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Package 39/251HostnameOS / ArchBUILDCHECKBUILD BIN
Biostrings 2.7.6
H. Pages
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biostrings
Last Changed Rev: 29007 / Revision: 29143
Last Changed Date: 2007-12-03 14:37:37 -0800 (Mon, 03 Dec 2007)
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 
lemming Windows Server 2003 (32-bit) / x64  OK [ WARNINGS ] OK 
Package: Biostrings
Version: 2.7.6
Command: D:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD check Biostrings_2.7.6.tar.gz
StartedAt: 2007-12-11 05:32:30 -0700 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 05:35:52 -0700 (Tue, 11 Dec 2007)
EllapsedTime: 202.2 seconds
RetCode: 0
Status: WARNINGS
CheckDir: Biostrings.Rcheck
Warnings: 4

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.2-bioc/meat/Biostrings.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.7.6'
* 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
  match_ULdna.c:341: warning: 'ans' is used uninitialized in this function
See 'D:/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
.read.uncompressed_fasta_file: no visible binding for global variable
  'i'
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 S4 classes:
  BOC_SubjectString BOC2_SubjectString PDict ULdna_PDict
Undocumented S4 methods:
  generic 'countPattern' and siglist 'BOC2_SubjectString'
  generic 'initialize' and siglist 'BOC_SubjectString'
  generic 'initialize' and siglist 'BOC2_SubjectString'
  generic 'initialize' and siglist 'ULdna_PDict'
  generic 'length' and siglist 'ULdna_PDict'
  generic 'matchPattern' and siglist 'BOC_SubjectString'
  generic 'matchPattern' and siglist 'BOC2_SubjectString'
  generic 'nchar' and siglist 'ULdna_PDict'
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 ... OK

WARNING: There were 4 warnings, see
  D:/biocbld/bbs-2.2-bioc/meat/Biostrings.Rcheck/00check.log
for details

Biostrings.Rcheck/00install.out:

installing R.css in D:/biocbld/bbs-2.2-bioc/meat/Biostrings.Rcheck


---------- Making package Biostrings ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making R_init_Biostrings.d from R_init_Biostrings.c
making XInteger.d from XInteger.c
making XRaw.d from XRaw.c
making align_needwunsQS.d from align_needwunsQS.c
making char_frequency.d from char_frequency.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_ULdna.d from match_ULdna.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 reverseComplement.d from reverseComplement.c
making utils.d from utils.c
making views_buffer.d from views_buffer.c
gcc  -std=gnu99  -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc  -std=gnu99  -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c XInteger.c -o XInteger.o
gcc  -std=gnu99  -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c XRaw.c -o XRaw.o
XRaw.c: In function 'XRaw_loadFASTA':
XRaw.c:701: warning: 'view_start' may be used uninitialized in this function
gcc  -std=gnu99  -Id:/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  -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c char_frequency.c -o char_frequency.o
gcc  -std=gnu99  -Id:/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  -Id:/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  -Id:/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  -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c match_ULdna.c -o match_ULdna.o
match_ULdna.c:293: warning: 'ULdna_exact_search' defined but not used
match_ULdna.c: In function 'ULdna_init_with_BStringList':
match_ULdna.c:341: warning: 'ans' is used uninitialized in this function
gcc  -std=gnu99  -Id:/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  -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c match_naive.c -o match_naive.o
gcc  -std=gnu99  -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c match_shiftor.c -o match_shiftor.o
gcc  -std=gnu99  -Id:/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  -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c pmatchPattern.c -o pmatchPattern.o
gcc  -std=gnu99  -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c reverseComplement.c -o reverseComplement.o
gcc  -std=gnu99  -Id:/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:478: warning: 'lkup_val.r' may be used uninitialized in this function
utils.c:478: warning: 'lkup_val.i' may be used uninitialized in this function
utils.c: In function '_Biostrings_reverse_translate_charcpy_from_i1i2':
utils.c:436: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function '_Biostrings_translate_charcpy_to_subset':
utils.c:357: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function '_Biostrings_translate_charcpy_to_i1i2':
utils.c:318: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function '_Biostrings_translate_charcpy_from_subset':
utils.c:278: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function '_Biostrings_translate_charcpy_from_i1i2':
utils.c:239: warning: 'lkup_val' may be used uninitialized in this function
gcc  -std=gnu99  -Id:/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 d:/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 R_init_Biostrings.o XInteger.o XRaw.o align_needwunsQS.o char_frequency.o find_palindromes.o match_BOC.o match_BOC2.o match_ULdna.o match_boyermoore.o match_naive.o match_shiftor.o normalize_views.o pmatchPattern.o reverseComplement.o utils.o views_buffer.o Biostrings_res.o  -Ld:/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 "toString" in "Biostrings"
Creating a new generic function for "nchar" in "Biostrings"
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.matrix" 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"
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"
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
  BString-class                     text    html    latex   example chm
  BStringAlign-class                text    html    latex   example chm
  BStringPartialMatches-class       text    html    latex   example chm
  BStringViews-class                text    html    latex   example chm
  BStringViews-constructors         text    html    latex   example chm
  BStringViews-io                   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
  IUPAC_CODE_MAP                    text    html    latex   example chm
  RNAString-class                   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
  matchLRPatterns                   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
  reverseComplement                 text    html    latex   example chm
  scoring_matrices                  text    html    latex   example chm
  subBString                        text    html    latex   example chm
  toComplex                         text    html    latex           chm
  yeastSEQCHR1                      text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.2-bioc\meat\Biostrings.Rcheck\00_pkg_src\Biostrings\chm\Biostrings.chm


Compile time: 0 minutes, 0 seconds
31	Topics
530	Local links
1	Internet link
1	Graphic


Created d:\biocbld\bbs-2.2-bioc\meat\Biostrings.Rcheck\00_pkg_src\Biostrings\chm\Biostrings.chm, 68,279 bytes
Compression decreased file by 130,139 bytes.
  adding MD5 sums

* DONE (Biostrings)