
xscat.c:36: warning: 'ans_length' is used uninitialized in this function
See 'E:/biocbld/bbs-2.4-bioc/meat/Biostrings.Rcheck/00install.out' for details.
* checking package directory ... OK
* checking for portable file names ... 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 ... OK
* checking Rd files against version 2 parser ... 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
WARNING: There was 1 warning, see
E:/biocbld/bbs-2.4-bioc/meat/Biostrings.Rcheck/00check.log
for details
* Installing *source* package 'Biostrings' ...
** libs
making DLL ...
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c BAB_class.c -o BAB_class.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c Dups_utils.c -o Dups_utils.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c MIndex_utils.c -o MIndex_utils.o
MIndex_utils.c: In function 'SparseMIndex_endIndex':
MIndex_utils.c:220: warning: unused variable 'poffsets_order'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c RoSeq_utils.c -o RoSeq_utils.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c SparseList_utils.c -o SparseList_utils.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c XStringSet_class.c -o XStringSet_class.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c XString_class.c -o XString_class.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:39: warning: 'lkup_val' may be used uninitialized in this function
align_needwunsQS.c:39: note: 'lkup_val' was declared here
align_needwunsQS.c:26: warning: 'sc' may be used uninitialized in this function
align_needwunsQS.c:26: note: 'sc' was declared here
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
align_pairwiseAlignment.c: In function 'pairwiseAlignment':
align_pairwiseAlignment.c:132: warning: unused variable 'prevMinus1'
align_pairwiseAlignment.c:132: warning: unused variable 'prev'
align_pairwiseAlignment.c:132: warning: unused variable 'currMinus1'
align_pairwiseAlignment.c:132: warning: unused variable 'curr'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -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 -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c char_translate.c -o char_translate.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c copy_seq.c -o copy_seq.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c fasta_io.c -o fasta_io.o
fasta_io.c:102: warning: 'add_desc_LENGTHONLY' defined but not used
fasta_io.c:137: warning: 'add_empty_seq_CHARAEAE' defined but not used
fasta_io.c:143: warning: 'append_to_last_seq_CHARAEAE' defined but not used
fasta_io.c:157: warning: 'add_desc1' defined but not used
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c find_palindromes.c -o find_palindromes.o
find_palindromes.c: In function 'find_palindromes':
find_palindromes.c:25: warning: 'letter0' may be used uninitialized in this function
find_palindromes.c:25: note: 'letter0' was declared here
find_palindromes.c:24: warning: 'all_letter0' may be used uninitialized in this function
find_palindromes.c:24: note: 'all_letter0' was declared here
find_palindromes.c:79: warning: 'letter0' may be used uninitialized in this function
find_palindromes.c:79: note: 'letter0' was declared here
find_palindromes.c:78: warning: 'lkup_val' may be used uninitialized in this function
find_palindromes.c:78: note: 'lkup_val' was declared here
find_palindromes.c:78: warning: 'all_letter0' may be used uninitialized in this function
find_palindromes.c:78: note: 'all_letter0' was declared here
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c inject_code.c -o inject_code.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c letter_frequency.c -o letter_frequency.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -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 -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -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 -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c match_PWM.c -o match_PWM.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c match_pattern.c -o match_pattern.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c match_pattern_at.c -o match_pattern_at.o
match_pattern_at.c: In function '_nedit_for_Proffset':
match_pattern_at.c:292: warning: unused variable 'Pc'
match_pattern_at.c:291: warning: unused variable 'j'
match_pattern_at.c:291: warning: unused variable 'jmin'
match_pattern_at.c:291: warning: unused variable 'iplus1'
match_pattern_at.c:291: warning: unused variable 'i'
match_pattern_at.c:291: warning: unused variable 'b'
match_pattern_at.c:291: warning: unused variable 'B'
match_pattern_at.c:290: warning: unused variable 'row_length'
match_pattern_at.c:290: warning: unused variable 'curr_row'
match_pattern_at.c:290: warning: unused variable 'prev_row'
match_pattern_at.c:290: warning: unused variable 'max_nedit_plus1'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
match_pattern_boyermoore.c: In function '_match_pattern_boyermoore':
match_pattern_boyermoore.c:374: warning: 'c' may be used uninitialized in this function
match_pattern_boyermoore.c:373: warning: 'j1' may be used uninitialized in this function
match_pattern_boyermoore.c:373: warning: 'i2' may be used uninitialized in this function
match_pattern_boyermoore.c:373: warning: 'i1' may be used uninitialized in this function
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c match_pattern_indels.c -o match_pattern_indels.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c match_pdict.c -o match_pdict.o
match_pdict.c: In function 'XStringSet_vmatch_pdict':
match_pdict.c:392: warning: 'ans_length' may be used uninitialized in this function
match_pdict.c:392: note: 'ans_length' was declared here
