BioC 2.11: CHECK report for Biostrings on lamb1

Package: Biostrings

Version: 2.26.3

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings Biostrings_2.26.3.tar.gz

StartedAt: 2013-03-24 23:41:20 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:51:40 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 620.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: Biostrings.Rcheck

Warnings: 2

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Biostrings.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘2.26.3’
* 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 whether package ‘Biostrings’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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(s) in documentation object ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Biostrings.Rcheck/00_pkg_src/Biostrings/man/MaskedXString-class.Rd’:
  ‘[IRanges]{Ranges-utils}’

Missing link(s) in documentation object ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Biostrings.Rcheck/00_pkg_src/Biostrings/man/MultipleAlignment-class.Rd’:
  ‘[IRanges:Ranges-utils]{narrow}’

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

* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'splitAsListReturnedClass' and siglist 'AAStringSet'
  generic 'splitAsListReturnedClass' and siglist 'BStringSet'
  generic 'splitAsListReturnedClass' and siglist 'DNAStringSet'
  generic 'splitAsListReturnedClass' and siglist 'RNAStringSet'
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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
matchPDict-exact   285.542  2.988 293.682
matchPDict-inexact  53.420  0.376  54.229
XStringSet-io       11.765  0.136  12.474
PDict-class         11.381  0.172  11.739
XStringSet-class     9.565  0.124   9.982
stringDist           7.489  0.012   7.648
findPalindromes      5.988  0.060   6.369
* 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 was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Biostrings.Rcheck/00check.log’
for details.

* installing *source* package ‘Biostrings’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c BAB_class.c -o BAB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c BitMatrix.c -o BitMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c gtestsim.c -o gtestsim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c letter_frequency.c -o letter_frequency.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c matchprobes.c -o matchprobes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c strutils.c -o strutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c translate.c -o translate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-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]
xscat.c:145:14: warning: ‘ans_element_type’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -shared -L/usr/local/lib64 -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-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-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’ 
   ‘MultipleAlignments.Rnw’ 
   ‘PairwiseAlignments.Rnw’ 
   ‘matchprobes.Rnw’ 
** testing if installed package can be loaded

* DONE (Biostrings)

name	user	system	elapsed
AAString-class	0.004	0.000	0.006
AMINO_ACID_CODE	0.004	0.000	0.002
AlignedXStringSet-class	0.300	0.000	0.313
DNAString-class	0.004	0.000	0.003
FASTA-io-legacy	0.000	0.000	0.001
GENETIC_CODE	0.004	0.000	0.004
HNF4alpha	0.048	0.004	0.054
IUPAC_CODE_MAP	0.012	0.000	0.012
MIndex-class	0	0	0
MaskedXString-class	0.520	0.012	0.850
MultipleAlignment-class	2.512	0.024	2.596
PDict-class	11.381	0.172	11.739
PairwiseAlignments-class	0.228	0.004	0.233
PairwiseAlignments-io	3.992	0.296	4.347
QualityScaledXStringSet-class	0.024	0.000	0.026
RNAString-class	0.008	0.000	0.011
XString-class	0.012	0.000	0.014
XStringQuality-class	0.14	0.00	0.14
XStringSet-class	9.565	0.124	9.982
XStringSet-comparison	4.616	0.120	4.770
XStringSet-io	11.765	0.136	12.474
XStringSetList-class	0.304	0.000	0.306
XStringViews-class	0.312	0.000	0.315
align-utils	0.048	0.004	0.051
chartr	0.728	0.020	0.802
detail	1.612	0.032	1.972
dinucleotideFrequencyTest	0.020	0.000	0.061
findPalindromes	5.988	0.060	6.369
getSeq	0.068	0.012	0.094
gregexpr2	0.000	0.000	0.003
injectHardMask	0.152	0.000	0.152
letter	0.02	0.00	0.02
letterFrequency	1.484	0.076	1.605
longestConsecutive	0	0	0
lowlevel-matching	0.612	0.004	0.631
maskMotif	1.904	0.024	2.151
match-utils	0.036	0.000	0.038
matchLRPatterns	0.680	0.016	0.818
matchPDict-exact	285.542	2.988	293.682
matchPDict-inexact	53.420	0.376	54.229
matchPWM	1.972	0.004	2.002
matchPattern	3.460	0.012	3.826
matchProbePair	1.564	0.016	1.584
matchprobes	0.344	0.000	0.344
misc	0.016	0.000	0.016
needwunsQS	0	0	0
nucleotideFrequency	0.884	0.028	1.032
pairwiseAlignment	1.044	0.000	1.045
phiX174Phage	0.724	0.004	0.729
pid	0.520	0.000	0.521
replaceLetterAt	0.744	0.016	0.770
reverseComplement	1.772	0.088	1.949
stringDist	7.489	0.012	7.648
substitution_matrices	0.652	0.008	0.681
toComplex	0.004	0.000	0.003
translate	1.516	0.020	1.545
trimLRPatterns	0.104	0.000	0.104
xscat	2.476	0.012	2.571
yeastSEQCHR1	0.004	0.000	0.004

Summary

Command output