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 'E:/biocbld/bbs-2.2-bioc/meat/Biostrings.Rcheck'
* using R version 2.7.0 Under development (unstable) (2008-03-10 r44730)
* 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 ... WARNING
Found the following significant warnings:
match_BOC.c:38: warning: 'pre4' is used uninitialized in this function
match_BOC2.c:54: warning: 'pre4' is used uninitialized in this function
See 'E:/biocbld/bbs-2.2-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 ... 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:
BOC_SubjectString BOC2_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 5 warnings, see
E:/biocbld/bbs-2.2-bioc/meat/Biostrings.Rcheck/00check.log
for details
installing R.css in E:/biocbld/bbs-2.2-bioc/meat/Biostrings.Rcheck
---------- Making package Biostrings ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making ACtree_utils.d from ACtree_utils.c
making IRanges_class.d from IRanges_class.c
making IRanges_utils.d from IRanges_utils.c
making MIndex_utils.d from MIndex_utils.c
making R_init_Biostrings.d from R_init_Biostrings.c
making XInteger.d from XInteger.c
making XRaw_class.d from XRaw_class.c
making XRaw_utils.d from XRaw_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 bufutils.d from bufutils.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 find_palindromes.d from find_palindromes.c
making match_BOC.d from match_BOC.c
making match_BOC2.d from match_BOC2.c
making match_TBdna.d from match_TBdna.c
making match_boyermoore.d from match_boyermoore.c
making match_naive.d from match_naive.c
making match_shiftor.d from match_shiftor.c
making normalize_views.d from normalize_views.c
making pmatchPattern.d from pmatchPattern.c
making replace_locs.d from replace_locs.c
making seqs_to_seqs.d from seqs_to_seqs.c
making utils.d from utils.c
making views_buffer.d from views_buffer.c
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c ACtree_utils.c -o ACtree_utils.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -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 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -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 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c XInteger.c -o XInteger.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c XRaw_class.c -o XRaw_class.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -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 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c XStringSet_class.c -o XStringSet_class.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c XString_class.c -o XString_class.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -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 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c bufutils.c -o bufutils.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -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 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c char_translate.c -o char_translate.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c copy_seq.c -o copy_seq.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/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-2.2-bioc/R/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'
match_BOC.c: In function 'match_BOC_preprocess':
match_BOC.c:29: warning: 'pre4' may be used uninitialized in this function
match_BOC.c:29: note: 'pre4' was declared here
match_BOC.c: In function 'match_BOC_exact':
match_BOC.c:38: warning: 'pre4' is used uninitialized in this function
match_BOC.c:29: note: 'pre4' was declared here
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/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'
match_BOC2.c: In function 'match_BOC2_exact':
match_BOC2.c:54: warning: 'pre4' is used uninitialized in this function
match_BOC2.c:45: note: 'pre4' was declared here
match_BOC2.c: In function 'match_BOC2_preprocess':
match_BOC2.c:45: warning: 'pre4' may be used uninitialized in this function
match_BOC2.c:45: note: 'pre4' was declared here
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c match_TBdna.c -o match_TBdna.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c match_boyermoore.c -o match_boyermoore.o
match_boyermoore.c: In function 'match_boyermoore':
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: 'i2' may be used uninitialized in this function
match_boyermoore.c:371: note: 'i2' 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 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c match_naive.c -o match_naive.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c match_shiftor.c -o match_shiftor.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c normalize_views.c -o normalize_views.o
normalize_views.c:49: warning: 'normalize_orderedbystartviews' defined but not used
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c replace_locs.c -o replace_locs.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -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 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -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 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c views_buffer.c -o views_buffer.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include -i Biostrings_res.rc -o Biostrings_res.o
gcc -std=gnu99 -shared -s -o Biostrings.dll Biostrings.def ACtree_utils.o IRanges_class.o IRanges_utils.o MIndex_utils.o R_init_Biostrings.o XInteger.o XRaw_class.o XRaw_utils.o XStringSet_class.o XString_class.o align_needwunsQS.o bufutils.o char_frequency.o char_translate.o copy_seq.o find_palindromes.o match_BOC.o match_BOC2.o match_TBdna.o match_boyermoore.o match_naive.o match_shiftor.o normalize_views.o pmatchPattern.o replace_locs.o seqs_to_seqs.o utils.o views_buffer.o Biostrings_res.o -Le:/biocbld/bbs-2.2-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
installing data files
preparing package Biostrings 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"
installing man source files
installing indices
not zipping data
installing help
Note: removing empty section \details
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 \details
Note: removing empty section \description
Note: removing empty section \examples
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 chm
AAString-class text html latex example chm
AMINO_ACID_CODE text html latex example chm
Biostrings-internals text html latex chm
DNAString-class text html latex example chm
GENETIC_CODE text html latex example chm
IRanges-class text html latex example chm
IRanges-utils text html latex example chm
IUPAC_CODE_MAP text html latex example chm
PDict-class text html latex example chm
RNAString-class text html latex example chm
XString-class text html latex example chm
XStringAlign-class text html latex example chm
XStringPartialMatches-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
findPalindromes text html latex example chm
gregexpr2 text html latex example chm
letter text html latex example chm
mask 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
matchPattern text html latex example chm
matchProbePair text html latex example chm
needwunsQS text html latex example chm
pmatchPattern text html latex example chm
readFASTA text html latex example chm
replaceLetterAtLoc text html latex example chm
reverseComplement text html latex example chm
subXString text html latex example chm
substitution_matrices text html latex example chm
toComplex text html latex chm
yeastSEQCHR1 text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.2-bioc\meat\Biostrings.Rcheck\00_pkg_src\Biostrings\chm\Biostrings.chm
Compile time: 0 minutes, 1 second
39 Topics
843 Local links
1 Internet link
1 Graphic
Created e:\biocbld\bbs-2.2-bioc\meat\Biostrings.Rcheck\00_pkg_src\Biostrings\chm\Biostrings.chm, 101,361 bytes
Compression decreased file by 235,705 bytes.
adding MD5 sums
* DONE (Biostrings)