Biostrings 2.7.44
H. Pages
| Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biostrings | | Last Changed Rev: 30943 / Revision: 30951 | | Last Changed Date: 2008-04-08 20:04:16 -0700 (Tue, 08 Apr 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | WARNINGS | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | WARNINGS | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | [ WARNINGS ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.1) / i386 | OK | WARNINGS | OK |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/Biostrings.Rcheck'
* using R version 2.7.0 beta (2008-04-07 r45159)
* using session charset: ISO8859-1
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.7.44'
* 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 ... WARNING
'library' or 'require' calls not declared from:
BSgenome.Hsapiens.UCSC.hg18
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cmp_BOC2vsBoyerMoore_exactmatching: no visible binding for global
variable 'Hsapiens'
* checking Rd files ... WARNING
Rd files without 'description':
matchLRPatterns.Rd
toComplex.Rd
These entries are required in an Rd file.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
cDNA chartr dna2rna rna2dna transcribe
Undocumented S4 classes:
BOC2_SubjectString BOC_SubjectString
Undocumented S4 methods:
generic 'chartr' and siglist 'XString'
generic 'chartr' and siglist 'XStringSet'
generic 'chartr' and siglist 'BStringViews'
generic 'countPattern' and siglist 'BOC2_SubjectString'
generic 'initialize' and siglist 'BOC_SubjectString'
generic 'initialize' and siglist 'BOC2_SubjectString'
generic 'matchPattern' and siglist 'BOC_SubjectString'
generic 'matchPattern' and siglist 'BOC2_SubjectString'
generic 'narrow' and siglist 'BStringViews'
generic 'restrict' and siglist 'BStringViews'
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 ... WARNING
Objects in \usage without \alias in documentation object 'matchPDict':
unlist
Functions with \usage entries need to have the appropriate \alias entries,
and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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 were 4 warnings, see
/loc/home/biocbuild/bbs-2.2-bioc/meat/Biostrings.Rcheck/00check.log
for details
* Installing *source* package 'Biostrings' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c ACtree_utils.c -o ACtree_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:38: warning: 'lkup_val' may be used uninitialized in this function
align_needwunsQS.c:38: note: 'lkup_val' was declared here
align_needwunsQS.c:25: warning: 'sc' may be used uninitialized in this function
align_needwunsQS.c:25: note: 'sc' was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c bufutils.c -o bufutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c char_frequency.c -o char_frequency.o
char_frequency.c: In function 'oligonucleotide_frequency':
char_frequency.c:159: warning: 'ans_offset' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c char_translate.c -o char_translate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c copy_seq.c -o copy_seq.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -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 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_utils.c -o IRanges_utils.o
IRanges_utils.c: In function 'reduce_IRanges':
IRanges_utils.c:191: warning: 'ans_inframe_start' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/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'
match_BOC2.c: In function 'make_pre4':
match_BOC2.c:45: warning: 'pre4' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/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'
match_BOC.c: In function 'get_pre4':
match_BOC.c:29: warning: 'pre4' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c match_boyermoore.c -o match_boyermoore.o
match_boyermoore.c: In function 'match_boyermoore':
match_boyermoore.c:371: warning: 'i2' may be used uninitialized in this function
match_boyermoore.c:371: note: 'i2' was declared here
match_boyermoore.c:372: warning: 'c' may be used uninitialized in this function
match_boyermoore.c:372: note: 'c' was declared here
match_boyermoore.c:371: warning: 'j1' may be used uninitialized in this function
match_boyermoore.c:371: note: 'j1' was declared here
match_boyermoore.c:371: warning: 'i1' may be used uninitialized in this function
match_boyermoore.c:371: note: 'i1' was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c match_naive.c -o match_naive.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c match_shiftor.c -o match_shiftor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c match_TBdna.c -o match_TBdna.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c MIndex_utils.c -o MIndex_utils.o
MIndex_utils.c: In function 'extract_endIndex':
MIndex_utils.c:95: warning: unused variable 'poffsets_order'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c normalize_views.c -o normalize_views.o
