BioC 3.2: CHECK report for Biostrings on zin1

Package: Biostrings

Version: 2.37.8

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Biostrings_2.37.8.tar.gz

StartedAt: 2015-08-23 22:03:16 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:12:17 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 540.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biostrings.Rcheck

Warnings: 2

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Biostrings_2.37.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/Biostrings.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biostrings/DESCRIPTION’ ... OK
* this is package ‘Biostrings’ version ‘2.37.8’
* 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 ... [17s/17s] OK
* checking installed package size ... NOTE
  installed size is 15.0Mb
  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.
Versioned 'LinkingTo' value for ‘S4Vectors’ is only usable in R >= 3.0.2
* 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’ ‘S4Vectors:::anyMissingOrOutside’
  ‘S4Vectors:::duplicatedIntegerPairs’
  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 ... WARNING
Missing link or links in documentation object 'translate.Rd':
  ‘[GenomicFeatures]{extractTranscriptsFromGenome}’

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

* 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 '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 compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [440s/441s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
matchPDict-exact   314.937  0.262 316.253
matchPDict-inexact  39.232  0.036  39.366
findPalindromes     26.440  0.208  26.778
XStringSet-class     7.721  0.168   8.013
matchPattern         5.538  0.016   5.554
* 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

Status: 2 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/Biostrings.Rcheck/00check.log’
for details.

