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CHECK report for Biostrings on merida2

This page was generated on 2019-04-09 13:22:32 -0400 (Tue, 09 Apr 2019).

Package 166/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biostrings 2.51.5
H. Pagès
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/Biostrings
Branch: master
Last Commit: 951902c
Last Changed Date: 2019-03-15 18:47:25 -0400 (Fri, 15 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: Biostrings
Version: 2.51.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Biostrings_2.51.5.tar.gz
StartedAt: 2019-04-08 23:33:29 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:43:55 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 626.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Biostrings.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Biostrings_2.51.5.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Biostrings.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biostrings/DESCRIPTION’ ... OK
* this is package ‘Biostrings’ version ‘2.51.5’
* 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 13.9Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    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:::show_IntegerRangesList’ ‘IRanges:::unlist_as_integer’
  ‘S4Vectors:::anyMissingOrOutside’ ‘XVector:::close_filexp’
  ‘XVector:::extract_character_from_XRaw_by_positions’
  ‘XVector:::extract_character_from_XRaw_by_ranges’
  ‘XVector:::new_XVectorList_from_list_of_XVector’
  ‘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 '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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
matchPDict-exact   329.079  4.680 336.364
matchPDict-inexact  54.715  1.002  56.332
findPalindromes     31.116  0.122  31.433
XStringSet-class    12.997  0.485  13.579
XStringSet-io        8.426  0.637   9.133
stringDist           7.794  0.031   7.872
matchPattern         7.211  0.220   7.494
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/Biostrings.Rcheck/00check.log’
for details.



Installation output

Biostrings.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Biostrings
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Biostrings’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c BAB_class.c -o BAB_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c BitMatrix.c -o BitMatrix.o
BitMatrix.c:299:13: warning: unused function 'BitMatrix_print' [-Wunused-function]
static void BitMatrix_print(BitMatrix *bitmat)
            ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MIndex_class.c -o MIndex_class.o
MIndex_class.c:184:20: warning: unused variable 'poffsets_order' [-Wunused-variable]
        IntAE *poffsets, *poffsets_order;
                          ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_Biostrings.c -o R_init_Biostrings.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RoSeqs_utils.c -o RoSeqs_utils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SparseList_utils.c -o SparseList_utils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c XStringSetList_class.c -o XStringSetList_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c XStringSet_class.c -o XStringSet_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c XString_class.c -o XString_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c align_needwunsQS.c -o align_needwunsQS.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c align_utils.c -o align_utils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c find_palindromes.c -o find_palindromes.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c gtestsim.c -o gtestsim.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c inject_code.c -o inject_code.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -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"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c lowlevel_matching.c -o lowlevel_matching.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c match_PWM.c -o match_PWM.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c match_pattern.c -o match_pattern.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c match_pattern_indels.c -o match_pattern_indels.o
match_pattern_indels.c:7:13: warning: unused function 'test_match_pattern_indels' [-Wunused-function]
static void test_match_pattern_indels(const char *p, const char *s,
            ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c match_pattern_shiftor.c -o match_pattern_shiftor.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c match_pdict.c -o match_pdict.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c:139:13: warning: unused function 'debug_node_counting_functions' [-Wunused-function]
static void debug_node_counting_functions(int maxdepth)
            ^
match_pdict_ACtree2.c:602:21: warning: unused function 'a_nice_max_nodeextbuf_nelt' [-Wunused-function]
static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
                    ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c match_pdict_Twobit.c -o match_pdict_Twobit.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c match_pdict_utils.c -o match_pdict_utils.o
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:712:6: warning: unused variable 'nelt' [-Wunused-variable]
        int nelt, nkey0, nkey1, nkey2, i, key;
            ^
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: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:260:13: 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"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c match_reporting.c -o match_reporting.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c matchprobes.c -o matchprobes.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c pmatchPattern.c -o pmatchPattern.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c read_fasta_files.c -o read_fasta_files.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c read_fastq_files.c -o read_fastq_files.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c replaceAt.c -o replaceAt.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c replace_letter_at.c -o replace_letter_at.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c strutils.c -o strutils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c translate.c -o translate.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c unstrsplit_methods.c -o unstrsplit_methods.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.c -o utils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I/usr/local/include   -fPIC  -Wall -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 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 read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet”
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)

Tests output

Biostrings.Rcheck/tests/run_unitTests.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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> require("Biostrings") || stop("unable to load Biostrings package")
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

[1] TRUE
> Biostrings:::.test()


RUNIT TEST PROTOCOL -- Mon Apr  8 23:43:40 2019 
*********************************************** 
Number of test functions: 39 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Biostrings RUnit Tests - 39 test functions, 0 errors, 0 failures
Number of test functions: 39 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 10.649   0.934  11.649 

Example timings

Biostrings.Rcheck/Biostrings-Ex.timings

nameusersystemelapsed
AAString-class0.0030.0000.004
AMINO_ACID_CODE0.0020.0000.003
AlignedXStringSet-class0.0800.0030.086
DNAString-class0.0030.0000.003
GENETIC_CODE0.0170.0040.021
HNF4alpha0.2100.0020.216
IUPAC_CODE_MAP0.1730.0040.180
MIndex-class0.0000.0000.001
MaskedXString-class0.2710.0320.330
MultipleAlignment-class1.7510.0461.805
PDict-class3.9680.1314.130
PairwiseAlignments-class0.7170.0090.731
PairwiseAlignments-io2.4690.2002.686
QualityScaledXStringSet-class0.1910.0040.199
RNAString-class0.0070.0000.007
XString-class0.0120.0010.013
XStringQuality-class0.2140.0030.217
XStringSet-class12.997 0.48513.579
XStringSet-comparison2.7240.2192.959
XStringSet-io8.4260.6379.133
XStringSetList-class0.2960.0050.306
XStringViews-class0.1140.0070.121
align-utils0.0440.0080.051
chartr0.8070.0490.861
detail0.3870.0170.405
dinucleotideFrequencyTest0.0150.0020.018
findPalindromes31.116 0.12231.433
getSeq0.0600.0030.063
gregexpr20.0010.0010.002
injectHardMask0.0420.0010.044
letter0.0180.0010.019
letterFrequency1.0690.0601.131
longestConsecutive000
lowlevel-matching0.4020.0520.457
maskMotif1.0290.0751.112
match-utils0.0190.0010.019
matchLRPatterns0.7260.0410.768
matchPDict-exact329.079 4.680336.364
matchPDict-inexact54.715 1.00256.332
matchPWM2.9640.0122.998
matchPattern7.2110.2207.494
matchProbePair1.4750.0461.523
matchprobes0.3420.0100.352
misc0.0260.0000.027
needwunsQS0.0000.0000.001
nucleotideFrequency0.9890.0541.048
padAndClip0.7270.0690.801
pairwiseAlignment0.9010.0670.975
phiX174Phage0.5860.0500.638
pid0.4280.0370.468
replaceAt3.2490.3623.620
replaceLetterAt0.6410.1060.749
reverseComplement1.3560.2301.598
stringDist7.7940.0317.872
substitution_matrices0.7450.0200.772
toComplex0.0020.0000.002
translate2.6530.0782.754
trimLRPatterns0.0830.0010.085
xscat1.2610.0441.318
yeastSEQCHR10.0040.0020.005