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Package 47/294HostnameOS / ArchBUILDCHECKBUILD BIN
Biostrings 2.10.22
H. Pages
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/Biostrings
Last Changed Rev: 38413 / Revision: 38965
Last Changed Date: 2009-04-02 10:19:41 -0700 (Thu, 02 Apr 2009)
wilson2 Linux (openSUSE 11.1) / x86_64  OK [ WARNINGS ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK  WARNINGS  OK 
Package: Biostrings
Version: 2.10.22
Command: /home/biocbuild/bbs-2.3-bioc/R/bin/R CMD check --no-vignettes Biostrings_2.10.22.tar.gz
StartedAt: 2009-04-18 15:05:50 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 15:10:28 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 277.4 seconds
RetCode: 0
Status: WARNINGS
CheckDir: Biostrings.Rcheck
Warnings: 1

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.3-bioc/meat/Biostrings.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: UTF-8
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.10.22'
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[[' and siglist 'ByName_MIndex'
  generic 'endIndex' and siglist 'ByName_MIndex'
  generic 'show' and siglist 'ByName_MIndex'
  generic 'startIndex' and siglist 'ByName_MIndex'
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 using pdflatex ... OK

WARNING: There was 1 warning, see
  /loc/home/biocbuild/bbs-2.3-bioc/meat/Biostrings.Rcheck/00check.log
for details

Biostrings.Rcheck/00install.out:

* Installing *source* package 'Biostrings' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function ‘align_needwunsQS’:
align_needwunsQS.c:26: warning: ‘sc’ may be used uninitialized in this function
align_needwunsQS.c:26: note: ‘sc’ was declared here
align_needwunsQS.c:39: warning: ‘lkup_val’ may be used uninitialized in this function
align_needwunsQS.c:39: note: ‘lkup_val’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c align_utils.c -o align_utils.o
align_utils.c: In function ‘PairwiseAlignedFixedSubject_align_aligned’:
align_utils.c:222: warning: ‘indelWidthSubject’ may be used uninitialized in this function
align_utils.c:222: warning: ‘indelStartSubject’ may be used uninitialized in this function
align_utils.c:222: warning: ‘indelWidthPattern’ may be used uninitialized in this function
align_utils.c:222: warning: ‘indelStartPattern’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c char_frequency.c -o char_frequency.o
char_frequency.c: In function ‘oligonucleotide_frequency’:
char_frequency.c:207: warning: ‘ans_offset’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c char_translate.c -o char_translate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c copy_seq.c -o copy_seq.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c Dups_utils.c -o Dups_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c fasta_io.c -o fasta_io.o
fasta_io.c:54: warning: ‘add_desc_LENGTHONLY’ defined but not used
fasta_io.c:89: warning: ‘add_empty_seq_CHARAEAE’ defined but not used
fasta_io.c:95: warning: ‘append_to_last_seq_CHARAEAE’ defined but not used
fasta_io.c:109: warning: ‘add_desc1’ defined but not used
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c find_palindromes.c -o find_palindromes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/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’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/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’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c match_pattern_at.c -o match_pattern_at.o
match_pattern_at.c: In function ‘_nedit_for_Proffset’:
match_pattern_at.c:292: warning: unused variable ‘Pc’
match_pattern_at.c:291: warning: unused variable ‘j’
match_pattern_at.c:291: warning: unused variable ‘jmin’
match_pattern_at.c:291: warning: unused variable ‘iplus1’
match_pattern_at.c:291: warning: unused variable ‘i’
match_pattern_at.c:291: warning: unused variable ‘b’
match_pattern_at.c:291: warning: unused variable ‘B’
match_pattern_at.c:290: warning: unused variable ‘row_length’
match_pattern_at.c:290: warning: unused variable ‘curr_row’
match_pattern_at.c:290: warning: unused variable ‘prev_row’
match_pattern_at.c:290: warning: unused variable ‘max_nedit_plus1’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
match_pattern_boyermoore.c: In function ‘_match_pattern_boyermoore’:
match_pattern_boyermoore.c:374: warning: ‘c’ may be used uninitialized in this function
match_pattern_boyermoore.c:373: warning: ‘j1’ may be used uninitialized in this function
match_pattern_boyermoore.c:373: warning: ‘i2’ may be used uninitialized in this function
match_pattern_boyermoore.c:373: warning: ‘i1’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c match_pattern_indels.c -o match_pattern_indels.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c match_pdict_ACtree.c -o match_pdict_ACtree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c match_pdict.c -o match_pdict.o
match_pdict.c: In function ‘XStringSet_vmatch_pdict’:
match_pdict.c:359: warning: ‘ans’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function ‘walk_subject’:
match_pdict_Twobit.c:187: warning: ‘twobit_sign’ may be used uninitialized in this function
match_pdict_Twobit.c: In function ‘build_Twobit’:
match_pdict_Twobit.c:132: warning: ‘twobit_sign2pos’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c MIndex_utils.c -o MIndex_utils.o
MIndex_utils.c: In function ‘ByName_MIndex_endIndex’:
MIndex_utils.c:220: warning: unused variable ‘poffsets_order’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c replace_letter_at.c -o replace_letter_at.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c RoSeq_utils.c -o RoSeq_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c utils.c -o utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c XString_class.c -o XString_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include"   -fpic  -g -O2 -Wall -c XStringSet_class.c -o XStringSet_class.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Biostrings.so align_needwunsQS.o align_pairwiseAlignment.o align_utils.o char_frequency.o char_translate.o copy_seq.o Dups_utils.o fasta_io.o find_palindromes.o inject_code.o IRanges_stubs.o match_BOC2.o match_BOC.o match_pattern_at.o match_pattern_boyermoore.o match_pattern.o match_pattern_indels.o match_pattern_shiftor.o match_pdict_ACtree2.o match_pdict_ACtree.o match_pdict.o match_pdict_Twobit.o match_PWM.o match_reporting.o MIndex_utils.o pmatchPattern.o PreprocessedTB_class.o replace_letter_at.o R_init_Biostrings.o RoSeq_utils.o SparseList_utils.o utils.o XString_class.o XStringSet_class.o   -L/home/biocbuild/bbs-2.3-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: IRanges

