BioC 3.1: CHECK report for Biostrings on morelia

Package: Biostrings

Version: 2.36.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biostrings_2.36.4.tar.gz

StartedAt: 2015-10-08 23:38:06 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:48:07 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 601.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biostrings.Rcheck

Warnings: 3

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biostrings_2.36.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/Biostrings.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biostrings/DESCRIPTION’ ... OK
* this is package ‘Biostrings’ version ‘2.36.4’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Biostrings’ can be installed ... [19s/19s] OK
* checking installed package size ... NOTE
  installed size is 14.2Mb
  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.
Versioned 'LinkingTo' value for ‘S4Vectors’ is only usable in R >= 3.0.2
* 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
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [473s/474s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
matchPDict-exact   312.685 14.862 327.904
matchPDict-inexact  40.272  2.084  42.426
findPalindromes     30.998  1.372  32.566
XStringSet-class     8.191  0.796   9.225
XStringSet-io        6.056  0.644   6.708
matchPattern         6.125  0.552   6.682
replaceAt            4.760  0.904   5.667
* 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: 3 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/Biostrings.Rcheck/00check.log’
for details.

* installing *source* package ‘Biostrings’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c BAB_class.c -o BAB_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c BitMatrix.c -o BitMatrix.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c MIndex_class.c -o MIndex_class.o
MIndex_class.c:193:18: warning: unused variable 'poffsets_order' [-Wunused-variable]
        IntAE poffsets, poffsets_order;
                        ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_Biostrings.c -o R_init_Biostrings.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RoSeqs_utils.c -o RoSeqs_utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c SparseList_utils.c -o SparseList_utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c XStringSetList_class.c -o XStringSetList_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c XStringSet_class.c -o XStringSet_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c XStringSet_io.c -o XStringSet_io.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c XString_class.c -o XString_class.o
XString_class.c:178:6: warning: variable 'lkup_length' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
        if (lkup == R_NilValue) {
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
XString_class.c:185:30: note: uninitialized use occurs here
                        INTEGER(start)[0], lkup0, lkup_length);
                                                  ^˜˜˜˜˜˜˜˜˜˜
XString_class.c:178:2: note: remove the 'if' if its condition is always false
        if (lkup == R_NilValue) {
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
XString_class.c:168:17: note: initialize the variable 'lkup_length' to silence this warning
        int lkup_length;
                       ^
                        = 0
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c align_needwunsQS.c -o align_needwunsQS.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c align_utils.c -o align_utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c find_palindromes.c -o find_palindromes.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c gtestsim.c -o gtestsim.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c inject_code.c -o inject_code.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c io_utils.c -o io_utils.o
io_utils.c:399:43: warning: variable 'subtype' is uninitialized when used here [-Wuninitialized]
                file = oZFile_open(expath, mode, ztype, subtype);
                                                        ^˜˜˜˜˜˜
io_utils.c:389:20: note: initialize the variable 'subtype' to silence this warning
        int ztype, subtype;
                          ^
                           = 0
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c letter_frequency.c -o letter_frequency.o
letter_frequency.c:956:13: warning: unused variable 'ans_dimnames' [-Wunused-variable]
  SEXP ans, ans_dimnames;
            ^
letter_frequency.c:957:48: warning: unused variable 'x_pos' [-Wunused-variable]
  int x_width, y_width, x_length, *ans_mat, i, x_pos;
                                               ^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c lowlevel_matching.c -o lowlevel_matching.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_BOC.c -o match_BOC.o
match_BOC.c:268:59: warning: unused variable 'offsets' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                 ^
match_BOC.c:268:55: warning: unused variable 'j' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                             ^
match_BOC.c:268:68: warning: unused variable 'noffsets' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                          ^
match_BOC.c:331:3: warning: unused label 'continue0' [-Wunused-label]
                continue0: ;
                ^˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_BOC2.c -o match_BOC2.o
match_BOC2.c:234:55: warning: unused variable 'j' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                             ^
match_BOC2.c:234:68: warning: unused variable 'noffsets' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                          ^
match_BOC2.c:234:59: warning: unused variable 'offsets' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                 ^
match_BOC2.c:288:3: warning: unused label 'continue0' [-Wunused-label]
                continue0: ;
                ^˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_PWM.c -o match_PWM.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_pattern.c -o match_pattern.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_pattern_indels.c -o match_pattern_indels.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_pattern_shiftor.c -o match_pattern_shiftor.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_pdict.c -o match_pdict.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c:640:21: warning: unused function 'a_nice_max_nodeextbuf_nelt' [-Wunused-function]
static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
                    ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_pdict_Twobit.c -o match_pdict_Twobit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c:681:49: warning: unused variable 'ncol' [-Wunused-variable]
        int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
                                                       ^
match_pdict_utils.c:741:6: warning: unused variable 'nelt' [-Wunused-variable]
        int nelt, nkey0, nkey1, nkey2, i;
            ^
match_pdict_utils.c:850:20: warning: unused variable 'ndup' [-Wunused-variable]
        unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                          ^
match_pdict_utils.c:850:26: warning: unused variable 'nloci' [-Wunused-variable]
        unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                                ^
match_pdict_utils.c:850:33: warning: unused variable 'NFC' [-Wunused-variable]
        unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                                       ^
match_pdict_utils.c:851:27: warning: unused variable 'total_NFC' [-Wunused-variable]
        static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                                 ^
match_pdict_utils.c:851:44: warning: unused variable 'subtotal_NFC' [-Wunused-variable]
        static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                                                  ^
match_pdict_utils.c:286:13: warning: unused function 'match_headtail_by_loc' [-Wunused-function]
static void match_headtail_by_loc(const HeadTail *headtail,
            ^
8 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c match_reporting.c -o match_reporting.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c matchprobes.c -o matchprobes.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pmatchPattern.c -o pmatchPattern.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c replace_letter_at.c -o replace_letter_at.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c strutils.c -o strutils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c translate.c -o translate.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c unstrsplit_methods.c -o unstrsplit_methods.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c utils.c -o utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c xscat.c -o xscat.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Biostrings.so 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 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 unstrsplit_methods.o utils.o xscat.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/Biostrings.Rcheck/Biostrings/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (Biostrings)

