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NOTES: (1) a maintainance reboot of lemming prevented these builds to complete on this machine (2) these are the last builds with R 2.6.0 (2007-06-03 r41797) on lamb1 and lemming, next builds will be with R 2.6.0 (2007-06-10 r41908) configured with --enable-strict-barrier
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Biostrings

2.5.9

H. Pages
Last Changed Date: 2007-06-06 03:57:52 -0700
Last Changed Rev: 25216
lamb1 Linux (SUSE 10.1) x86_64  OK  WARNINGS 
wellington Linux (SUSE 9.2) i686  OK  WARNINGS 
churchill Solaris 2.9 sparc  OK [ WARNINGS ]
lemming Windows Server 2003 (32-bit) x64  OK  WARNINGS skipped
Package: Biostrings
Version: 2.5.9
Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check Biostrings_2.5.9.tar.gz
RetCode: 0
Time: 252.1 seconds
Status: WARNINGS
CheckDir: Biostrings.Rcheck
Warnings: 2

Command output

* checking for working latex ... OK
* using log directory '/loc/biocbuild/bbs-2.1-bioc/meat/Biostrings.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-06-03 r41797)
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.5.9'
* 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:
       missing link(s):  scoring\_matrices
See '/loc/biocbuild/bbs-2.1-bioc/meat/Biostrings.Rcheck/00install.out' for details.
* 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 ... NOTE
testBiostrings: no visible global function definition for
  'defineTestSuite'
testBiostrings: no visible global function definition for
  'runTestSuite'
testBiostrings: no visible global function definition for
  'printTextProtocol'
* checking Rd files ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object 'needwunsQS.Rd':
  scoring\_matrices

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... 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 2 warnings, see
  /loc/biocbuild/bbs-2.1-bioc/meat/Biostrings.Rcheck/00check.log
for details

Biostrings.Rcheck/00install.out:

* Installing *source* package 'Biostrings' ...
** libs
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-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/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c XInteger.c -o XInteger.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c XRaw.c -o XRaw.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-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:25: warning: 'sc' may be used uninitialized in this function
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c char_frequency.c -o char_frequency.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-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: 'c' may be used uninitialized in this function
match_boyermoore.c:370: warning: 'j1' may be used uninitialized in this function
match_boyermoore.c:370: warning: 'i2' may be used uninitialized in this function
match_boyermoore.c:370: warning: 'i1' may be used uninitialized in this function
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c match_naive.c -o match_naive.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c match_shiftor.c -o match_shiftor.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c reverseComplement.c -o reverseComplement.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-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:479: warning: 'lkup_val.r' may be used uninitialized in this function
utils.c:479: warning: 'lkup_val.i' may be used uninitialized in this function
utils.c: In function 'Biostrings_reverse_translate_charcpy_from_i1i2':
utils.c:437: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function 'Biostrings_translate_charcpy_to_subset':
utils.c:358: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function 'Biostrings_translate_charcpy_to_i1i2':
utils.c:319: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function 'Biostrings_translate_charcpy_from_subset':
utils.c:279: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function 'Biostrings_translate_charcpy_from_i1i2':
utils.c:240: warning: 'lkup_val' may be used uninitialized in this function
gcc -std=gnu99 -G -L/usr/local/lib -o Biostrings.so R_init_Biostrings.o XInteger.o XRaw.o align_needwunsQS.o char_frequency.o match_boyermoore.o match_naive.o match_shiftor.o reverseComplement.o utils.o   -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** data
** inst
** preparing package 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 "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"
Creating a new generic function for "split" in "Biostrings"
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
  BString-class                     text    html    latex   example
  BStringAlign-class                text    html    latex   example
  BStringViews-class                text    html    latex
  BStringViews-constructors         text    html    latex   example
  Biostrings-internals              text    html    latex
  DNAString-class                   text    html    latex   example
  GENETIC_CODE                      text    html    latex   example
  IUPAC_CODE_MAP                    text    html    latex   example
  RNAString-class                   text    html    latex   example
  alphabetFrequency                 text    html    latex   example
  gregexpr2                         text    html    latex   example
  matchPattern                      text    html    latex   example
  matchProbePair                    text    html    latex   example
  needwunsQS                        text    html    latex   example
     missing link(s):  scoring\_matrices
  readFASTA                         text    html    latex   example
  reverseComplement                 text    html    latex   example
  scoring_matrices                  text    html    latex   example
  toComplex                         text    html    latex   example
  yeastSEQCHR1                      text    html    latex   example
** building package indices ...
* DONE (Biostrings)