Biostrings 2.38.4
H. Pages
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Biostrings | | Last Changed Rev: 113428 / Revision: 116712 | | Last Changed Date: 2016-02-08 13:40:08 -0800 (Mon, 08 Feb 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf Biostrings.buildbin-libdir Biostrings.Rcheck && mkdir Biostrings.buildbin-libdir Biostrings.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Biostrings.buildbin-libdir Biostrings_2.38.4.tar.gz >Biostrings.Rcheck\00install.out 2>&1 && cp Biostrings.Rcheck\00install.out Biostrings-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=Biostrings.buildbin-libdir --install="check:Biostrings-install.out" --force-multiarch --no-vignettes --timings Biostrings_2.38.4.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/Biostrings.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.38.4'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'Biostrings' can be installed ... OK
* checking installed package size ... NOTE
installed size is 14.4Mb
sub-directories of 1Mb or more:
doc 1.1Mb
extdata 11.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'methods' 'BiocGenerics' 'IRanges' 'XVector'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'BiocGenerics:::testPackage' 'IRanges:::.showAtomicList'
'IRanges:::showRangesList' 'S4Vectors:::anyMissingOrOutside'
'S4Vectors:::duplicatedIntegerPairs'
See the note in ?`:::` about the use of this operator.
* 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 or links in documentation object 'translate.Rd':
'[GenomicFeatures]{extractTranscriptsFromGenome}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'twoWayAlphabetFrequency'
Undocumented S4 methods:
generic 'compare' and siglist 'Vector,XStringSet'
generic 'compare' and siglist 'XStringSet,Vector'
generic 'compare' and siglist 'XStringSet,vector'
generic 'compare' and siglist 'vector,XStringSet'
generic 'match' and siglist 'Vector,XStringSet'
generic 'match' and siglist 'XStringSet,Vector'
generic 'match' and siglist 'XStringSet,vector'
generic 'match' and siglist 'vector,XStringSet'
generic 'relistToClass' and siglist 'XString'
generic 'relistToClass' and siglist 'XStringSet'
generic 'twoWayAlphabetFrequency' and siglist 'XString,XString'
generic 'twoWayAlphabetFrequency' and siglist 'XString,XStringSet'
generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XString'
generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XStringSet'
generic 'unstrsplit' and siglist 'XStringSet'
generic 'unstrsplit' and siglist 'XStringSetList'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.2-bioc/meat/Biostrings.buildbin-libdir/Biostrings/libs/i386/Biostrings.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/Biostrings.buildbin-libdir/Biostrings/libs/x64/Biostrings.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [10m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
matchPDict-exact 394.20 1.31 395.51
matchPDict-inexact 58.42 0.27 58.72
findPalindromes 46.68 0.61 48.17
XStringSet-class 15.02 0.39 16.15
stringDist 13.03 0.01 13.05
matchPattern 10.25 0.03 10.28
XStringSet-io 9.35 0.37 9.73
PDict-class 5.89 0.10 6.31
XStringSet-comparison 5.56 0.20 5.75
replaceAt 4.89 0.14 5.02
** running examples for arch 'x64' ... [10m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
matchPDict-exact 408.18 1.27 409.53
matchPDict-inexact 51.82 0.19 52.01
findPalindromes 50.87 0.50 51.37
XStringSet-class 12.99 0.31 13.79
matchPattern 10.82 0.09 10.96
stringDist 7.79 0.03 7.81
XStringSet-io 7.30 0.23 9.91
PDict-class 6.70 0.08 6.77
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 5 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/Biostrings.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'Biostrings' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c BAB_class.c -o BAB_class.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/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 [enabled by default]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/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:193:20: warning: unused variable 'poffsets_order' [-Wunused-variable]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c SparseList_utils.c -o SparseList_utils.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c XStringSetList_class.c -o XStringSetList_class.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/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:123:32: warning: 'lkup_length' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/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:812:7: warning: 'load_rec' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/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:125:33: warning: 'lkup_length' may be used uninitialized in this function [-Wuninitialized]
XString_class.c:168:6: note: 'lkup_length' was declared here
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/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:173:22: warning: 'sc' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignmentsSingleSubject_align_aligned':
align_utils.c:254:14: warning: 'indelWidthSubject' may be used uninitialized in this function [-Wuninitialized]
align_utils.c:235:42: warning: 'indelStartSubject' may be used uninitialized in this function [-Wuninitialized]
align_utils.c:242:6: warning: 'indelWidthPattern' may be used uninitialized in this function [-Wuninitialized]
