BioC 2.12: CHECK report for Biostrings on george2

Package: Biostrings

Version: 2.28.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Biostrings_2.28.0.tar.gz

StartedAt: 2013-10-09 00:28:56 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:43:56 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 899.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biostrings.Rcheck

Warnings: 2

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘2.28.0’
* 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 ... [33s/35s] 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      404.197  1.636 415.964
matchPDict-inexact     87.606  0.692  90.521
PDict-class            19.465  0.260  20.164
XStringSet-class       14.957  0.332  16.257
XStringSet-io          13.217  0.132  14.175
stringDist              6.944  0.000   6.955
XStringSet-comparison   6.300  0.276   6.806
findPalindromes         6.097  0.056   6.168
* 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]
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: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-2.12-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]
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
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 ‘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
** testing if installed package can be loaded
* DONE (Biostrings)

name	user	system	elapsed
AAString-class	0.016	0.004	0.024
AMINO_ACID_CODE	0.312	0.008	0.318
AlignedXStringSet-class	0.160	0.008	0.165
DNAString-class	0.024	0.000	0.022
GENETIC_CODE	0.020	0.004	0.023
HNF4alpha	0.056	0.000	0.057
IUPAC_CODE_MAP	0.032	0.000	0.033
MIndex-class	0.012	0.000	0.015
MaskedXString-class	0.872	0.012	0.884
MultipleAlignment-class	3.480	0.044	3.815
PDict-class	19.465	0.260	20.164
PairwiseAlignments-class	0.840	0.012	0.857
PairwiseAlignments-io	4.213	0.168	4.647
QualityScaledXStringSet-class	0.056	0.000	0.054
RNAString-class	0.028	0.000	0.030
XString-class	0.036	0.004	0.050
XStringQuality-class	0.228	0.004	0.237
XStringSet-class	14.957	0.332	16.257
XStringSet-comparison	6.300	0.276	6.806
XStringSet-io	13.217	0.132	14.175
XStringSetList-class	0.500	0.004	0.514
XStringViews-class	0.492	0.000	0.498
align-utils	0.216	0.000	0.217
chartr	0.900	0.040	0.942
detail	1.832	0.080	1.914
dinucleotideFrequencyTest	0.032	0.008	0.040
findPalindromes	6.097	0.056	6.168
getSeq	0.076	0.016	0.094
gregexpr2	0.180	0.004	0.185
injectHardMask	0.084	0.000	0.084
letter	0.040	0.004	0.041
letterFrequency	2.300	0.076	2.544
longestConsecutive	0.004	0.000	0.007
lowlevel-matching	2.076	0.012	2.253
maskMotif	2.452	0.036	2.528
match-utils	0.064	0.000	0.063
matchLRPatterns	0.880	0.024	0.939
matchPDict-exact	404.197	1.636	415.964
matchPDict-inexact	87.606	0.692	90.521
matchPWM	2.376	0.032	2.441
matchPattern	4.816	0.052	4.873
matchProbePair	1.868	0.012	1.890
matchprobes	0.436	0.012	0.450
misc	0.036	0.000	0.039
needwunsQS	0.012	0.000	0.015
nucleotideFrequency	1.225	0.032	1.257
pairwiseAlignment	1.584	0.004	1.590
phiX174Phage	0.932	0.000	0.934
pid	0.760	0.004	0.762
replaceLetterAt	1.268	0.008	1.276
reverseComplement	2.316	0.092	2.410
stringDist	6.944	0.000	6.955
substitution_matrices	1.036	0.000	1.037
toComplex	0.016	0.000	0.015
translate	3.277	0.012	3.303
trimLRPatterns	0.192	0.004	0.194
xscat	3.732	0.008	3.745
yeastSEQCHR1	0.012	0.000	0.012