Back to the "Multiple platform build/check report" A [B] C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 76/609HostnameOS / ArchBUILDCHECKBUILD BIN
Biostrings 2.26.3
H. Pages
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/Biostrings
Last Changed Rev: 72941 / Revision: 74773
Last Changed Date: 2013-01-25 16:51:14 -0800 (Fri, 25 Jan 2013)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 

Summary

Package: Biostrings
Version: 2.26.3
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biostrings_2.26.3.tar.gz
StartedAt: 2013-03-24 22:44:58 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 22:57:07 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 728.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Biostrings.Rcheck
Warnings: 3

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/Biostrings.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.26.3'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'Biostrings' can be installed ... WARNING
Found the following significant warnings:
  XStringSet_io.c:368: warning: 'loader_ext.cached_ans_elt.length' is used uninitialized in this function
  XStringSet_io.c:368: warning: 'loader_ext.cached_ans_elt.seq' is used uninitialized in this function
  xscat.c:94: warning: 'ans_length' is used uninitialized in this function
  xscat.c:36: warning: 'ans_length' is used uninitialized in this function
See '/Users/biocbuild/bbs-2.11-bioc/meat/Biostrings.Rcheck/00install.out' for details.
* checking installed package size ... 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 for left-over 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 package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object '/Users/biocbuild/bbs-2.11-bioc/meat/Biostrings.Rcheck/00_pkg_src/Biostrings/man/MaskedXString-class.Rd':
  '[IRanges]{Ranges-utils}'

Missing link(s) in documentation object '/Users/biocbuild/bbs-2.11-bioc/meat/Biostrings.Rcheck/00_pkg_src/Biostrings/man/MultipleAlignment-class.Rd':
  '[IRanges:Ranges-utils]{narrow}'

See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'splitAsListReturnedClass' and siglist 'AAStringSet'
  generic 'splitAsListReturnedClass' and siglist 'BStringSet'
  generic 'splitAsListReturnedClass' and siglist 'DNAStringSet'
  generic 'splitAsListReturnedClass' and siglist 'RNAStringSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
matchPDict-exact      342.525  7.828 356.644
matchPDict-inexact     68.588  2.636  73.850
XStringSet-class       10.884  2.108  13.271
XStringSet-io          11.346  1.610  13.299
stringDist              9.942  0.244  10.868
PDict-class             9.529  0.627  10.270
findPalindromes         8.283  0.108   8.486
XStringSet-comparison   5.191  1.561   7.160
PairwiseAlignments-io   3.434  1.359   5.317
matchPattern            4.499  0.209   5.465
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 3 warnings.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/Biostrings.Rcheck/00check.log'
for details.

Biostrings.Rcheck/00install.out:

