BioC 3.4: CHECK report for Biostrings on zin1

Package: Biostrings

Version: 2.41.4

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Biostrings_2.41.4.tar.gz

StartedAt: 2016-09-20 03:49:23 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 03:58:09 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 526.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biostrings.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Biostrings_2.41.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Biostrings.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biostrings/DESCRIPTION’ ... OK
* this is package ‘Biostrings’ version ‘2.41.4’
* package encoding: UTF-8
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 14.9Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    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
* 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:::new_Views’ ‘IRanges:::showRangesList’
  ‘S4Vectors:::anyMissingOrOutside’ ‘XVector:::finalize_filexp’
  ‘XVector:::new_XVectorList_from_list_of_XVector’
  ‘XVector:::open_input_files’ ‘XVector:::open_output_file’
  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 ... NOTE
writePairwiseAlignments: no visible global function definition for
  ‘packageVersion’
encoding,XStringQuality: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  packageVersion setNames
Consider adding
  importFrom("stats", "setNames")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘twoWayAlphabetFrequency’
Undocumented S4 methods:
  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 'pcompare' and siglist 'Vector,XStringSet'
  generic 'pcompare' and siglist 'XStringSet,Vector'
  generic 'pcompare' and siglist 'XStringSet,vector'
  generic 'pcompare' and siglist 'vector,XStringSet'
  generic 'relistToClass' and siglist 'XString'
  generic 'relistToClass' and siglist 'XStringSet'
  generic 'showAsCell' and siglist 'XStringSetList'
  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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
matchPDict-exact   287.308  8.876 296.208
matchPDict-inexact  40.680  0.196  40.887
findPalindromes     24.812  0.528  25.486
XStringSet-class     8.312  1.544  10.122
matchPattern         5.148  0.244   5.425
XStringSet-io        4.152  1.224   5.373
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/Biostrings.Rcheck/00check.log’
for details.