align_utils.c:236:50: warning: 'indelStartPattern' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c find_palindromes.c -o find_palindromes.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c gtestsim.c -o gtestsim.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c inject_code.c -o inject_code.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function 'XStringSet_two_way_letter_frequency':
letter_frequency.c:957:48: warning: unused variable 'x_pos' [-Wunused-variable]
letter_frequency.c:956:13: warning: unused variable 'ans_dimnames' [-Wunused-variable]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c lowlevel_matching.c -o lowlevel_matching.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/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 [-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 -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/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 [-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 -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c match_PWM.c -o match_PWM.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c match_pattern.c -o match_pattern.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c match_pattern_indels.c -o match_pattern_indels.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c match_pdict.c -o match_pdict.o
match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet':
match_pdict.c:442:12: warning: 'ans_col' may be used uninitialized in this function [-Wuninitialized]
match_pdict.c:415:58: note: 'ans_col' was declared here
match_pdict.c: In function 'vmatch_XStringSet_XStringSet':
match_pdict.c:493:13: warning: 'ans_elt' may be used uninitialized in this function [-Wuninitialized]
match_pdict.c:464:57: note: 'ans_elt' was declared here
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -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 -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/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:91:2: warning: 'twobit_sign2pos' may be used uninitialized in this function [-Wuninitialized]
match_pdict_Twobit.c:126:12: note: 'twobit_sign2pos' was declared here
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/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:674:49: warning: unused variable 'ncol' [-Wunused-variable]
match_pdict_utils.c: In function 'match_ppheadtail':
match_pdict_utils.c:734:6: warning: unused variable 'nelt' [-Wunused-variable]
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:841:44: warning: unused variable 'subtotal_NFC' [-Wunused-variable]
match_pdict_utils.c:841:27: warning: unused variable 'total_NFC' [-Wunused-variable]
match_pdict_utils.c:840:33: warning: unused variable 'NFC' [-Wunused-variable]
match_pdict_utils.c:840:26: warning: unused variable 'nloci' [-Wunused-variable]
match_pdict_utils.c:840:20: warning: unused variable 'ndup' [-Wunused-variable]
match_pdict_utils.c: At top level:
match_pdict_utils.c:282:13: warning: 'match_headtail_by_loc' defined but not used [-Wunused-function]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c match_reporting.c -o match_reporting.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c matchprobes.c -o matchprobes.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c pmatchPattern.c -o pmatchPattern.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c replaceAt.c -o replaceAt.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c replace_letter_at.c -o replace_letter_at.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c strutils.c -o strutils.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c translate.c -o translate.o
translate.c: In function 'DNAStringSet_translate':
translate.c:126:29: warning: 'if_ambig0' may be used uninitialized in this function [-Wuninitialized]
translate.c:126:14: warning: 'if_non_ambig0' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature':
utils.c:210:2: warning: 'twobit_sign' may be used uninitialized in this function [-Wuninitialized]
utils.c: In function '_get_twobit_signature_at':
utils.c:217:12: warning: 'twobit_sign' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c xscat.c -o xscat.o
xscat.c: In function 'XString_xscat':
xscat.c:38:2: 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:92:2: warning: 'ans_length' may be used uninitialized in this function [-Wuninitialized]
xscat.c:110:14: warning: 'ans_element_type' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -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 S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.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 replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/Biostrings.buildbin-libdir/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
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'Biostrings' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c BAB_class.c -o BAB_class.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -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 [enabled by default]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function 'SparseMIndex_endIndex':
MIndex_class.c:193:20: warning: unused variable 'poffsets_order' [-Wunused-variable]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c SparseList_utils.c -o SparseList_utils.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c XStringSetList_class.c -o XStringSetList_class.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -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:123:32: warning: 'lkup_length' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function 'parse_FASTQ_file':