* installing *source* package 'Biostrings' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c BAB_class.c -o BAB_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c BitMatrix.c -o BitMatrix.o
BitMatrix.c: In function 'debug_BitMatrix':
BitMatrix.c:382: warning: left shift count >= width of type
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function 'SparseMIndex_endIndex':
MIndex_class.c:192: warning: unused variable 'poffsets_order'
MIndex_class.c: In function '_get_cachedMIndex_elt':
MIndex_class.c:93: warning: 'cached_iranges.end' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c SparseList_utils.c -o SparseList_utils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
XStringSet_class.c:92: warning: 'lkup_length' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function 'parse_FASTQ_file':
XStringSet_io.c:594: warning: 'load_record' may be used uninitialized in this function
XStringSet_io.c: In function 'read_fastq_in_XStringSet':
XStringSet_io.c:558: warning: 'loader_ext.lkup_length' may be used uninitialized in this function
XStringSet_io.c:558: note: 'loader_ext.lkup_length' was declared here
XStringSet_io.c: In function 'fasta_info':
XStringSet_io.c:113: warning: 'loader.lkup_length' may be used uninitialized in this function
XStringSet_io.c:113: note: 'loader.lkup_length' was declared here
XStringSet_io.c: In function 'read_fasta_in_XStringSet':
XStringSet_io.c:368: warning: 'loader_ext.cached_ans_elt.length' is used uninitialized in this function
XStringSet_io.c:368: warning: 'loader_ext.cached_ans_elt.seq' is used uninitialized in this function
XStringSet_io.c:177: warning: 'loader.lkup_length' may be used uninitialized in this function
XStringSet_io.c:177: note: 'loader.lkup_length' was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c XString_class.c -o XString_class.o
XString_class.c: In function 'new_XString_from_CHARACTER':
XString_class.c:162: warning: 'lkup_length' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -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 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignmentsSingleSubject_align_aligned':
align_utils.c:223: warning: 'indelWidthSubject' may be used uninitialized in this function
align_utils.c:223: warning: 'indelStartSubject' may be used uninitialized in this function
align_utils.c:223: warning: 'indelWidthPattern' may be used uninitialized in this function
align_utils.c:223: warning: 'indelStartPattern' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c find_palindromes.c -o find_palindromes.o
find_palindromes.c: In function 'find_palindromes':
find_palindromes.c:26: warning: 'letter0' may be used uninitialized in this function
find_palindromes.c:26: note: 'letter0' was declared here
find_palindromes.c:25: warning: 'all_letter0' may be used uninitialized in this function
find_palindromes.c:25: note: 'all_letter0' was declared here
find_palindromes.c:82: warning: 'letter0' may be used uninitialized in this function
find_palindromes.c:82: note: 'letter0' was declared here
find_palindromes.c:81: warning: 'lkup_val' may be used uninitialized in this function
find_palindromes.c:81: note: 'lkup_val' was declared here
find_palindromes.c:81: warning: 'all_letter0' may be used uninitialized in this function
find_palindromes.c:81: note: 'all_letter0' was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c gtestsim.c -o gtestsim.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c inject_code.c -o inject_code.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c io_utils.c -o io_utils.o
io_utils.c: In function 'open_input_file':
io_utils.c:70: warning: unused variable 'buf'
io_utils.c:69: warning: unused variable 'ret'
io_utils.c: In function 'new_input_ExternalFilePtr':
io_utils.c:68: warning: 'fp' may be used uninitialized in this function
io_utils.c:68: note: 'fp' was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c letter_frequency.c -o letter_frequency.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c lowlevel_matching.c -o lowlevel_matching.o
lowlevel_matching.c: In function 'XStringSet_vmatch_pattern_at':
lowlevel_matching.c:586: warning: 'ans' may be used uninitialized in this function
lowlevel_matching.c:584: warning: 'ans_nrow' may be used uninitialized in this function
lowlevel_matching.c:584: warning: 'ans_elt' may be used uninitialized in this function
lowlevel_matching.c: In function 'XString_match_pattern_at':
lowlevel_matching.c:536: warning: 'ans' may be used uninitialized in this function
lowlevel_matching.c:534: warning: 'ans_elt' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_BOC.c -o match_BOC.o
match_BOC.c: In function 'BOC_preprocess':
match_BOC.c:82: warning: overflow in implicit constant conversion
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 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -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 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_PWM.c -o match_PWM.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_pattern.c -o match_pattern.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
match_pattern_boyermoore.c: In function '_match_pattern_boyermoore':
match_pattern_boyermoore.c:401: warning: 'c' may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: 'j1' may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: 'i2' may be used uninitialized in this function
match_pattern_boyermoore.c:399: warning: 'i1' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_pattern_indels.c -o match_pattern_indels.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_pdict.c -o match_pdict.o
match_pdict.c: In function 'init_vcount_collapsed_ans':
match_pdict.c:110: warning: 'ans_length' may be used uninitialized in this function
match_pdict.c: In function 'vmatch_XStringSet_XStringSet':
match_pdict.c:463: warning: 'ans_elt' may be used uninitialized in this function
match_pdict.c:463: note: 'ans_elt' was declared here
match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet':
match_pdict.c:414: warning: 'ans_col' may be used uninitialized in this function
match_pdict.c:414: note: 'ans_col' was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c:641: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function 'build_Twobit':
match_pdict_Twobit.c:125: warning: 'twobit_sign2pos' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function 'match_ppheadtail0':
match_pdict_utils.c:664: warning: unused variable 'ncol'
match_pdict_utils.c: In function 'match_ppheadtail':
match_pdict_utils.c:722: warning: unused variable 'nelt'
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:821: warning: unused variable 'subtotal_NFC'
match_pdict_utils.c:821: warning: unused variable 'total_NFC'
match_pdict_utils.c:820: warning: unused variable 'NFC'
match_pdict_utils.c:820: warning: unused variable 'nloci'
match_pdict_utils.c:820: warning: unused variable 'ndup'
match_pdict_utils.c: At top level:
match_pdict_utils.c:279: warning: 'match_headtail_by_loc' defined but not used
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c match_reporting.c -o match_reporting.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c matchprobes.c -o matchprobes.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c pmatchPattern.c -o pmatchPattern.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c replace_letter_at.c -o replace_letter_at.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c strutils.c -o strutils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c translate.c -o translate.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature_at':
utils.c:210: warning: 'twobit_sign' may be used uninitialized in this function
utils.c: In function '_get_twobit_signature':
utils.c:196: warning: 'twobit_sign' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c xscat.c -o xscat.o
xscat.c: In function 'XStringSet_xscat':
xscat.c:94: warning: 'ans_length' is used uninitialized in this function
xscat.c:70: warning: 'ans_element_type' may be used uninitialized in this function
xscat.c: In function 'XString_xscat':
xscat.c:36: warning: 'ans_length' is used uninitialized in this function
xscat.c:18: warning: 'ans_classname' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o SparseList_utils.o XStringSet_class.o XStringSet_io.o XString_class.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o io_utils.o letter_frequency.o lowlevel_matching.o match_BOC.o match_BOC2.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replace_letter_at.o strutils.o translate.o utils.o xscat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/Biostrings.Rcheck/Biostrings/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'setequal' from package 'base' in package 'Biostrings'
Creating a generic function for 'ls' from package 'base' in package 'Biostrings'
Creating a new generic function for 'offset' in package 'Biostrings'
** help
*** installing help indices
** building package indices
** installing vignettes
   'Biostrings2Classes.Rnw' 
   'MultipleAlignments.Rnw' 
   'PairwiseAlignments.Rnw' 
   'matchprobes.Rnw' 
** testing if installed package can be loaded