name	user	system	elapsed
AAString-class	0.005	0.000	0.006
AMINO_ACID_CODE	0.001	0.000	0.002
AlignedXStringSet-class	0.062	0.005	0.067
DNAString-class	0.001	0.000	0.002
GENETIC_CODE	0.011	0.005	0.015
HNF4alpha	0.030	0.015	0.044
IUPAC_CODE_MAP	0.004	0.002	0.005
MIndex-class	0.000	0.000	0.001
MaskedXString-class	0.275	0.010	0.332
MultipleAlignment-class	1.237	0.039	1.278
PDict-class	3.979	0.338	4.364
PairwiseAlignments-class	0.156	0.013	0.169
PairwiseAlignments-io	2.383	0.283	2.671
QualityScaledXStringSet-class	0.023	0.001	0.023
RNAString-class	0.011	0.001	0.011
XString-class	0.011	0.000	0.012
XStringQuality-class	0.075	0.000	0.076
XStringSet-class	8.191	0.796	9.225
XStringSet-comparison	2.837	0.490	3.346
XStringSet-io	6.056	0.644	6.708
XStringSetList-class	0.565	0.027	0.593
XStringViews-class	0.156	0.029	0.186
align-utils	0.052	0.002	0.053
chartr	0.784	0.123	0.920
detail	0.568	0.023	0.590
dinucleotideFrequencyTest	0.015	0.001	0.016
findPalindromes	30.998	1.372	32.566
getSeq	0.084	0.002	0.086
gregexpr2	0.001	0.000	0.002
injectHardMask	0.046	0.001	0.047
letter	0.017	0.000	0.017
letterFrequency	1.428	0.222	1.650
longestConsecutive	0.001	0.000	0.001
lowlevel-matching	0.574	0.084	0.659
maskMotif	1.251	0.109	1.367
match-utils	0.02	0.00	0.02
matchLRPatterns	0.744	0.119	0.957
matchPDict-exact	312.685	14.862	327.904
matchPDict-inexact	40.272	2.084	42.426
matchPWM	3.553	0.089	3.642
matchPattern	6.125	0.552	6.682
matchProbePair	1.336	0.062	1.404
matchprobes	0.279	0.005	0.284
misc	0.011	0.000	0.011
needwunsQS	0.002	0.000	0.002
nucleotideFrequency	0.780	0.078	0.858
padAndClip	0.621	0.058	0.684
pairwiseAlignment	0.678	0.150	0.828
phiX174Phage	0.575	0.118	0.693
pid	0.284	0.030	0.314
replaceAt	4.760	0.904	5.667
replaceLetterAt	0.812	0.190	1.005
reverseComplement	1.448	0.198	1.648
stringDist	4.697	0.287	4.988
substitution_matrices	0.510	0.146	0.657
toComplex	0.002	0.001	0.002
translate	0.882	0.020	0.902
trimLRPatterns	0.051	0.001	0.052
xscat	1.590	0.165	1.755
yeastSEQCHR1	0.004	0.000	0.004