Attaching package: 'IRanges'


	The following object(s) are masked from package:base :

	 cbind,
	 rbind,
	 sapply 

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 "XStringSet" no definition for class: "AsIs"
Creating a generic for "order" in package  "Biostrings"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ:  (...), (na.last, decreasing))
Creating a new generic function for "sort" in "Biostrings"
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "BStringViews" no definition for class: "file"
Creating a generic for "substr" in package  "Biostrings"
    (the supplied definition differs from and overrides the implicit generic in package "base": Formal arguments differ (in default values?))
Creating a generic for "substring" in package  "Biostrings"
    (the supplied definition differs from and overrides the implicit generic in package "base": Formal arguments differ (in default values?))
Creating a generic for "chartr" in package  "Biostrings"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ:  (x), (old, new, x))
Creating a new generic function for "ls" in "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"
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
  AlignedXStringSet-class           text    html    latex   example
  BOC_SubjectString-class           text    html    latex
  Biostrings-internals              text    html    latex
  DNAString-class                   text    html    latex   example
  GENETIC_CODE                      text    html    latex   example
  IUPAC_CODE_MAP                    text    html    latex   example
Note: removing empty section \examples in file 'InDel-class.Rd'
  InDel-class                       text    html    latex
  MIndex-class                      text    html    latex   example
  MaskedXString-class               text    html    latex   example
  PDict-class                       text    html    latex   example
  PairwiseAlignedFixedSubject-class text    html    latex   example
  QualityScaledXStringSet-class     text    html    latex   example
  RNAString-class                   text    html    latex   example
  XString-class                     text    html    latex   example
  XStringPartialMatches-class       text    html    latex
  XStringQuality-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
  chartr                            text    html    latex   example
  findPalindromes                   text    html    latex   example
  gregexpr2                         text    html    latex   example
  injectHardMask                    text    html    latex   example
  letter                            text    html    latex   example
  maskMotif                         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
  matchPWM                          text    html    latex   example
  matchPattern                      text    html    latex   example
  matchProbePair                    text    html    latex   example
  needwunsQS                        text    html    latex   example
  pairwiseAlignment                 text    html    latex   example
  phiX174Phage                      text    html    latex   example
  pid                               text    html    latex   example
  pmatchPattern                     text    html    latex
  readFASTA                         text    html    latex   example
  replaceLetterAt                   text    html    latex   example
  reverse                           text    html    latex   example
  stringDist                        text    html    latex   example
  subXString                        text    html    latex
  substitution_matrices             text    html    latex   example
  toComplex                         text    html    latex   example
  translate                         text    html    latex   example
  yeastSEQCHR1                      text    html    latex   example
** building package indices ...
* DONE (Biostrings)