* DONE (Biostrings)

Biostrings.Rcheck/Biostrings-Ex.timings:

nameusersystemelapsed
AAString-class0.0070.0000.007
AMINO_ACID_CODE0.0030.0000.003
AlignedXStringSet-class0.2150.0080.224
DNAString-class0.0020.0010.003
FASTA-io-legacy0.0000.0010.000
GENETIC_CODE0.0040.0010.005
HNF4alpha0.0460.0020.048
IUPAC_CODE_MAP0.0090.0000.010
MIndex-class0.0000.0010.000
MaskedXString-class0.4570.0210.523
MultipleAlignment-class2.4640.0262.503
PDict-class 9.529 0.62710.270
PairwiseAlignments-class0.2560.0270.310
PairwiseAlignments-io3.4341.3595.317
QualityScaledXStringSet-class0.0280.0010.029
RNAString-class0.0140.0010.015
XString-class0.0170.0010.018
XStringQuality-class0.1340.0010.135
XStringSet-class10.884 2.10813.271
XStringSet-comparison5.1911.5617.160
XStringSet-io11.346 1.61013.299
XStringSetList-class0.1910.0160.207
XStringViews-class0.3020.0270.330
align-utils0.0580.0040.062
chartr1.1720.0921.281
detail1.5620.0701.809
dinucleotideFrequencyTest0.0200.0080.028
findPalindromes8.2830.1088.486
getSeq0.0920.0270.123
gregexpr20.0020.0000.003
injectHardMask0.0810.0190.102
letter0.0200.0040.025
letterFrequency2.1840.6062.890
longestConsecutive000
lowlevel-matching0.7210.2001.022
maskMotif2.0040.3122.388
match-utils0.0410.0010.042
matchLRPatterns0.7900.0680.886
matchPDict-exact342.525 7.828356.644
matchPDict-inexact68.588 2.63673.850
matchPWM3.2200.0433.411
matchPattern4.4990.2095.465
matchProbePair2.0730.0792.282
matchprobes0.4800.0330.583
misc0.0180.0020.021
needwunsQS0.0000.0010.000
nucleotideFrequency1.3410.1851.722
pairwiseAlignment0.9570.6222.060
phiX174Phage0.7270.2541.262
pid0.4790.3711.036
replaceLetterAt0.8460.3741.596
reverseComplement2.6080.8374.485
stringDist 9.942 0.24410.868
substitution_matrices0.6120.3341.356
toComplex0.0020.0000.002
translate1.6400.0441.837
trimLRPatterns0.1190.0010.156
xscat2.7360.4923.505
yeastSEQCHR10.0040.0020.006