BioC 2.13: CHECK report for Biostrings on zin1

Package: Biostrings

Version: 2.30.1

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings Biostrings_2.30.1.tar.gz

StartedAt: 2014-04-04 23:52:51 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-05 00:00:58 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 487.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biostrings.Rcheck

Warnings: 1

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/Biostrings.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘2.30.1’
* 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 ... [18s/19s] OK
* checking installed package size ... OK
* 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:
  ‘IRanges:::.showAtomicList’ ‘IRanges:::extractROWS’
  ‘IRanges:::normalizeDoubleBracketSubscript’
  ‘IRanges:::showRangesList’
  See the note in ?`:::` about the use of this operator.
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 ... 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 'splitAsListReturnedClass' and siglist 'AAStringSet'
  generic 'splitAsListReturnedClass' and siglist 'BStringSet'
  generic 'splitAsListReturnedClass' and siglist 'DNAStringSet'
  generic 'splitAsListReturnedClass' and siglist 'RNAStringSet'
  generic 'twoWayAlphabetFrequency' and siglist 'XString,XString'
  generic 'twoWayAlphabetFrequency' and siglist 'XString,XStringSet'
  generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XString'
  generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XStringSet'
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 ... NOTE
File ‘/home/biocbuild/bbs-2.13-bioc/meat/Biostrings.Rcheck/Biostrings/libs/Biostrings.so’:
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Object: ‘align_pairwiseAlignment.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘Biostrings2Classes.Rnw’, ‘BiostringsQuickOverview.Rnw’,
  ‘MultipleAlignments.Rnw’, ‘PairwiseAlignments.Rnw’, ‘matchprobes.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [357s/359s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
matchPDict-exact   236.891  0.448 238.255
matchPDict-inexact  40.675  0.168  40.959
findPalindromes      6.608  0.496   7.161
XStringSet-io        6.953  0.032   7.099
XStringSet-class     6.469  0.096   6.690
replaceAt            6.208  0.056   6.279
PDict-class          5.992  0.088   6.093
stringDist           5.604  0.004   5.620
* 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

WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/Biostrings.Rcheck/00check.log’
for details.

