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Package 68/462HostnameOS / ArchBUILDCHECKBUILD BIN
Biostrings 2.21.1
H. Pages
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biostrings
Last Changed Rev: 54976 / Revision: 55359
Last Changed Date: 2011-04-19 22:47:05 -0700 (Tue, 19 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: Biostrings
Version: 2.21.1
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings Biostrings_2.21.1.tar.gz
StartedAt: 2011-05-09 12:47:21 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 12:57:13 -0700 (Mon, 09 May 2011)
EllapsedTime: 591.8 seconds
RetCode: 0
Status:  OK  
CheckDir: Biostrings.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/Biostrings.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.21.1'
* checking package name space 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 whether package 'Biostrings' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... NOTE
.checkFormat: no visible binding for global variable 'filepath'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' call not declared from: 'BSgenome.Hsapiens.UCSC.hg18'
* 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 examples ... OK
* 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

Biostrings.Rcheck/00install.out:

* installing *source* package 'Biostrings' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c BAB_class.c -o BAB_class.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c BitMatrix.c -o BitMatrix.o
BitMatrix.c: In function 'debug_BitMatrix':
BitMatrix.c:382:3: warning: left shift count >= width of type
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -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'
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c SparseList_utils.c -o SparseList_utils.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
XStringSet_class.c:92:18: warning: 'lkup_length' may be used uninitialized in this function
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function 'parse_FASTQ_file':
XStringSet_io.c:546:27: warning: 'load_record' may be used uninitialized in this function
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c XString_class.c -o XString_class.o
XString_class.c: In function 'new_XString_from_CHARACTER':
XString_class.c:162:6: warning: 'lkup_length' may be used uninitialized in this function
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:26:12: warning: 'sc' may be used uninitialized in this function
align_needwunsQS.c:26:12: note: 'sc' was declared here
align_needwunsQS.c:39:8: warning: 'lkup_val' may be used uninitialized in this function
align_needwunsQS.c:39:8: note: 'lkup_val' was declared here
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignedFixedSubject_align_aligned':
align_utils.c:223:7: warning: 'indelStartPattern' may be used uninitialized in this function
align_utils.c:223:26: warning: 'indelWidthPattern' may be used uninitialized in this function
align_utils.c:223:45: warning: 'indelStartSubject' may be used uninitialized in this function
align_utils.c:223:64: warning: 'indelWidthSubject' may be used uninitialized in this function
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c find_palindromes.c -o find_palindromes.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c gtestsim.c -o gtestsim.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c inject_code.c -o inject_code.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -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'
io_utils.c:69:6: warning: unused variable 'ret'
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c letter_frequency.c -o letter_frequency.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c lowlevel_matching.c -o lowlevel_matching.o
lowlevel_matching.c: In function 'XString_match_pattern_at':
lowlevel_matching.c:534:69: warning: 'ans_elt' may be used uninitialized in this function
lowlevel_matching.c:536:7: warning: 'ans' may be used uninitialized in this function
lowlevel_matching.c: In function 'XStringSet_vmatch_pattern_at':
lowlevel_matching.c:584:18: warning: 'ans_elt' may be used uninitialized in this function
lowlevel_matching.c:584:27: warning: 'ans_nrow' may be used uninitialized in this function
lowlevel_matching.c:586:7: warning: 'ans' may be used uninitialized in this function
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -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
match_BOC.c:268:68: warning: unused variable 'noffsets'
match_BOC.c:268:59: warning: unused variable 'offsets'
match_BOC.c:268:55: warning: unused variable 'j'
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -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
match_BOC2.c:234:68: warning: unused variable 'noffsets'
match_BOC2.c:234:59: warning: unused variable 'offsets'
match_BOC2.c:234:55: warning: unused variable 'j'
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c match_PWM.c -o match_PWM.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c match_WCP.c -o match_WCP.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c match_pattern.c -o match_pattern.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
match_pattern_boyermoore.c: In function '_match_pattern_boyermoore':
match_pattern_boyermoore.c:399:35: warning: 'i1' may be used uninitialized in this function
match_pattern_boyermoore.c:399:39: warning: 'i2' may be used uninitialized in this function
match_pattern_boyermoore.c:399:43: warning: 'j1' may be used uninitialized in this function
match_pattern_boyermoore.c:401:16: warning: 'c' may be used uninitialized in this function
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c match_pattern_indels.c -o match_pattern_indels.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c match_pdict.c -o match_pdict.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c:640:21: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function 'build_Twobit':
match_pdict_Twobit.c:125:12: warning: 'twobit_sign2pos' may be used uninitialized in this function
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function 'match_ppheadtail0':
match_pdict_utils.c:653:43: warning: unused variable 'ncol'
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:806:44: warning: unused variable 'subtotal_NFC'
match_pdict_utils.c:806:27: warning: unused variable 'total_NFC'
match_pdict_utils.c:805:33: warning: unused variable 'NFC'
match_pdict_utils.c:805:26: warning: unused variable 'nloci'
match_pdict_utils.c:805:20: warning: unused variable 'ndup'
match_pdict_utils.c: At top level:
match_pdict_utils.c:268:13: warning: 'match_headtail_by_loc' defined but not used
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c match_reporting.c -o match_reporting.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c matchprobes.c -o matchprobes.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c pmatchPattern.c -o pmatchPattern.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c replace_letter_at.c -o replace_letter_at.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c strutils.c -o strutils.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c translate.c -o translate.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature':
utils.c:196:9: warning: 'twobit_sign' may be used uninitialized in this function
utils.c: In function '_get_twobit_signature_at':
utils.c:210:12: warning: 'twobit_sign' may be used uninitialized in this function
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -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
xscat.c:18:14: warning: 'ans_classname' may be used uninitialized in this function
xscat.c: In function 'XStringSet_xscat':
xscat.c:94:2: warning: 'ans_length' may be used uninitialized in this function
xscat.c:70:14: warning: 'ans_element_type' may be used uninitialized in this function
gcc -shared -s -static-libgcc -o Biostrings.dll tmp.def 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_WCP.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 -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/Biostrings.Rcheck/Biostrings/libs/i386
** R
** data
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Creating a new generic function for "setequal" in "Biostrings"
Creating a new generic function for "ls" in "Biostrings"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'Alignments.Rnw' 
   'Biostrings2Classes.Rnw' 
   'MultipleAlignments.Rnw' 
   'matchprobes.Rnw' 
** testing if installed package can be loaded

