BioC 3.0: CHECK report for Biostrings on zin1

Package: Biostrings

Version: 2.34.1

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings Biostrings_2.34.1.tar.gz

StartedAt: 2015-04-09 22:00:54 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 22:11:35 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 641.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biostrings.Rcheck

Warnings: 2

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###
### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings Biostrings_2.34.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/Biostrings.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biostrings/DESCRIPTION’ ... OK
* this is package ‘Biostrings’ version ‘2.34.1’
* 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 for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Biostrings’ can be installed ... [20s/20s] OK
* checking installed package size ... NOTE
  installed size is 14.9Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata  11.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘BiocGenerics’ ‘IRanges’ ‘XVector’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’ ‘IRanges:::.showAtomicList’
  ‘IRanges:::showRangesList’
  See the note in ?`:::` about the use of this operator.
* 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 ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘twoWayAlphabetFrequency’
Undocumented S4 methods:
  generic 'compare' and siglist 'Vector,XStringSet'
  generic 'compare' and siglist 'XStringSet,Vector'
  generic 'compare' and siglist 'XStringSet,vector'
  generic 'compare' and siglist 'vector,XStringSet'
  generic 'match' and siglist 'Vector,XStringSet'
  generic 'match' and siglist 'XStringSet,Vector'
  generic 'match' and siglist 'XStringSet,vector'
  generic 'match' and siglist 'vector,XStringSet'
  generic 'relistToClass' and siglist 'XString'
  generic 'relistToClass' and siglist 'XStringSet'
  generic 'splitAsListReturnedClass' and siglist 'XString'
  generic 'splitAsListReturnedClass' and siglist 'XStringSet'
  generic 'twoWayAlphabetFrequency' and siglist 'XString,XString'
  generic 'twoWayAlphabetFrequency' and siglist 'XString,XStringSet'
  generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XString'
  generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XStringSet'
  generic 'unstrsplit' and siglist 'XStringSet'
  generic 'unstrsplit' and siglist 'XStringSetList'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [510s/512s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
matchPDict-exact   380.531  0.604 382.772
matchPDict-inexact  40.439  0.156  40.663
findPalindromes     14.533  0.304  14.923
matchPattern        11.909  0.040  12.024
XStringSet-class     8.877  0.268   9.206
stringDist           5.776  0.004   5.788
PDict-class          5.440  0.080   5.582
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

WARNING: There were 2 warnings.
NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/Biostrings.Rcheck/00check.log’
for details.