* installing *source* package ‘Biostrings’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c BAB_class.c -o BAB_class.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c BitMatrix.c -o BitMatrix.o
BitMatrix.c:299:13: warning: ‘BitMatrix_print’ defined but not used [-Wunused-function]
 static void BitMatrix_print(BitMatrix *bitmat)
             ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function ‘SparseMIndex_endIndex’:
MIndex_class.c:179:20: warning: unused variable ‘poffsets_order’ [-Wunused-variable]
  IntAE *poffsets, *poffsets_order;
                    ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c XStringSetList_class.c -o XStringSetList_class.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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:109:3: warning: ‘lkup_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
   ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function ‘parse_FASTQ_file’:
XStringSet_io.c:799:7: warning: ‘load_rec’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (load_rec && loader->load_qual != NULL)
       ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c XString_class.c -o XString_class.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function ‘align_needwunsQS’:
align_needwunsQS.c:155:22: warning: ‘sc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  INTEGER(ans_elt)[0] = score;
                      ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -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 [-Wmaybe-uninitialized]
     jPattern += indelWidthSubject;
              ^
align_utils.c:235:42: warning: ‘indelStartSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
                                          ^
align_utils.c:225:26: warning: ‘indelWidthPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
                          ^
align_utils.c:236:50: warning: ‘indelStartPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
                                                  ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c find_palindromes.c -o find_palindromes.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c gtestsim.c -o gtestsim.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c inject_code.c -o inject_code.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -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]
   int x_width, y_width, x_length, *ans_mat, i, x_pos;
                                                ^
letter_frequency.c:956:13: warning: unused variable ‘ans_dimnames’ [-Wunused-variable]
   SEXP ans, ans_dimnames;
             ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c lowlevel_matching.c -o lowlevel_matching.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_PWM.c -o match_PWM.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pattern.c -o match_pattern.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pattern_indels.c -o match_pattern_indels.o
match_pattern_indels.c:7:13: warning: ‘test_match_pattern_indels’ defined but not used [-Wunused-function]
 static void test_match_pattern_indels(const char *p, const char *s,
             ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pdict.c -o match_pdict.o
match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’:
match_pdict.c:419:12: warning: ‘ans_col’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    ans_col += tb_length;
            ^
match_pdict.c:392:58: note: ‘ans_col’ was declared here
  int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
                                                          ^
match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’:
match_pdict.c:470:13: warning: ‘ans_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     ans_elt += P_length;
             ^
match_pdict.c:441:57: note: ‘ans_elt’ was declared here
  int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
                                                         ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c: In function ‘split_and_move_pointers’:
match_pdict_ACtree2.c:1031:10: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable]
  ACnode *node0, *node1, *node2;
          ^
match_pdict_ACtree2.c: In function ‘merge_pointers’:
match_pdict_ACtree2.c:1076:10: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable]
  ACnode *node0, *node1, *node2;
          ^
match_pdict_ACtree2.c: At top level:
match_pdict_ACtree2.c:139:13: warning: ‘debug_node_counting_functions’ defined but not used [-Wunused-function]
 static void debug_node_counting_functions(int maxdepth)
             ^
match_pdict_ACtree2.c:602:21: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used [-Wunused-function]
 static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
                     ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
In file included from /home/biocbuild/bbs-3.4-bioc/R/include/Rdefines.h:36:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from match_pdict_Twobit.c:10:
match_pdict_Twobit.c: In function ‘build_Twobit’:
/home/biocbuild/bbs-3.4-bioc/R/include/Rinternals.h:661:20: warning: ‘twobit_sign2pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^
match_pdict_Twobit.c:110:12: note: ‘twobit_sign2pos’ was declared here
  SEXP ans, twobit_sign2pos;
            ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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:652:49: warning: unused variable ‘ncol’ [-Wunused-variable]
  int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
                                                 ^
match_pdict_utils.c: In function ‘match_ppheadtail’:
match_pdict_utils.c:712:6: warning: unused variable ‘nelt’ [-Wunused-variable]
  int nelt, nkey0, nkey1, nkey2, i, key;
      ^
match_pdict_utils.c: In function ‘_match_pdict_all_flanks’:
match_pdict_utils.c:819:44: warning: unused variable ‘subtotal_NFC’ [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                                            ^
match_pdict_utils.c:819:27: warning: unused variable ‘total_NFC’ [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                           ^
match_pdict_utils.c:818:33: warning: unused variable ‘NFC’ [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                                 ^
match_pdict_utils.c:818:26: warning: unused variable ‘nloci’ [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                          ^
match_pdict_utils.c:818:20: warning: unused variable ‘ndup’ [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                    ^
match_pdict_utils.c: At top level:
match_pdict_utils.c:260:13: warning: ‘match_headtail_by_loc’ defined but not used [-Wunused-function]
 static void match_headtail_by_loc(const HeadTail *headtail,
             ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c match_reporting.c -o match_reporting.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c matchprobes.c -o matchprobes.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c replaceAt.c -o replaceAt.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c replace_letter_at.c -o replace_letter_at.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c strutils.c -o strutils.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -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 [-Wmaybe-uninitialized]
     if (if_ambig == TRANSLATE_ERROR) {
        ^
translate.c:126:29: note: ‘if_ambig0’ was declared here
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
                             ^
translate.c:97:8: warning: ‘if_non_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (if_non_ambig == TRANSLATE_TO_X)
        ^
translate.c:126:14: note: ‘if_non_ambig0’ was declared here
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
              ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c utils.c -o utils.o
utils.c: In function ‘_get_twobit_signature’:
utils.c:157:9: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  return twobit_sign;
         ^
utils.c: In function ‘_get_twobit_signature_at’:
utils.c:164:12: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  int i, j, twobit_sign;
            ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c xscat.c -o xscat.o
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function ‘XString_xscat’:
/home/biocbuild/bbs-3.4-bioc/R/include/Rdefines.h:94:21: warning: ‘ans_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define NEW_RAW(n)  Rf_allocVector(RAWSXP,n)
                     ^
xscat.c:18:13: note: ‘ans_length’ was declared here
  int nargs, ans_length, tag_offset, j;
             ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/include/Rdefines.h:36:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
/home/biocbuild/bbs-3.4-bioc/R/include/Rinternals.h:661:20: warning: ‘ans_classname’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^
xscat.c:20:14: note: ‘ans_classname’ was declared here
  const char *ans_classname;
              ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function ‘XStringSet_xscat’:
/home/biocbuild/bbs-3.4-bioc/R/include/Rdefines.h:88:25: warning: ‘ans_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define NEW_INTEGER(n)  Rf_allocVector(INTSXP,n)
                         ^
xscat.c:66:32: note: ‘ans_length’ was declared here
  int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
                                ^
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/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 letter_frequency.o lowlevel_matching.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 -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/Biostrings.Rcheck/Biostrings/libs
** R
** data
** inst
** preparing package for lazy loading
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
* DONE (Biostrings)

