Biostrings 2.8.17
H. Pages
| Snapshot Date: 2008-08-08 00:12:03 -0700 (Fri, 08 Aug 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/Biostrings | | Last Changed Rev: 32289 / Revision: 33132 | | Last Changed Date: 2008-06-14 08:43:15 -0700 (Sat, 14 Jun 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | [ OK ] | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
* checking for file 'Biostrings/DESCRIPTION' ... OK
* preparing 'Biostrings':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
installing R.css in E:/biocbld/bbs-2.2-bioc/tmpdir/Rinst117631356
---------- 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 SparseList_utils.d from SparseList_utils.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 align_pairwiseAlignment.d from align_pairwiseAlignment.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 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_TBdna.d from match_TBdna.c
making match_pattern.d from match_pattern.c
making match_pattern_boyermoore.d from match_pattern_boyermoore.c
making match_pattern_shiftor.d from match_pattern_shiftor.c
making match_reporting.d from match_reporting.c
making match_utils.d from match_utils.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
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:77: 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 SparseList_utils.c -o SparseList_utils.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 align_pairwiseAlignment.c -o align_pairwiseAlignment.o
align_pairwiseAlignment.c: In function 'align_pairwiseAlignment':
align_pairwiseAlignment.c:125: warning: 'lookupValue' may be used uninitialized in this function
align_pairwiseAlignment.c:125: note: 'lookupValue' 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 inject_code.c -o inject_code.o
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:332: warning: label 'continue0' defined but not used
match_BOC.c:269: warning: unused variable 'noffsets'
match_BOC.c:269: warning: unused variable 'offsets'
match_BOC.c:269: warning: unused variable 'j'
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:289: warning: label 'continue0' defined but not used
match_BOC2.c:235: warning: unused variable 'noffsets'
match_BOC2.c:235: warning: unused variable 'offsets'
match_BOC2.c:235: warning: unused variable 'j'
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c match_PWM.c -o match_PWM.o
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_pattern.c -o match_pattern.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/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:371: warning: 'i1' may be used uninitialized in this function
match_pattern_boyermoore.c:372: warning: 'c' may be used uninitialized in this function
match_pattern_boyermoore.c:371: warning: 'j1' may be used uninitialized in this function
match_pattern_boyermoore.c:371: warning: 'i2' may be used uninitialized in this function
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c match_utils.c -o match_utils.o
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
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 SparseList_utils.o XInteger.o XRaw_class.o XRaw_utils.o XStringSet_class.o XString_class.o align_needwunsQS.o align_pairwiseAlignment.o bufutils.o char_frequency.o char_translate.o copy_seq.o find_palindromes.o inject_code.o match_BOC.o match_BOC2.o match_PWM.o match_TBdna.o match_pattern.o match_pattern_boyermoore.o match_pattern_shiftor.o match_reporting.o match_utils.o pmatchPattern.o replace_locs.o seqs_to_seqs.o utils.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 "update" 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 "append" in "Biostrings"
Creating a new generic function for "ls" in "Biostrings"
Creating a new generic function for "as.list" in "Biostrings"
Creating a new generic function for "toString" in "Biostrings"
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 "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"
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "coverage" no definition for class: "MIndex"
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 \details
Note: removing empty section \details
Note: removing empty section \examples
Note: removing empty section \details
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
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
IRanges-class text html latex example chm
IRanges-utils text html latex example chm
IUPAC_CODE_MAP text html latex example chm
MaskCollection-class text html latex example chm
MaskedXString-class 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 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
pmatchPattern text html latex example chm
read.Mask text html latex example chm
readFASTA text html latex example chm
replaceLetterAtLoc text html latex example chm
reverse 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\chm\Biostrings.chm
Compile time: 0 minutes, 2 seconds
47 Topics
1,163 Local links
1 Internet link
1 Graphic
Created e:\biocbld\bbs-2.2-bioc\meat\Biostrings\chm\Biostrings.chm, 128,569 bytes
Compression decreased file by 331,304 bytes.
adding MD5 sums
* DONE (Biostrings)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'Biostrings_2.8.17.tar.gz'