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 '/loc/home/biocbuild/bbs-2.3-bioc/meat/Biostrings.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: UTF-8
* 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 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 ... 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
/loc/home/biocbuild/bbs-2.3-bioc/meat/Biostrings.Rcheck/00check.log
for details
* Installing *source* package 'Biostrings' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-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-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-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: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 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -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 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c char_translate.c -o char_translate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c copy_seq.c -o copy_seq.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c Dups_utils.c -o Dups_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -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 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c find_palindromes.c -o find_palindromes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-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-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-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-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -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 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-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: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 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-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-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-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-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-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-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-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:359: warning: ‘ans’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-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 ‘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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -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 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-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-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-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-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c RoSeq_utils.c -o RoSeq_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c utils.c -o utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c XString_class.c -o XString_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c XStringSet_class.c -o XStringSet_class.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Biostrings.so align_needwunsQS.o align_pairwiseAlignment.o align_utils.o char_frequency.o char_translate.o copy_seq.o Dups_utils.o fasta_io.o find_palindromes.o inject_code.o IRanges_stubs.o match_BOC2.o match_BOC.o match_pattern_at.o match_pattern_boyermoore.o match_pattern.o match_pattern_indels.o match_pattern_shiftor.o match_pdict_ACtree2.o match_pdict_ACtree.o match_pdict.o match_pdict_Twobit.o match_PWM.o match_reporting.o MIndex_utils.o pmatchPattern.o PreprocessedTB_class.o replace_letter_at.o R_init_Biostrings.o RoSeq_utils.o SparseList_utils.o utils.o XString_class.o XStringSet_class.o -L/home/biocbuild/bbs-2.3-bioc/R/lib -lR
** R
** data
** inst
** preparing package 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"
** help
>>> Building/Updating help pages for package 'Biostrings'
Formats: text html latex example
AAString-class text html latex example
AMINO_ACID_CODE text html latex example
AlignedXStringSet-class text html latex example
BOC_SubjectString-class text html latex
Biostrings-internals text html latex
DNAString-class text html latex example
GENETIC_CODE text html latex example
IUPAC_CODE_MAP text html latex example
Note: removing empty section \examples in file 'InDel-class.Rd'
InDel-class text html latex
MIndex-class text html latex example
MaskedXString-class text html latex example
PDict-class text html latex example
PairwiseAlignedFixedSubject-class text html latex example
QualityScaledXStringSet-class text html latex example
RNAString-class text html latex example
XString-class text html latex example
XStringPartialMatches-class text html latex
XStringQuality-class text html latex example
XStringSet-class text html latex example
XStringSet-io text html latex example
XStringViews-class text html latex example
XStringViews-constructors text html latex example
align-utils text html latex example
alphabetFrequency text html latex example
chartr text html latex example
findPalindromes text html latex example
gregexpr2 text html latex example
injectHardMask text html latex example
letter text html latex example
maskMotif text html latex example
match-utils text html latex example
matchLRPatterns text html latex example
matchPDict-exact text html latex example
matchPDict-inexact text html latex example
matchPWM text html latex example
matchPattern text html latex example
matchProbePair text html latex example
needwunsQS text html latex example
pairwiseAlignment text html latex example
phiX174Phage text html latex example
pid text html latex example
pmatchPattern text html latex
readFASTA text html latex example
replaceLetterAt text html latex example
reverse text html latex example
stringDist text html latex example
subXString text html latex
substitution_matrices text html latex example
toComplex text html latex example
translate text html latex example
yeastSEQCHR1 text html latex example
** building package indices ...
* DONE (Biostrings)