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c match_pdict_ACtree.c -o match_pdict_ACtree.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -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 -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -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 -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c match_reporting.c -o match_reporting.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c matchprobes.c -o matchprobes.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c pmatchPattern.c -o pmatchPattern.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c replace_letter_at.c -o replace_letter_at.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c strutils.c -o strutils.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature':
utils.c:225: warning: 'twobit_sign' may be used uninitialized in this function
utils.c: In function '_get_twobit_signature_at':
utils.c:239: warning: 'twobit_sign' may be used uninitialized in this function
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -O3 -Wall -std=gnu99 -c xscat.c -o xscat.o
xscat.c: In function 'XStringSet_xscat':
xscat.c:86: warning: 'ans_length' is used uninitialized in this function
xscat.c:62: warning: 'ans_baseClass' may be used uninitialized in this function
xscat.c:62: warning: 'ans_classname' may be used uninitialized in this function
xscat.c: In function 'XString_xscat':
xscat.c:36: warning: 'ans_classname' is used uninitialized in this function
xscat.c:36: warning: 'ans_length' is used uninitialized in this function
gcc -shared -s -o Biostrings.dll tmp.def BAB_class.o Dups_utils.o IRanges_stubs.o MIndex_utils.o PreprocessedTB_class.o R_init_Biostrings.o RoSeq_utils.o SparseList_utils.o XStringSet_class.o XString_class.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o char_translate.o copy_seq.o fasta_io.o find_palindromes.o inject_code.o letter_frequency.o match_BOC.o match_BOC2.o match_PWM.o match_pattern.o match_pattern_at.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_reporting.o matchprobes.o pmatchPattern.o replace_letter_at.o strutils.o utils.o xscat.o -Le:/biocbld/bbs-2.4-bioc/R/bin -lR
... done
** R
** data
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from package:base :
cbind,
duplicated,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rank,
rbind,
rep.int,
sapply,
sort,
table,
unique
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"
Creating a new generic function for "setequal" in "Biostrings"
Creating a new generic function for "match" in "Biostrings"
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "BStringViews" no definition for class: "file"
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"
** help
*** installing help indices
>>> Building/Updating help pages for package 'Biostrings'
Formats: text html latex example chm
AAString-class text html latex example chm
AMINO_ACID_CODE text html latex example chm
AlignedXStringSet-class text html latex example chm
BOC_SubjectString-class text html latex chm
Biostrings-internals text html latex chm
DNAString-class text html latex example chm
GENETIC_CODE text html latex example chm
IUPAC_CODE_MAP text html latex example chm
Note: removing empty section \examples in file 'InDel-class.Rd'
Note: removing empty section \examples in file 'InDel-class.Rd'
InDel-class text html latex chm
MIndex-class text html latex example chm
MaskedXString-class text html latex example chm
PDict-class text html latex example chm
PairwiseAlignedXStringSet-class text html latex example chm
QualityScaledXStringSet-class text html latex example chm
RNAString-class text html latex example chm
XString-class text html latex example chm
XStringPartialMatches-class text html latex chm
XStringQuality-class text html latex example chm
XStringSet-class text html latex example chm
XStringSet-io text html latex example chm
XStringViews-class text html latex example chm
XStringViews-constructors text html latex example chm
align-utils text html latex example chm
basecontent text html latex example chm
chartr text html latex example chm
complementSeq text html latex example chm
findPalindromes text html latex example chm
gregexpr2 text html latex example chm
injectHardMask text html latex example chm
letter text html latex example chm
letterFrequency text html latex example chm
longestConsecutive text html latex example chm
maskMotif text html latex example chm
match-utils text html latex example chm
matchLRPatterns text html latex example chm
matchPDict-exact text html latex example chm
matchPDict-inexact text html latex example chm
matchPWM text html latex example chm
matchPattern text html latex example chm
matchProbePair text html latex example chm
matchprobes text html latex example chm
needwunsQS text html latex example chm
nucleotideFrequency text html latex example chm
pairwiseAlignment text html latex example chm
phiX174Phage text html latex example chm
pid text html latex example chm
pmatchPattern text html latex chm
readFASTA text html latex example chm
replaceLetterAt text html latex example chm
reverse text html latex example chm
reverseSeq text html latex example chm
stringDist text html latex example chm
subXString text html latex chm
substitution_matrices text html latex example chm
toComplex text html latex example chm
translate text html latex example chm
trimLRPatterns text html latex example chm
xscat text html latex example chm
yeastSEQCHR1 text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\BBS-2~1.4-B\meat\BIOSTR~1.RCH\00_PKG~1\BIOSTR~1\chm\Biostrings.chm
Compile time: 0 minutes, 2 seconds
60 Topics
1,500 Local links
4 Internet links
1 Graphic
Created e:\biocbld\BBS-2~1.4-B\meat\BIOSTR~1.RCH\00_PKG~1\BIOSTR~1\chm\Biostrings.chm, 182,147 bytes
Compression decreased file by 464,566 bytes.
** building package indices ...
** MD5 sums
* DONE (Biostrings)