XStringSet_io.c:812:7: warning: 'load_rec' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -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:184:31: warning: 'lkup_length' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:173:22: warning: 'sc' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignmentsSingleSubject_align_aligned':
align_utils.c:254:14: warning: 'indelWidthSubject' may be used uninitialized in this function [-Wuninitialized]
align_utils.c:235:42: warning: 'indelStartSubject' may be used uninitialized in this function [-Wuninitialized]
align_utils.c:159:6: warning: 'indelWidthPattern' may be used uninitialized in this function [-Wuninitialized]
align_utils.c:236:50: warning: 'indelStartPattern' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c find_palindromes.c -o find_palindromes.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c gtestsim.c -o gtestsim.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c inject_code.c -o inject_code.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function 'XStringSet_two_way_letter_frequency':
letter_frequency.c:957:48: warning: unused variable 'x_pos' [-Wunused-variable]
letter_frequency.c:956:13: warning: unused variable 'ans_dimnames' [-Wunused-variable]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c lowlevel_matching.c -o lowlevel_matching.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -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 [-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 -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -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 [-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 -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c match_PWM.c -o match_PWM.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c match_pattern.c -o match_pattern.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c match_pattern_indels.c -o match_pattern_indels.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c match_pdict.c -o match_pdict.o
match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet':
match_pdict.c:442:12: warning: 'ans_col' may be used uninitialized in this function [-Wuninitialized]
match_pdict.c:415:58: note: 'ans_col' was declared here
match_pdict.c: In function 'vmatch_XStringSet_XStringSet':
match_pdict.c:493:13: warning: 'ans_elt' may be used uninitialized in this function [-Wuninitialized]
match_pdict.c:464:57: note: 'ans_elt' was declared here
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -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 -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -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:91:2: warning: 'twobit_sign2pos' may be used uninitialized in this function [-Wuninitialized]
match_pdict_Twobit.c:126:12: note: 'twobit_sign2pos' was declared here
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -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:674:49: warning: unused variable 'ncol' [-Wunused-variable]
match_pdict_utils.c: In function 'match_ppheadtail':
match_pdict_utils.c:734:6: warning: unused variable 'nelt' [-Wunused-variable]
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:841:44: warning: unused variable 'subtotal_NFC' [-Wunused-variable]
match_pdict_utils.c:841:27: warning: unused variable 'total_NFC' [-Wunused-variable]
match_pdict_utils.c:840:33: warning: unused variable 'NFC' [-Wunused-variable]
match_pdict_utils.c:840:26: warning: unused variable 'nloci' [-Wunused-variable]
match_pdict_utils.c:840:20: warning: unused variable 'ndup' [-Wunused-variable]
match_pdict_utils.c: At top level:
match_pdict_utils.c:282:13: warning: 'match_headtail_by_loc' defined but not used [-Wunused-function]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c match_reporting.c -o match_reporting.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c matchprobes.c -o matchprobes.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c pmatchPattern.c -o pmatchPattern.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c replaceAt.c -o replaceAt.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c replace_letter_at.c -o replace_letter_at.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c strutils.c -o strutils.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c translate.c -o translate.o
translate.c: In function 'DNAStringSet_translate':
translate.c:101:8: warning: 'if_ambig0' may be used uninitialized in this function [-Wuninitialized]
translate.c:126:29: note: 'if_ambig0' was declared here
translate.c:97:8: warning: 'if_non_ambig0' may be used uninitialized in this function [-Wuninitialized]
translate.c:126:14: note: 'if_non_ambig0' was declared here
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature':
utils.c:210:2: warning: 'twobit_sign' may be used uninitialized in this function [-Wuninitialized]
utils.c: In function '_get_twobit_signature_at':
utils.c:217:12: warning: 'twobit_sign' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c xscat.c -o xscat.o
xscat.c: In function 'XString_xscat':
xscat.c:38:2: 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:92:2: warning: 'ans_length' may be used uninitialized in this function [-Wuninitialized]
xscat.c:110:14: warning: 'ans_element_type' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -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 S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.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 replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/Biostrings.buildbin-libdir/Biostrings/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Biostrings' as Biostrings_2.38.4.zip
* DONE (Biostrings)