BioC 2.12: CHECK report for Biostrings on george2

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘2.27.12’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘Rmpi’
* 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 ... [34s/37s] OK
* checking installed package size ... OK
* checking package directory ... 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 or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00_pkg_src/Biostrings/man/MaskedXString-class.Rd’:
  ‘[IRanges]{Ranges-utils}’

Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00_pkg_src/Biostrings/man/MultipleAlignment-class.Rd’:
  ‘[IRanges:Ranges-utils]{narrow}’

Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00_pkg_src/Biostrings/man/XStringViews-class.Rd’:
  ‘[IRanges:IRanges-setops]{gaps}’

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

* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [10m/11m] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
matchPDict-exact      395.265  1.644 409.546
matchPDict-inexact     84.129  0.828  87.628
PDict-class            19.513  0.236  20.675
XStringSet-class       15.865  0.316  16.473
XStringSet-io          13.597  0.144  14.676
stringDist              8.889  0.012   9.479
findPalindromes         6.941  0.036   7.031
XStringSet-comparison   6.272  0.268   7.264
matchPattern            4.829  0.092   5.053
* 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 2 warnings.
NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00check.log’
for details.

* installing *source* package ‘Biostrings’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c BAB_class.c -o BAB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c BitMatrix.c -o BitMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/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:113:33: warning: ‘lkup_length’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function ‘parse_FASTQ_file’:
XStringSet_io.c:658:7: warning: ‘load_record’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/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:178:32: warning: ‘lkup_length’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function ‘align_needwunsQS’:
align_needwunsQS.c:172:22: warning: ‘sc’ may be used uninitialized in this function [-Wuninitialized]
align_needwunsQS.c:44:37: warning: ‘lkup_val’ may be used uninitialized in this function [-Wuninitialized]
align_needwunsQS.c:39:8: note: ‘lkup_val’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c align_utils.c -o align_utils.o
align_utils.c: In function ‘PairwiseAlignmentsSingleSubject_align_aligned’:
align_utils.c:252:14: warning: ‘indelWidthSubject’ may be used uninitialized in this function [-Wuninitialized]
align_utils.c:233:42: warning: ‘indelStartSubject’ may be used uninitialized in this function [-Wuninitialized]
align_utils.c:157:6: warning: ‘indelWidthPattern’ may be used uninitialized in this function [-Wuninitialized]
align_utils.c:234:50: warning: ‘indelStartPattern’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c find_palindromes.c -o find_palindromes.o
find_palindromes.c: In function ‘find_palindromes’:
find_palindromes.c:122:22: warning: ‘letter0’ may be used uninitialized in this function [-Wuninitialized]
find_palindromes.c:82:7: note: ‘letter0’ was declared here
find_palindromes.c:101:27: warning: ‘lkup_val’ may be used uninitialized in this function [-Wuninitialized]
find_palindromes.c:81:66: note: ‘lkup_val’ 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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c gtestsim.c -o gtestsim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/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]
io_utils.c: In function ‘new_input_ExternalFilePtr’:
io_utils.c:130:2: warning: ‘fp’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/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:854:48: warning: unused variable ‘x_pos’ [-Wunused-variable]
letter_frequency.c:853:13: warning: unused variable ‘ans_dimnames’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c lowlevel_matching.c -o lowlevel_matching.o
lowlevel_matching.c: In function ‘XString_match_pattern_at’:
lowlevel_matching.c:568:2: warning: ‘ans’ may be used uninitialized in this function [-Wuninitialized]
lowlevel_matching.c:563:18: warning: ‘ans_elt’ may be used uninitialized in this function [-Wuninitialized]
lowlevel_matching.c: In function ‘XStringSet_vmatch_pattern_at’:
lowlevel_matching.c:625:2: warning: ‘ans’ may be used uninitialized in this function [-Wuninitialized]
lowlevel_matching.c:584:27: warning: ‘ans_nrow’ may be used uninitialized in this function [-Wuninitialized]
lowlevel_matching.c:617:41: warning: ‘ans_elt’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c match_BOC.c -o match_BOC.o
match_BOC.c: In function ‘BOC_exact_search’:
match_BOC.c:331:3: 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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c match_BOC2.c -o match_BOC2.o
match_BOC2.c: In function ‘BOC2_exact_search’:
match_BOC2.c:288:3: 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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c match_pattern_indels.c -o match_pattern_indels.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c match_pdict.c -o match_pdict.o
match_pdict.c: In function ‘init_vcount_collapsed_ans’:
match_pdict.c:107:13: warning: ‘ans_length’ may be used uninitialized in this function [-Wuninitialized]
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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function ‘build_Twobit’:
match_pdict_Twobit.c:90:2: warning: ‘twobit_sign2pos’ may be used uninitialized in this function [-Wuninitialized]
match_pdict_Twobit.c:125:12: note: ‘twobit_sign2pos’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/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:664:49: warning: unused variable ‘ncol’ [-Wunused-variable]
match_pdict_utils.c: In function ‘match_ppheadtail’:
match_pdict_utils.c:722:6: warning: unused variable ‘nelt’ [-Wunused-variable]
match_pdict_utils.c: In function ‘_match_pdict_all_flanks’:
match_pdict_utils.c:821:44: warning: unused variable ‘subtotal_NFC’ [-Wunused-variable]
match_pdict_utils.c:821:27: warning: unused variable ‘total_NFC’ [-Wunused-variable]
match_pdict_utils.c:820:33: warning: unused variable ‘NFC’ [-Wunused-variable]
match_pdict_utils.c:820:26: warning: unused variable ‘nloci’ [-Wunused-variable]
match_pdict_utils.c:820:20: 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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c matchprobes.c -o matchprobes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c replace_letter_at.c -o replace_letter_at.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c strutils.c -o strutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c translate.c -o translate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c utils.c -o utils.o
utils.c: In function ‘_get_twobit_signature’:
utils.c:203:2: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wuninitialized]
utils.c: In function ‘_get_twobit_signature_at’:
utils.c:210:12: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c xscat.c -o xscat.o
xscat.c: In function ‘XString_xscat’:
xscat.c:36:2: 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:94:2: 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 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-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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
   ‘Biostrings2Classes.Rnw’ 
   ‘BiostringsQuickOverview.Rnw’ 
   ‘MultipleAlignments.Rnw’ 
   ‘PairwiseAlignments.Rnw’ 
   ‘matchprobes.Rnw’ 
** testing if installed package can be loaded
* DONE (Biostrings)