normalize_views.c:49: warning: 'normalize_orderedbystartviews' defined but not used
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c replace_locs.c -o replace_locs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c seqs_to_seqs.c -o seqs_to_seqs.o
seqs_to_seqs.c: In function 'copy_subXRaw':
seqs_to_seqs.c:191: warning: unused variable 'ans'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o
utils.c: In function '_Biostrings_coerce_to_complex_from_i1i2':
utils.c:492: warning: 'lkup_val.r' may be used uninitialized in this function
utils.c:492: warning: 'lkup_val.i' may be used uninitialized in this function
utils.c: In function '_Biostrings_reverse_translate_charcpy_from_i1i2':
utils.c:448: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function '_Biostrings_translate_charcpy_to_subset':
utils.c:367: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function '_Biostrings_translate_charcpy_to_i1i2':
utils.c:326: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function '_Biostrings_translate_charcpy_from_subset':
utils.c:286: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function '_Biostrings_translate_charcpy_from_i1i2':
utils.c:245: warning: 'lkup_val' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c views_buffer.c -o views_buffer.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c XInteger.c -o XInteger.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c XRaw_class.c -o XRaw_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c XRaw_utils.c -o XRaw_utils.o
XRaw_utils.c: In function 'XRaw_loadFASTA':
XRaw_utils.c:552: warning: 'view_start' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c XString_class.c -o XString_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c XStringSet_class.c -o XStringSet_class.o
gcc -std=gnu99 -shared -L/usr/local/lib -o Biostrings.so ACtree_utils.o align_needwunsQS.o bufutils.o char_frequency.o char_translate.o copy_seq.o find_palindromes.o IRanges_class.o IRanges_utils.o match_BOC2.o match_BOC.o match_boyermoore.o match_naive.o match_shiftor.o match_TBdna.o MIndex_utils.o normalize_views.o pmatchPattern.o replace_locs.o R_init_Biostrings.o seqs_to_seqs.o utils.o views_buffer.o XInteger.o XRaw_class.o XRaw_utils.o XString_class.o XStringSet_class.o -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "start" in "Biostrings"
Creating a new generic function for "end" in "Biostrings"
Creating a new generic function for "as.data.frame" in "Biostrings"
Creating a new generic function for "duplicated" in "Biostrings"
Creating a new generic function for "as.matrix" in "Biostrings"
Creating a new generic function for "update" in "Biostrings"
Creating a new generic function for "toString" in "Biostrings"
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "XString" no definition for class: "AsIs"
Creating a new generic function for "nchar" in "Biostrings"
Creating a new generic function for "as.list" 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 "XStringSet" no definition for class: "AsIs"
New generic for "substr" does not agree with implicit generic from package "base"; a new generic will be assigned with package "Biostrings"
New generic for "substring" does not agree with implicit generic from package "base"; a new generic will be assigned with package "Biostrings"
New generic for "chartr" does not agree with implicit generic from package "base"; a new generic will be assigned with package "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"
Creating a new generic function for "unlist" in "Biostrings"
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "eq" no definition for class: "BioString"
** help
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \description
Note: removing empty section \details
Note: removing empty section \description
Note: removing empty section \examples
>>> 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
Biostrings-internals text html latex
DNAString-class text html latex example
GENETIC_CODE text html latex example
IRanges-class text html latex example
IRanges-utils text html latex example
IUPAC_CODE_MAP text html latex example
PDict-class text html latex example
RNAString-class text html latex example
XString-class text html latex example
XStringAlign-class text html latex example
XStringPartialMatches-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
findPalindromes text html latex example
gregexpr2 text html latex example
letter text html latex example
mask 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
matchPattern text html latex example
matchProbePair text html latex example
needwunsQS text html latex example
pmatchPattern text html latex example
readFASTA text html latex example
replaceLetterAtLoc text html latex example
reverseComplement text html latex example
subXString text html latex example
substitution_matrices text html latex example
toComplex text html latex
yeastSEQCHR1 text html latex example
** building package indices ...
* DONE (Biostrings)