Biostrings 2.18.4
H. Pages
| Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/Biostrings | | Last Changed Rev: 53339 / Revision: 54281 | | Last Changed Date: 2011-03-01 14:56:14 -0800 (Tue, 01 Mar 2011) |
| lamb2 | Linux (openSUSE 11.2) / 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 | WARNINGS | OK |
* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/Biostrings.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.18.4'
* 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 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 ... NOTE
prepare_Rd: InDel-class.Rd:50-51: Dropping empty section \examples
prepare_Rd: WCP.Rd:32-33: Dropping empty section \details
prepare_Rd: WCP.Rd:42-43: Dropping empty section \examples
prepare_Rd: XKeySortedData.Rd:39-40: Dropping empty section \details
prepare_Rd: XKeySortedData.Rd:49-50: Dropping empty section \examples
prepare_Rd: XKeySortedDataList.Rd:30-31: Dropping empty section \details
prepare_Rd: XKeySortedDataList.Rd:40-41: Dropping empty section \examples
prepare_Rd: matchWCP.Rd:70-71: Dropping empty section \examples
* 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' calls not declared from:
BSgenome.Hsapiens.UCSC.hg18 hgu133aprobe
* checking data for non-ASCII characters ... 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 package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package 'Biostrings' ...
** libs
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c BAB_class.c -o BAB_class.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -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
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -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'
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c PreprocessedTB_class.c -o PreprocessedTB_class.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c R_init_Biostrings.c -o R_init_Biostrings.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c RoSeqs_utils.c -o RoSeqs_utils.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c SparseList_utils.c -o SparseList_utils.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -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
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function 'parse_FASTQ_file':
XStringSet_io.c:544:27: warning: 'load_record' may be used uninitialized in this function
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -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
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -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
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -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
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c extract_transcripts.c -o extract_transcripts.o
extract_transcripts.c: In function 'tlocs2rlocs':
extract_transcripts.c:243:44: warning: 'nlocs' may be used uninitialized in this function
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c find_palindromes.c -o find_palindromes.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c gtestsim.c -o gtestsim.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c inject_code.c -o inject_code.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -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'
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c letter_frequency.c -o letter_frequency.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -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
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -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'
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -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'
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c match_PWM.c -o match_PWM.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c match_WCP.c -o match_WCP.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c match_pattern.c -o match_pattern.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -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
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c match_pattern_indels.c -o match_pattern_indels.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c match_pattern_shiftor.c -o match_pattern_shiftor.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c match_pdict.c -o match_pdict.o
match_pdict.c: In function 'init_vcount_collapsed_ans':
match_pdict.c:110:6: warning: 'ans_length' may be used uninitialized in this function
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -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
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -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
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -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
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c match_reporting.c -o match_reporting.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c matchprobes.c -o matchprobes.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c pmatchPattern.c -o pmatchPattern.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c replace_letter_at.c -o replace_letter_at.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c strutils.c -o strutils.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c translate.c -o translate.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -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
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include" -O2 -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
x86_64-w64-mingw32-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 extract_transcripts.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 -LD:/biocbld/BBS-2˜1.7-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.7-bioc/meat/Biostrings.Rcheck/Biostrings/libs/x64
** R
** data
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin,
pmin.int, rbind, rep.int, table
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 ...
** testing if installed package can be loaded
* DONE (Biostrings)