name	user	system	elapsed
AAString-class	0.024	0.000	0.025
AMINO_ACID_CODE	0.312	0.008	0.321
AlignedXStringSet-class	0.160	0.008	0.171
DNAString-class	0.028	0.000	0.047
GENETIC_CODE	0.024	0.000	0.025
HNF4alpha	0.068	0.008	0.076
IUPAC_CODE_MAP	0.032	0.000	0.036
MIndex-class	0.028	0.000	0.038
MaskedXString-class	0.564	0.020	0.596
MultipleAlignment-class	4.012	0.040	4.260
PDict-class	19.513	0.236	20.675
PairwiseAlignments-class	1.056	0.072	1.128
PairwiseAlignments-io	4.713	0.192	4.903
QualityScaledXStringSet-class	0.052	0.000	0.054
RNAString-class	0.028	0.000	0.027
XString-class	0.044	0.000	0.046
XStringQuality-class	0.216	0.012	0.231
XStringSet-class	15.865	0.316	16.473
XStringSet-comparison	6.272	0.268	7.264
XStringSet-io	13.597	0.144	14.676
XStringSetList-class	0.504	0.012	0.516
XStringViews-class	0.536	0.004	0.540
align-utils	0.228	0.000	0.231
chartr	0.936	0.028	0.964
detail	1.976	0.080	2.080
dinucleotideFrequencyTest	0.032	0.004	0.039
findPalindromes	6.941	0.036	7.031
getSeq	0.092	0.012	0.104
gregexpr2	0.992	0.040	1.054
injectHardMask	0.092	0.000	0.093
letter	0.044	0.000	0.043
letterFrequency	2.592	0.088	2.690
longestConsecutive	0.004	0.000	0.006
lowlevel-matching	1.076	0.004	1.081
maskMotif	2.652	0.092	3.095
match-utils	0.056	0.000	0.057
matchLRPatterns	0.876	0.036	1.070
matchPDict-exact	395.265	1.644	409.546
matchPDict-inexact	84.129	0.828	87.628
matchPWM	2.344	0.012	2.571
matchPattern	4.829	0.092	5.053
matchProbePair	1.920	0.020	1.949
matchprobes	0.432	0.012	0.475
misc	0.036	0.000	0.034
needwunsQS	0.012	0.000	0.012
nucleotideFrequency	1.244	0.032	1.277
pairwiseAlignment	1.824	0.004	2.220
phiX174Phage	1.312	0.000	1.468
pid	0.880	0.000	0.881
replaceLetterAt	1.428	0.008	1.437
reverseComplement	2.532	0.064	2.764
stringDist	8.889	0.012	9.479
substitution_matrices	1.100	0.016	1.262
toComplex	0.024	0.000	0.024
translate	2.556	0.008	2.704
trimLRPatterns	0.344	0.000	0.521
xscat	3.616	0.012	3.880
yeastSEQCHR1	0.012	0.000	0.012

Summary

Command output