* installing *source* package ‘Biostrings’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c BAB_class.c -o BAB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c BitMatrix.c -o BitMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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:192:18: warning: unused variable ‘poffsets_order’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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:114:33: warning: ‘lkup_length’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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:659:7: warning: ‘load_record’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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:180:32: warning: ‘lkup_length’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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:253:14: warning: ‘indelWidthSubject’ may be used uninitialized in this function [-Wuninitialized]
align_utils.c:234:42: warning: ‘indelStartSubject’ may be used uninitialized in this function [-Wuninitialized]
align_utils.c:158:6: warning: ‘indelWidthPattern’ may be used uninitialized in this function [-Wuninitialized]
align_utils.c:235:50: warning: ‘indelStartPattern’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c find_palindromes.c -o find_palindromes.o
find_palindromes.c: In function ‘find_palindromes’:
find_palindromes.c:110:10: warning: ‘letter0’ may be used uninitialized in this function [-Wuninitialized]
find_palindromes.c:82:7: note: ‘letter0’ was declared here
find_palindromes.c:119:36: warning: ‘all_letter0’ may be used uninitialized in this function [-Wuninitialized]
find_palindromes.c:81:43: note: ‘all_letter0’ was declared here
find_palindromes.c:46:10: warning: ‘letter0’ may be used uninitialized in this function [-Wuninitialized]
find_palindromes.c:26:7: note: ‘letter0’ was declared here
find_palindromes.c:55:36: warning: ‘all_letter0’ may be used uninitialized in this function [-Wuninitialized]
find_palindromes.c:25:43: note: ‘all_letter0’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c gtestsim.c -o gtestsim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c io_utils.c -o io_utils.o
io_utils.c: In function ‘open_input_file’:
io_utils.c:70:14: warning: unused variable ‘buf’ [-Wunused-variable]
io_utils.c:69:6: warning: unused variable ‘ret’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c lowlevel_matching.c -o lowlevel_matching.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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:58:26: warning: variable ‘fixedP’ set but not used [-Wunused-but-set-variable]
match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’:
match_pdict.c:441:12: warning: ‘ans_col’ may be used uninitialized in this function [-Wuninitialized]
match_pdict.c:414:58: note: ‘ans_col’ was declared here
match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’:
match_pdict.c:492:13: warning: ‘ans_elt’ may be used uninitialized in this function [-Wuninitialized]
match_pdict.c:463:57: note: ‘ans_elt’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c matchprobes.c -o matchprobes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c strutils.c -o strutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c translate.c -o translate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c xscat.c -o xscat.o
xscat.c: In function ‘XString_xscat’:
xscat.c:37:2: warning: ‘ans_length’ may be used uninitialized in this function [-Wuninitialized]
xscat.c:51:2: warning: ‘ans_classname’ may be used uninitialized in this function [-Wuninitialized]
xscat.c: In function ‘XStringSet_xscat’:
xscat.c:91:2: warning: ‘ans_length’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -shared -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 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 utils.o xscat.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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	0.012	0.000	0.010
AMINO_ACID_CODE	0.000	0.004	0.005
AlignedXStringSet-class	0.076	0.008	0.087
DNAString-class	0.004	0.004	0.006
GENETIC_CODE	0.008	0.000	0.005
HNF4alpha	0.024	0.000	0.025
IUPAC_CODE_MAP	0.008	0.000	0.010
MIndex-class	0.000	0.000	0.003
MaskedXString-class	0.240	0.020	0.284
MultipleAlignment-class	2.148	0.020	2.169
PDict-class	5.992	0.088	6.093
PairwiseAlignments-class	0.388	0.040	0.428
PairwiseAlignments-io	2.604	0.056	2.666
QualityScaledXStringSet-class	0.024	0.000	0.021
RNAString-class	0.008	0.000	0.009
XString-class	0.012	0.000	0.013
XStringQuality-class	0.084	0.004	0.091
XStringSet-class	6.469	0.096	6.690
XStringSet-comparison	3.740	0.096	4.029
XStringSet-io	6.953	0.032	7.099
XStringSetList-class	0.876	0.020	0.898
XStringViews-class	0.220	0.004	0.227
align-utils	0.040	0.000	0.042
chartr	0.648	0.020	0.669
detail	0.828	0.028	0.859
dinucleotideFrequencyTest	0.020	0.000	0.017
findPalindromes	6.608	0.496	7.161
getSeq	0.056	0.008	0.065
gregexpr2	0.024	0.000	0.027
injectHardMask	0.072	0.000	0.074
letter	0.016	0.000	0.018
letterFrequency	1.564	0.072	1.663
longestConsecutive	0.004	0.000	0.001
lowlevel-matching	0.588	0.008	0.598
maskMotif	1.468	0.036	1.518
match-utils	0.036	0.000	0.039
matchLRPatterns	0.684	0.028	0.763
matchPDict-exact	236.891	0.448	238.255
matchPDict-inexact	40.675	0.168	40.959
matchPWM	2.460	0.016	2.513
matchPattern	4.388	0.040	4.443
matchProbePair	1.652	0.020	1.679
matchprobes	0.332	0.016	0.351
misc	0.016	0.000	0.018
needwunsQS	0.000	0.000	0.002
nucleotideFrequency	0.824	0.028	0.856
padAndClip	0.808	0.008	0.819
pairwiseAlignment	1.012	0.028	1.050
phiX174Phage	0.717	0.000	0.719
pid	0.424	0.000	0.437
replaceAt	6.208	0.056	6.279
replaceLetterAt	0.644	0.008	0.681
reverseComplement	1.472	0.028	1.503
stringDist	5.604	0.004	5.620
substitution_matrices	0.724	0.000	0.725
toComplex	0.004	0.000	0.004
translate	1.245	0.004	1.251
trimLRPatterns	0.104	0.004	0.107
xscat	1.808	0.012	1.820
yeastSEQCHR1	0.004	0.000	0.004