Biostrings 2.10.22
H. Pages
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/Biostrings | | Last Changed Rev: 38413 / Revision: 38965 | | Last Changed Date: 2009-04-02 10:19:41 -0700 (Thu, 02 Apr 2009) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ WARNINGS ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.6) / i386 | OK | WARNINGS | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.3-bioc/meat/Biostrings.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.10.22'
* 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 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 cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[[' and siglist 'ByName_MIndex'
generic 'endIndex' and siglist 'ByName_MIndex'
generic 'show' and siglist 'ByName_MIndex'
generic 'startIndex' and siglist 'ByName_MIndex'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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
* creating Biostrings-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating Biostrings-manual.tex ... OK
* checking Biostrings-manual.tex using pdflatex ... OK
WARNING: There was 1 warning, see
E:/biocbld/bbs-2.3-bioc/meat/Biostrings.Rcheck/00check.log
for details
installing R.css in E:/biocbld/bbs-2.3-bioc/meat/Biostrings.Rcheck
---------- Making package Biostrings ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making Dups_utils.d from Dups_utils.c
making IRanges_stubs.d from IRanges_stubs.c
making MIndex_utils.d from MIndex_utils.c
making PreprocessedTB_class.d from PreprocessedTB_class.c
making R_init_Biostrings.d from R_init_Biostrings.c
making RoSeq_utils.d from RoSeq_utils.c
making SparseList_utils.d from SparseList_utils.c
making XStringSet_class.d from XStringSet_class.c
making XString_class.d from XString_class.c
making align_needwunsQS.d from align_needwunsQS.c
making align_pairwiseAlignment.d from align_pairwiseAlignment.c
making align_utils.d from align_utils.c
making char_frequency.d from char_frequency.c
making char_translate.d from char_translate.c
making copy_seq.d from copy_seq.c
making fasta_io.d from fasta_io.c
making find_palindromes.d from find_palindromes.c
making inject_code.d from inject_code.c
making match_BOC.d from match_BOC.c
making match_BOC2.d from match_BOC2.c
making match_PWM.d from match_PWM.c
making match_pattern.d from match_pattern.c
making match_pattern_at.d from match_pattern_at.c
making match_pattern_boyermoore.d from match_pattern_boyermoore.c
making match_pattern_indels.d from match_pattern_indels.c
making match_pattern_shiftor.d from match_pattern_shiftor.c
making match_pdict.d from match_pdict.c
making match_pdict_ACtree.d from match_pdict_ACtree.c
making match_pdict_ACtree2.d from match_pdict_ACtree2.c
making match_pdict_Twobit.d from match_pdict_Twobit.c
making match_reporting.d from match_reporting.c
making pmatchPattern.d from pmatchPattern.c
making replace_letter_at.d from replace_letter_at.c
making utils.d from utils.c
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c Dups_utils.c -o Dups_utils.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c MIndex_utils.c -o MIndex_utils.o
MIndex_utils.c: In function 'ByName_MIndex_endIndex':
MIndex_utils.c:220: warning: unused variable 'poffsets_order'
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c RoSeq_utils.c -o RoSeq_utils.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c XStringSet_class.c -o XStringSet_class.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c XString_class.c -o XString_class.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -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 -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignedFixedSubject_align_aligned':
align_utils.c:222: warning: 'indelWidthSubject' may be used uninitialized in this function
align_utils.c:222: warning: 'indelStartSubject' may be used uninitialized in this function
align_utils.c:222: warning: 'indelWidthPattern' may be used uninitialized in this function
align_utils.c:222: warning: 'indelStartPattern' may be used uninitialized in this function
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c char_frequency.c -o char_frequency.o
char_frequency.c: In function 'oligonucleotide_frequency':
char_frequency.c:207: warning: 'ans_offset' may be used uninitialized in this function
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c char_translate.c -o char_translate.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c copy_seq.c -o copy_seq.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c fasta_io.c -o fasta_io.o
fasta_io.c:54: warning: 'add_desc_LENGTHONLY' defined but not used
fasta_io.c:89: warning: 'add_empty_seq_CHARAEAE' defined but not used
fasta_io.c:95: warning: 'append_to_last_seq_CHARAEAE' defined but not used
fasta_io.c:109: warning: 'add_desc1' defined but not used
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -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 -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c inject_code.c -o inject_code.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -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 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -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 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -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 -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -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 -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c match_pattern_indels.c -o match_pattern_indels.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c match_pdict.c -o match_pdict.o
match_pdict.c: In function 'XStringSet_vmatch_pdict':
match_pdict.c:359: warning: 'ans' may be used uninitialized in this function
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c match_pdict_ACtree.c -o match_pdict_ACtree.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function 'walk_subject':
match_pdict_Twobit.c:187: warning: 'twobit_sign' may be used uninitialized in this function
match_pdict_Twobit.c: In function 'build_Twobit':
match_pdict_Twobit.c:132: warning: 'twobit_sign2pos' may be used uninitialized in this function
match_pdict_Twobit.c: In function '_match_Twobit':
match_pdict_Twobit.c:187: warning: 'twobit_sign' may be used uninitialized in this function
match_pdict_Twobit.c:187: note: 'twobit_sign' was declared here
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c replace_letter_at.c -o replace_letter_at.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -O3 -Wall -c utils.c -o utils.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.3-bioc/R/include -i Biostrings_res.rc -o Biostrings_res.o
gcc -std=gnu99 -shared -s -o Biostrings.dll Biostrings.def 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_frequency.o char_translate.o copy_seq.o fasta_io.o find_palindromes.o inject_code.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 pmatchPattern.o replace_letter_at.o utils.o Biostrings_res.o -Le:/biocbld/bbs-2.3-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
installing data files
preparing package Biostrings for lazy loading
Loading required package: IRanges
Attaching package: 'IRanges'
The following object(s) are masked from package:base :
cbind,
rbind,
sapply
Creating a new generic function for "nchar" in "Biostrings"
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 generic for "order" in package "Biostrings"
(the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ: (...), (na.last, decreasing))
Creating a new generic function for "sort" in "Biostrings"
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "BStringViews" no definition for class: "file"
Creating a generic for "substr" in package "Biostrings"
(the supplied definition differs from and overrides the implicit generic in package "base": Formal arguments differ (in default values?))
Creating a generic for "substring" in package "Biostrings"
(the supplied definition differs from and overrides the implicit generic in package "base": Formal arguments differ (in default values?))
Creating a generic for "chartr" in package "Biostrings"
(the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ: (x), (old, new, x))
Creating a new generic function for "ls" in "Biostrings"
Creating a new generic function for "head" in "Biostrings"
Creating a new generic function for "tail" 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 "eq" no definition for class: "BioString"
installing man source files
installing indices
not zipping data
installing help
>>> 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
PairwiseAlignedFixedSubject-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
alphabetFrequency text html latex example chm
chartr 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
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
needwunsQS 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
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
yeastSEQCHR1 text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.3-bioc\meat\Biostrings.Rcheck\00_pkg_src\Biostrings\chm\Biostrings.chm
Compile time: 0 minutes, 1 second
52 Topics
1,313 Local links
4 Internet links
1 Graphic
Created e:\biocbld\bbs-2.3-bioc\meat\Biostrings.Rcheck\00_pkg_src\Biostrings\chm\Biostrings.chm, 153,655 bytes
Compression decreased file by 395,330 bytes.
adding MD5 sums
* DONE (Biostrings)