Biostrings 2.24.1
H. Pages
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/Biostrings | | Last Changed Rev: 64835 / Revision: 69725 | | Last Changed Date: 2012-04-03 09:53:06 -0700 (Tue, 03 Apr 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ WARNINGS ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/Biostrings.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘2.24.1’
* 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 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
.needwunsQS: warning in matrix(0, nr = n1 + 1, nc = n2 + 1): partial
argument match of 'nr' to 'nrow'
.needwunsQS: warning in matrix(0, nr = n1 + 1, nc = n2 + 1): partial
argument match of 'nc' to 'ncol'
g.test: warning in pchisq(STATISTIC, PARAMETER, lower = FALSE): partial
argument match of 'lower' to 'lower.tail'
* 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 ... WARNING
‘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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: ‘readFASTA’ is deprecated.
Warning: ‘writeFASTA’ is deprecated.
Warning: ‘writeFASTA’ is deprecated.
Warning: ‘writeFASTA’ is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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
‘/loc/home/biocbuild/bbs-2.10-bioc/meat/Biostrings.Rcheck/00check.log’
for details.
* installing *source* package ‘Biostrings’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c BAB_class.c -o BAB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c BitMatrix.c -o BitMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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:92:18: warning: ‘lkup_length’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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:546:27: warning: ‘load_record’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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:162:6: warning: ‘lkup_length’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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: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 -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c find_palindromes.c -o find_palindromes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c gtestsim.c -o gtestsim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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’
io_utils.c:69:6: warning: unused variable ‘ret’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c letter_frequency.c -o letter_frequency.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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: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 -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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
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 -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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
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 -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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:110:6: warning: ‘ans_length’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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:125:12: warning: ‘twobit_sign2pos’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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’
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 -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c matchprobes.c -o matchprobes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c strutils.c -o strutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c translate.c -o translate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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
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 -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-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-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)