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BioC 3.5: CHECK report for Biostrings on malbec2

This page was generated on 2017-08-16 13:12:15 -0400 (Wed, 16 Aug 2017).

Package 135/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biostrings 2.44.2
H. Pagès
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/Biostrings
Last Changed Rev: 131443 / Revision: 131943
Last Changed Date: 2017-07-20 15:20:57 -0400 (Thu, 20 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Biostrings
Version: 2.44.2
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Biostrings_2.44.2.tar.gz
StartedAt: 2017-08-15 21:32:53 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:41:26 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 512.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Biostrings.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Biostrings_2.44.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/Biostrings.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.44.2’
* 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       1.1Mb
    extdata  11.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
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:::regroupBySupergroup’
  ‘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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘strsplit’ ‘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 'parallelSlotNames' and siglist 'ByPos_MIndex'
  generic 'parallelSlotNames' and siglist 'MIndex'
  generic 'parallelSlotNames' and siglist 'PairwiseAlignments'
  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 'strsplit' 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 ... 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   280.840  1.464 282.491
matchPDict-inexact  40.280  0.108  40.413
findPalindromes     23.556  0.020  23.746
XStringSet-class     9.844  0.112  10.123
matchPattern         5.028  0.264   5.295
XStringSet-io        5.012  0.036   5.050
* 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, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/Biostrings.Rcheck/00check.log’
for details.


Biostrings.Rcheck/00install.out:

* installing *source* package ‘Biostrings’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c BAB_class.c -o BAB_class.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function ‘SparseMIndex_endIndex’:
MIndex_class.c:184:20: warning: unused variable ‘poffsets_order’ [-Wunused-variable]
  IntAE *poffsets, *poffsets_order;
                    ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c XStringSetList_class.c -o XStringSetList_class.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/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:111:3: warning: ‘lkup_len’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
   ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c XString_class.c -o XString_class.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c find_palindromes.c -o find_palindromes.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c gtestsim.c -o gtestsim.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c inject_code.c -o inject_code.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c lowlevel_matching.c -o lowlevel_matching.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c match_PWM.c -o match_PWM.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c match_pattern.c -o match_pattern.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
In file included from /home/biocbuild/bbs-3.5-bioc/R/include/Rdefines.h:40:0,
                 from /home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.5-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-3.5-bioc/R/include/Rinternals.h:691:20: 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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c match_reporting.c -o match_reporting.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c matchprobes.c -o matchprobes.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c replaceAt.c -o replaceAt.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c replace_letter_at.c -o replace_letter_at.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c strutils.c -o strutils.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c translate.c -o translate.o
translate.c: In function ‘DNAStringSet_translate’:
translate.c:110:8: warning: ‘if_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (if_ambig == TRANSLATE_ERROR) {
        ^
translate.c:136:29: note: ‘if_ambig0’ was declared here
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
                             ^
translate.c:106:8: warning: ‘if_non_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (if_non_ambig == TRANSLATE_TO_X)
        ^
translate.c:136:14: note: ‘if_non_ambig0’ was declared here
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
              ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c xscat.c -o xscat.o
In file included from /home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from /home/biocbuild/bbs-3.5-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-3.5-bioc/R/include/Rdefines.h:98:21: 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-3.5-bioc/R/include/Rdefines.h:40:0,
                 from /home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.5-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-3.5-bioc/R/include/Rinternals.h:691:20: 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-3.5-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from /home/biocbuild/bbs-3.5-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-3.5-bioc/R/include/Rdefines.h:92:25: 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-3.5-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-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/Biostrings.Rcheck/Biostrings/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘strsplit’ 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
* DONE (Biostrings)

Biostrings.Rcheck/Biostrings-Ex.timings:

nameusersystemelapsed
AAString-class0.0040.0000.004
AMINO_ACID_CODE0.0240.0000.026
AlignedXStringSet-class0.3120.0000.313
DNAString-class0.0000.0040.002
GENETIC_CODE0.0360.0000.035
HNF4alpha0.0120.0000.013
IUPAC_CODE_MAP0.1920.0000.192
MIndex-class0.0000.0000.001
MaskedXString-class0.3760.0000.398
MultipleAlignment-class1.3680.0121.382
PDict-class4.1080.0564.264
PairwiseAlignments-class0.2800.0000.278
PairwiseAlignments-io2.0240.0922.117
QualityScaledXStringSet-class0.0120.0000.011
RNAString-class0.0000.0040.006
XString-class0.0080.0000.009
XStringQuality-class0.2120.0040.218
XStringSet-class 9.844 0.11210.123
XStringSet-comparison2.2880.0122.301
XStringSet-io5.0120.0365.050
XStringSetList-class0.1760.0000.176
XStringViews-class0.1480.0000.148
align-utils0.0280.0000.028
chartr0.5480.0120.562
detail0.5320.0400.581
dinucleotideFrequencyTest0.2120.0120.229
findPalindromes23.556 0.02023.746
getSeq0.0680.0040.070
gregexpr20.0240.0040.026
injectHardMask0.0840.0040.087
letter0.0320.0040.035
letterFrequency1.0080.0121.021
longestConsecutive000
lowlevel-matching0.4760.0040.480
maskMotif1.5320.0361.571
match-utils0.0280.0000.028
matchLRPatterns0.5800.0800.731
matchPDict-exact280.840 1.464282.491
matchPDict-inexact40.280 0.10840.413
matchPWM1.9880.0041.992
matchPattern5.0280.2645.295
matchProbePair1.2360.0041.240
matchprobes0.2560.0040.259
misc0.0120.0000.013
needwunsQS0.0000.0000.001
nucleotideFrequency0.6080.0160.626
padAndClip0.4080.0000.409
pairwiseAlignment0.4120.0040.416
phiX174Phage0.4280.0000.431
pid0.1800.0000.182
replaceAt1.8840.0041.889
replaceLetterAt0.3640.0000.363
reverseComplement0.9320.0200.952
stringDist3.8200.0443.867
substitution_matrices0.2440.0600.303
toComplex0.0040.0000.002
translate1.1760.0041.179
trimLRPatterns0.0840.0040.089
xscat0.8400.0000.839
yeastSEQCHR10.0040.0000.004