* installing *source* package ‘Biostrings’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c BAB_class.c -o BAB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c BitMatrix.c -o BitMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function ‘SparseMIndex_endIndex’:
MIndex_class.c:193:18: warning: unused variable ‘poffsets_order’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c XStringSetList_class.c -o XStringSetList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function ‘new_XStringSet_from_CHARACTER’:
XStringSet_class.c:123:32: warning: ‘lkup_length’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function ‘parse_FASTQ_file’:
XStringSet_io.c:704:7: warning: ‘load_rec’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c XString_class.c -o XString_class.o
XString_class.c: In function ‘new_XString_from_CHARACTER’:
XString_class.c:180:31: warning: ‘lkup_length’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function ‘align_needwunsQS’:
align_needwunsQS.c:173:22: warning: ‘sc’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c align_utils.c -o align_utils.o
align_utils.c: In function ‘PairwiseAlignmentsSingleSubject_align_aligned’:
align_utils.c:254:14: warning: ‘indelWidthSubject’ may be used uninitialized in this function [-Wuninitialized]
align_utils.c:235:42: warning: ‘indelStartSubject’ may be used uninitialized in this function [-Wuninitialized]
align_utils.c:159:6: warning: ‘indelWidthPattern’ may be used uninitialized in this function [-Wuninitialized]
align_utils.c:236:50: warning: ‘indelStartPattern’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c find_palindromes.c -o find_palindromes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c gtestsim.c -o gtestsim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c io_utils.c -o io_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function ‘XStringSet_two_way_letter_frequency’:
letter_frequency.c:957:48: warning: unused variable ‘x_pos’ [-Wunused-variable]
letter_frequency.c:956:13: warning: unused variable ‘ans_dimnames’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c lowlevel_matching.c -o lowlevel_matching.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_BOC.c -o match_BOC.o
match_BOC.c: In function ‘BOC_exact_search’:
match_BOC.c:331:3: warning: label ‘continue0’ defined but not used [-Wunused-label]
match_BOC.c:268:68: warning: unused variable ‘noffsets’ [-Wunused-variable]
match_BOC.c:268:59: warning: unused variable ‘offsets’ [-Wunused-variable]
match_BOC.c:268:55: warning: unused variable ‘j’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_BOC2.c -o match_BOC2.o
match_BOC2.c: In function ‘BOC2_exact_search’:
match_BOC2.c:288:3: warning: label ‘continue0’ defined but not used [-Wunused-label]
match_BOC2.c:234:68: warning: unused variable ‘noffsets’ [-Wunused-variable]
match_BOC2.c:234:59: warning: unused variable ‘offsets’ [-Wunused-variable]
match_BOC2.c:234:55: warning: unused variable ‘j’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pattern_indels.c -o match_pattern_indels.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pdict.c -o match_pdict.o
match_pdict.c: In function ‘match_pdict’:
match_pdict.c:59:26: warning: variable ‘fixedP’ set but not used [-Wunused-but-set-variable]
match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’:
match_pdict.c:442:12: warning: ‘ans_col’ may be used uninitialized in this function [-Wuninitialized]
match_pdict.c:415:58: note: ‘ans_col’ was declared here
match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’:
match_pdict.c:493:13: warning: ‘ans_elt’ may be used uninitialized in this function [-Wuninitialized]
match_pdict.c:464:57: note: ‘ans_elt’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c: In function ‘split_and_move_pointers’:
match_pdict_ACtree2.c:1069:10: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable]
match_pdict_ACtree2.c: In function ‘merge_pointers’:
match_pdict_ACtree2.c:1114:10: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable]
match_pdict_ACtree2.c: At top level:
match_pdict_ACtree2.c:640:21: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used [-Wunused-function]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function ‘build_Twobit’:
match_pdict_Twobit.c:91:2: warning: ‘twobit_sign2pos’ may be used uninitialized in this function [-Wuninitialized]
match_pdict_Twobit.c:126:12: note: ‘twobit_sign2pos’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function ‘match_ppheadtail0’:
match_pdict_utils.c:665:49: warning: unused variable ‘ncol’ [-Wunused-variable]
match_pdict_utils.c: In function ‘match_ppheadtail’:
match_pdict_utils.c:723:6: warning: unused variable ‘nelt’ [-Wunused-variable]
match_pdict_utils.c: In function ‘_match_pdict_all_flanks’:
match_pdict_utils.c:823:44: warning: unused variable ‘subtotal_NFC’ [-Wunused-variable]
match_pdict_utils.c:823:27: warning: unused variable ‘total_NFC’ [-Wunused-variable]
match_pdict_utils.c:822:33: warning: unused variable ‘NFC’ [-Wunused-variable]
match_pdict_utils.c:822:26: warning: unused variable ‘nloci’ [-Wunused-variable]
match_pdict_utils.c:822:20: warning: unused variable ‘ndup’ [-Wunused-variable]
match_pdict_utils.c: At top level:
match_pdict_utils.c:275:13: warning: ‘match_headtail_by_loc’ defined but not used [-Wunused-function]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c matchprobes.c -o matchprobes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c replace_letter_at.c -o replace_letter_at.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c strutils.c -o strutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c translate.c -o translate.o
translate.c: In function ‘DNAStringSet_translate’:
translate.c:101:8: warning: ‘if_ambig0’ may be used uninitialized in this function [-Wuninitialized]
translate.c:126:29: note: ‘if_ambig0’ was declared here
translate.c:97:8: warning: ‘if_non_ambig0’ may be used uninitialized in this function [-Wuninitialized]
translate.c:126:14: note: ‘if_non_ambig0’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c utils.c -o utils.o
utils.c: In function ‘_get_twobit_signature’:
utils.c:210:2: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wuninitialized]
utils.c: In function ‘_get_twobit_signature_at’:
utils.c:217:12: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c xscat.c -o xscat.o
xscat.c: In function ‘XString_xscat’:
xscat.c:38:2: warning: ‘ans_length’ may be used uninitialized in this function [-Wuninitialized]
xscat.c:52:2: warning: ‘ans_classname’ may be used uninitialized in this function [-Wuninitialized]
xscat.c: In function ‘XStringSet_xscat’:
xscat.c:92:2: warning: ‘ans_length’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -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 S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.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 unstrsplit_methods.o utils.o xscat.o -lz -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/Biostrings.Rcheck/Biostrings/libs
** 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
** testing if installed package can be loaded
* DONE (Biostrings)