name	user	system	elapsed
AAString-class	0.004	0.000	0.004
AMINO_ACID_CODE	0.004	0.000	0.002
AlignedXStringSet-class	0.048	0.008	0.054
DNAString-class	0.000	0.000	0.002
GENETIC_CODE	0.012	0.000	0.011
HNF4alpha	0.016	0.000	0.014
IUPAC_CODE_MAP	0.004	0.000	0.004
MIndex-class	0.000	0.000	0.001
MaskedXString-class	0.176	0.000	0.216
MultipleAlignment-class	1.000	0.012	1.012
PDict-class	3.484	0.824	4.328
PairwiseAlignments-class	0.124	0.000	0.125
PairwiseAlignments-io	1.904	0.696	2.603
QualityScaledXStringSet-class	0.008	0.000	0.011
RNAString-class	0.024	0.000	0.026
XString-class	0.004	0.004	0.008
XStringQuality-class	0.132	0.000	0.132
XStringSet-class	8.312	1.544	10.122
XStringSet-comparison	1.612	1.840	3.454
XStringSet-io	4.152	1.224	5.373
XStringSetList-class	0.172	0.004	0.177
XStringViews-class	0.112	0.000	0.112
align-utils	0.032	0.000	0.033
chartr	0.528	0.600	1.162
detail	0.316	0.028	0.350
dinucleotideFrequencyTest	0.012	0.000	0.012
findPalindromes	24.812	0.528	25.486
getSeq	0.056	0.004	0.063
gregexpr2	0.000	0.000	0.001
injectHardMask	0.032	0.000	0.033
letter	0.016	0.000	0.014
letterFrequency	1.324	0.036	1.365
longestConsecutive	0.000	0.000	0.001
lowlevel-matching	0.348	0.112	0.461
maskMotif	1.052	0.540	1.625
match-utils	0.02	0.00	0.02
matchLRPatterns	0.404	1.352	1.797
matchPDict-exact	287.308	8.876	296.208
matchPDict-inexact	40.680	0.196	40.887
matchPWM	2.300	0.000	2.301
matchPattern	5.148	0.244	5.425
matchProbePair	1.208	0.012	1.220
matchprobes	0.256	0.004	0.267
misc	0.012	0.000	0.013
needwunsQS	0.000	0.000	0.001
nucleotideFrequency	0.640	0.004	0.646
padAndClip	0.416	0.000	0.416
pairwiseAlignment	0.58	0.00	0.58
phiX174Phage	0.484	0.000	0.484
pid	0.224	0.000	0.225
replaceAt	2.12	0.00	2.12
replaceLetterAt	0.392	0.004	0.396
reverseComplement	1.076	0.188	1.270
stringDist	4.176	0.004	4.181
substitution_matrices	0.356	0.000	0.355
toComplex	0.004	0.000	0.002
translate	0.760	0.000	0.758
trimLRPatterns	0.056	0.000	0.056
xscat	1.052	0.004	1.058
yeastSEQCHR1	0.004	0.000	0.004