Back to Multiple platform build/check report for BioC 3.8
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for Biostrings on merida1

This page was generated on 2019-04-16 11:54:05 -0400 (Tue, 16 Apr 2019).

Package 159/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biostrings 2.50.2
H. Pag├Ęs
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/Biostrings
Branch: RELEASE_3_8
Last Commit: 025e734
Last Changed Date: 2019-01-03 09:57:07 -0400 (Thu, 03 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Biostrings
Version: 2.50.2
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_2.50.2.tar.gz
StartedAt: 2019-04-15 22:38:27 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:49:16 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 648.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Biostrings.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_2.50.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Biostrings.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.50.2’
* 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 13.9Mb
  sub-directories of 1Mb or more:
    R         1.6Mb
    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:::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   338.084  4.631 345.644
matchPDict-inexact  55.130  0.840  56.560
findPalindromes     32.043  0.172  32.505
XStringSet-class    12.422  0.514  13.070
XStringSet-io       10.312  0.563  11.095
stringDist           8.922  0.037   9.065
matchPattern         7.182  0.254   7.537
* 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-3.8-bioc/meat/Biostrings.Rcheck/00check.log’
for details.



Installation output

Biostrings.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Biostrings’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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:818:20: 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: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: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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/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 version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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, lengths, 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 15 22:48:59 2019 
*********************************************** 
Number of test functions: 38 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Biostrings RUnit Tests - 38 test functions, 0 errors, 0 failures
Number of test functions: 38 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 11.702   0.910  12.675 

Example timings

Biostrings.Rcheck/Biostrings-Ex.timings

nameusersystemelapsed
AAString-class0.0070.0010.008
AMINO_ACID_CODE0.0760.0010.080
AlignedXStringSet-class0.2940.0040.305
DNAString-class0.0020.0000.001
GENETIC_CODE0.0160.0030.020
HNF4alpha0.0220.0020.026
IUPAC_CODE_MAP0.1970.0090.207
MIndex-class0.0000.0000.001
MaskedXString-class0.2990.0370.340
MultipleAlignment-class2.0450.0492.110
PDict-class4.1890.1414.517
PairwiseAlignments-class0.7890.0060.803
PairwiseAlignments-io2.8630.1983.105
QualityScaledXStringSet-class0.2670.0070.274
RNAString-class0.0090.0000.008
XString-class0.0160.0010.016
XStringQuality-class0.2320.0020.235
XStringSet-class12.422 0.51413.070
XStringSet-comparison3.0800.2963.413
XStringSet-io10.312 0.56311.095
XStringSetList-class0.3590.0100.391
XStringViews-class0.1920.0290.226
align-utils0.0680.0090.078
chartr0.7810.0520.847
detail0.6070.1320.748
dinucleotideFrequencyTest0.0190.0030.022
findPalindromes32.043 0.17232.505
getSeq0.0970.0040.101
gregexpr20.0030.0000.003
injectHardMask0.0510.0020.053
letter0.0210.0000.021
letterFrequency2.0510.1192.195
longestConsecutive0.0020.0000.002
lowlevel-matching0.5190.0570.577
maskMotif1.2020.0911.301
match-utils0.0210.0000.022
matchLRPatterns0.8020.0440.859
matchPDict-exact338.084 4.631345.644
matchPDict-inexact55.13 0.8456.56
matchPWM3.3140.0123.363
matchPattern7.1820.2547.537
matchProbePair1.5780.0481.652
matchprobes0.4320.0080.464
misc0.0290.0000.035
needwunsQS0.0030.0000.003
nucleotideFrequency0.9590.0641.043
padAndClip0.6070.0590.670
pairwiseAlignment0.9760.0641.048
phiX174Phage0.6040.0540.668
pid0.5510.1320.687
replaceAt3.2460.2853.559
replaceLetterAt0.5870.1060.699
reverseComplement1.2210.1131.359
stringDist8.9220.0379.065
substitution_matrices1.0660.1901.259
toComplex0.0030.0000.004
translate1.4370.0241.467
trimLRPatterns0.0910.0010.094
xscat1.4750.0451.525
yeastSEQCHR10.0050.0020.007