* installing *source* package ‘Biostrings’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c BAB_class.c -o BAB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c BitMatrix.c -o BitMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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:193:20: warning: unused variable ‘poffsets_order’ [-Wunused-variable]
  IntAE *poffsets, *poffsets_order;
                    ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c XStringSetList_class.c -o XStringSetList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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 [-Wmaybe-uninitialized]
   _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
                                ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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:812:7: warning: ‘load_rec’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (load_rec && loader->load_qual != NULL)
       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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:184:31: warning: ‘lkup_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  _copy_CHARSXP_to_Chars_holder(&ans_holder, x_elt,
                               ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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 [-Wmaybe-uninitialized]
  INTEGER(ans_elt)[0] = score;
                      ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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 [-Wmaybe-uninitialized]
     jPattern += indelWidthSubject;
              ^
align_utils.c:235:42: warning: ‘indelStartSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
                                          ^
align_utils.c:225:26: warning: ‘indelWidthPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
                          ^
align_utils.c:236:50: warning: ‘indelStartPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
                                                  ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c find_palindromes.c -o find_palindromes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c gtestsim.c -o gtestsim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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]
   int x_width, y_width, x_length, *ans_mat, i, x_pos;
                                                ^
letter_frequency.c:956:13: warning: unused variable ‘ans_dimnames’ [-Wunused-variable]
   SEXP ans, ans_dimnames;
             ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c lowlevel_matching.c -o lowlevel_matching.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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]
   continue0: ;
   ^
match_BOC.c:268:68: warning: unused variable ‘noffsets’ [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                    ^
match_BOC.c:268:59: warning: unused variable ‘offsets’ [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                           ^
match_BOC.c:268:55: warning: unused variable ‘j’ [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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]
   continue0: ;
   ^
match_BOC2.c:234:68: warning: unused variable ‘noffsets’ [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                    ^
match_BOC2.c:234:59: warning: unused variable ‘offsets’ [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                           ^
match_BOC2.c:234:55: warning: unused variable ‘j’ [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pdict.c -o match_pdict.o
match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’:
match_pdict.c:442:12: warning: ‘ans_col’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    ans_col += tb_length;
            ^
match_pdict.c:415:58: note: ‘ans_col’ was declared here
  int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
                                                          ^
match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’:
match_pdict.c:493:13: warning: ‘ans_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     ans_elt += P_length;
             ^
match_pdict.c:464:57: note: ‘ans_elt’ was declared here
  int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
                                                         ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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]
  ACnode *node0, *node1, *node2;
          ^
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]
  ACnode *node0, *node1, *node2;
          ^
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]
 static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
                     ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
In file included from /home/biocbuild/bbs-3.2-bioc/R/include/Rdefines.h:29:0,
                 from /home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from match_pdict_Twobit.c:10:
match_pdict_Twobit.c: In function ‘build_Twobit’:
/home/biocbuild/bbs-3.2-bioc/R/include/Rinternals.h:652:30: warning: ‘twobit_sign2pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                              ^
match_pdict_Twobit.c:126:12: note: ‘twobit_sign2pos’ was declared here
  SEXP ans, twobit_sign2pos;
            ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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:674:49: warning: unused variable ‘ncol’ [-Wunused-variable]
  int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
                                                 ^
match_pdict_utils.c: In function ‘match_ppheadtail’:
match_pdict_utils.c:734:6: warning: unused variable ‘nelt’ [-Wunused-variable]
  int nelt, nkey0, nkey1, nkey2, i, key;
      ^
match_pdict_utils.c: In function ‘_match_pdict_all_flanks’:
match_pdict_utils.c:841:44: warning: unused variable ‘subtotal_NFC’ [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                                            ^
match_pdict_utils.c:841:27: warning: unused variable ‘total_NFC’ [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                           ^
match_pdict_utils.c:840:33: warning: unused variable ‘NFC’ [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                                 ^
match_pdict_utils.c:840:26: warning: unused variable ‘nloci’ [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                          ^
match_pdict_utils.c:840:20: warning: unused variable ‘ndup’ [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                    ^
match_pdict_utils.c: At top level:
match_pdict_utils.c:282:13: warning: ‘match_headtail_by_loc’ defined but not used [-Wunused-function]
 static void match_headtail_by_loc(const HeadTail *headtail,
             ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c matchprobes.c -o matchprobes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c strutils.c -o strutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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 [-Wmaybe-uninitialized]
     if (if_ambig == TRANSLATE_ERROR) {
        ^
translate.c:126:29: note: ‘if_ambig0’ was declared here
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
                             ^
translate.c:97:8: warning: ‘if_non_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (if_non_ambig == TRANSLATE_TO_X)
        ^
translate.c:126:14: note: ‘if_non_ambig0’ was declared here
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
              ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-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 [-Wmaybe-uninitialized]
  return twobit_sign;
  ^
utils.c: In function ‘_get_twobit_signature_at’:
utils.c:217:12: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  int i, j, twobit_sign;
            ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c xscat.c -o xscat.o
In file included from /home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from /home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function ‘XString_xscat’:
/home/biocbuild/bbs-3.2-bioc/R/include/Rdefines.h:78:32: warning: ‘ans_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define NEW_RAW(n)  allocVector(RAWSXP,n)
                                ^
xscat.c:18:13: note: ‘ans_length’ was declared here
  int nargs, ans_length, tag_offset, j;
             ^
In file included from /home/biocbuild/bbs-3.2-bioc/R/include/Rdefines.h:29:0,
                 from /home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
/home/biocbuild/bbs-3.2-bioc/R/include/Rinternals.h:652:30: warning: ‘ans_classname’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                              ^
xscat.c:20:14: note: ‘ans_classname’ was declared here
  const char *ans_classname;
              ^
In file included from /home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from /home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function ‘XStringSet_xscat’:
/home/biocbuild/bbs-3.2-bioc/R/include/Rdefines.h:72:36: warning: ‘ans_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define NEW_INTEGER(n)  allocVector(INTSXP,n)
                                    ^
xscat.c:66:32: note: ‘ans_length’ was declared here
  int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
                                ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-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 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 -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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	0.005	0.000	0.006
AMINO_ACID_CODE	0.002	0.000	0.002
AlignedXStringSet-class	0.064	0.000	0.064
DNAString-class	0.002	0.000	0.002
GENETIC_CODE	0.013	0.000	0.013
HNF4alpha	0.016	0.004	0.020
IUPAC_CODE_MAP	0.01	0.00	0.01
MIndex-class	0.001	0.000	0.001
MaskedXString-class	0.208	0.004	0.234
MultipleAlignment-class	1.098	0.000	1.101
PDict-class	3.819	0.052	3.925
PairwiseAlignments-class	0.15	0.00	0.15
PairwiseAlignments-io	2.720	0.040	2.775
QualityScaledXStringSet-class	0.015	0.000	0.015
RNAString-class	0.008	0.000	0.007
XString-class	0.01	0.00	0.01
XStringQuality-class	0.057	0.000	0.058
XStringSet-class	7.721	0.168	8.013
XStringSet-comparison	2.860	0.088	2.966
XStringSet-io	4.637	0.088	4.731
XStringSetList-class	0.310	0.004	0.313
XStringViews-class	0.109	0.008	0.118
align-utils	0.08	0.00	0.08
chartr	0.550	0.000	0.578
detail	0.372	0.016	0.389
dinucleotideFrequencyTest	0.009	0.004	0.013
findPalindromes	26.440	0.208	26.778
getSeq	0.09	0.00	0.09
gregexpr2	0.001	0.000	0.001
injectHardMask	0.037	0.004	0.037
letter	0.010	0.000	0.013
letterFrequency	1.452	0.028	1.479
longestConsecutive	0.001	0.000	0.000
lowlevel-matching	0.536	0.004	0.540
maskMotif	1.164	0.012	1.207
match-utils	0.021	0.000	0.021
matchLRPatterns	0.456	0.012	0.517
matchPDict-exact	314.937	0.262	316.253
matchPDict-inexact	39.232	0.036	39.366
matchPWM	2.447	0.000	2.448
matchPattern	5.538	0.016	5.554
matchProbePair	1.327	0.004	1.329
matchprobes	0.286	0.000	0.287
misc	0.013	0.000	0.013
needwunsQS	0.001	0.000	0.001
nucleotideFrequency	0.758	0.004	0.764
padAndClip	0.583	0.000	0.583
pairwiseAlignment	0.952	0.000	0.952
phiX174Phage	0.601	0.000	0.603
pid	0.375	0.000	0.375
replaceAt	4.180	0.076	4.255
replaceLetterAt	0.581	0.004	0.601
reverseComplement	1.343	0.012	1.354
stringDist	4.985	0.000	4.981
substitution_matrices	0.469	0.000	0.469
toComplex	0.001	0.000	0.002
translate	0.793	0.000	0.792
trimLRPatterns	0.062	0.000	0.061
xscat	1.162	0.000	1.161
yeastSEQCHR1	0.003	0.000	0.004