Biostrings 2.22.0
H. Pages
| Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/Biostrings | | Last Changed Rev: 59932 / Revision: 61898 | | Last Changed Date: 2011-10-31 17:53:57 -0700 (Mon, 31 Oct 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 SP1 (64-bit) / x64 | OK | OK | OK |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/Biostrings.Rcheck'
* using R version 2.14.1 (2011-12-22)
* 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 '2.22.0'
* 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 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 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 ... 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 compiled code ... NOTE
File 'E:/biocbld/bbs-2.9-bioc/meat/Biostrings.Rcheck/Biostrings/libs/i386/Biostrings.dll':
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console. The detected symbols
are linked into the code but might come from libraries and not actually
be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
* 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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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'
match_pdict_utils.c: In function 'match_ppheadtail':
match_pdict_utils.c:722:6: warning: unused variable 'nelt'
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:821:44: warning: unused variable 'subtotal_NFC'
match_pdict_utils.c:821:27: warning: unused variable 'total_NFC'
match_pdict_utils.c:820:33: warning: unused variable 'NFC'
match_pdict_utils.c:820:26: warning: unused variable 'nloci'
match_pdict_utils.c:820:20: warning: unused variable 'ndup'
match_pdict_utils.c: At top level:
match_pdict_utils.c:275:13: 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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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
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 ...
*** tangling vignette sources ...
'Alignments.Rnw'
'Biostrings2Classes.Rnw'
'MultipleAlignments.Rnw'
'matchprobes.Rnw'
** testing if installed package can be loaded
* DONE (Biostrings)