name	user	system	elapsed
AAString-class	0.008	0.000	0.006
AMINO_ACID_CODE	0.004	0.000	0.003
AlignedXStringSet-class	0.072	0.000	0.070
DNAString-class	0.004	0.000	0.002
GENETIC_CODE	0.012	0.000	0.012
HNF4alpha	0.140	0.000	0.142
IUPAC_CODE_MAP	0.008	0.000	0.007
MIndex-class	0.000	0.000	0.001
MaskedXString-class	0.352	0.000	0.358
MultipleAlignment-class	1.468	0.008	1.507
PDict-class	5.440	0.080	5.582
PairwiseAlignments-class	0.184	0.016	0.199
PairwiseAlignments-io	2.388	0.032	2.422
QualityScaledXStringSet-class	0.016	0.000	0.017
RNAString-class	0.008	0.000	0.008
XString-class	0.008	0.000	0.010
XStringQuality-class	0.064	0.000	0.062
XStringSet-class	8.877	0.268	9.206
XStringSet-comparison	2.888	0.040	2.936
XStringSet-io	3.512	0.052	3.571
XStringSetList-class	0.404	0.008	0.412
XStringViews-class	0.192	0.000	0.190
align-utils	0.040	0.000	0.038
chartr	0.620	0.012	0.634
detail	0.784	0.016	0.806
dinucleotideFrequencyTest	0.008	0.008	0.015
findPalindromes	14.533	0.304	14.923
getSeq	0.116	0.008	0.125
gregexpr2	0.004	0.000	0.002
injectHardMask	0.040	0.004	0.045
letter	0.016	0.000	0.017
letterFrequency	1.872	0.064	1.944
longestConsecutive	0.000	0.000	0.001
lowlevel-matching	0.661	0.012	0.671
maskMotif	1.504	0.032	1.553
match-utils	0.028	0.000	0.027
matchLRPatterns	0.644	0.012	0.713
matchPDict-exact	380.531	0.604	382.772
matchPDict-inexact	40.439	0.156	40.663
matchPWM	2.420	0.004	2.428
matchPattern	11.909	0.040	12.024
matchProbePair	1.640	0.020	1.666
matchprobes	0.328	0.004	0.335
misc	0.016	0.000	0.015
needwunsQS	0.004	0.000	0.001
nucleotideFrequency	0.828	0.032	0.861
padAndClip	0.692	0.012	0.707
pairwiseAlignment	1.076	0.000	1.077
phiX174Phage	0.652	0.008	0.661
pid	0.412	0.000	0.415
replaceAt	4.853	0.064	4.927
replaceLetterAt	0.576	0.000	0.589
reverseComplement	1.236	0.028	1.267
stringDist	5.776	0.004	5.788
substitution_matrices	0.604	0.004	0.607
toComplex	0.004	0.000	0.002
translate	1.064	0.004	1.095
trimLRPatterns	0.080	0.000	0.082
xscat	1.480	0.008	1.610
yeastSEQCHR1	0.004	0.000	0.004