* DONE (Biostrings)

Biostrings.Rcheck/Biostrings-Ex.timings:

nameusersystemelapsed
AAString-class0.010.000.01
AMINO_ACID_CODE000
AlignedXStringSet-class0.170.000.22
DNAString-class000
FASTA-io-legacy20.32 0.5027.16
GENETIC_CODE000
HNF4alpha0.050.000.05
IUPAC_CODE_MAP0.010.000.02
MIndex-class000
MaskedXString-class0.360.031.28
MultipleAlignment-class2.490.022.51
PDict-class5.980.046.10
PairwiseAlignedXStringSet-class0.230.000.24
QualityScaledXStringSet-class0.030.000.03
RNAString-class000
XString-class0.020.000.01
XStringQuality-class0.110.000.11
XStringSet-class10.20 0.4310.80
XStringSet-io6.570.366.97
XStringSetList-class0.060.000.06
XStringViews-class0.220.000.22
XStringViews-constructor0.050.000.05
align-utils0.090.000.09
chartr0.610.000.61
detail0.940.000.94
dinucleotideFrequencyTest0.030.000.03
findPalindromes5.660.015.92
gregexpr2000
injectHardMask0.070.000.08
letter0.020.000.01
letterFrequency3.110.063.22
longestConsecutive000
lowlevel-matching1.310.041.38
maskMotif1.660.011.92
match-utils0.030.000.03
matchLRPatterns0.590.021.06
matchPDict-exact263.93 1.36266.91
matchPDict-inexact49.53 0.3250.06
matchPWM1.770.021.79
matchPattern3.450.033.54
matchProbePair1.200.031.25
matchprobes1.290.001.28
misc0.020.000.01
needwunsQS000
nucleotideFrequency1.890.052.02
pairwiseAlignment1.220.001.21
phiX174Phage0.920.000.94
pid0.550.010.56
replaceLetterAt1.520.021.54
reverse2.710.132.84
stringDist9.190.009.21
substitution_matrices0.790.000.80
toComplex0.020.000.02
translate1.360.001.36
trimLRPatterns0.250.000.25
xscat3.640.013.65
yeastSEQCHR1000