Package: Biostrings

Version: 2.54.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Biostrings_2.54.0.tar.gz

StartedAt: 2020-04-15 00:10:59 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:21:13 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 614.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biostrings.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Biostrings_2.54.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/Biostrings.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.54.0’
* 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 ... WARNING
Found the following significant warnings:
  read_fasta_files.c:186:9: warning: ‘*((void *)&loader_ext+64)’ is used uninitialized in this function [-Wuninitialized]
  read_fasta_files.c:186:9: warning: ‘*((void *)&loader_ext+72)’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/biocbuild/bbs-3.10-bioc/meat/Biostrings.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 14.7Mb
  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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
matchPDict-exact   341.176  0.736 342.751
matchPDict-inexact  56.704  0.108  56.926
findPalindromes     31.876  0.064  32.192
XStringSet-class    12.800  0.364  13.315
XStringSet-io        9.424  0.112   9.613
matchPattern         6.948  0.044   6.997
stringDist           5.168  0.000   5.193
* 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: 2 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/Biostrings.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL Biostrings
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘Biostrings’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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:124:3: warning: ‘lkup_len’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     INTEGER(start)[i], lkup0, lkup_len);
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c gtestsim.c -o gtestsim.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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;
          ^~~~~
At top level:
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)
                     ^~~~~~~~~~~~~~~~~~~~~~~~~~
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)
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include/Rdefines.h:40:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.10-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-3.10-bioc/R/include/Rinternals.h:852:20: 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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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
                    ^~~~
At top level:
match_pdict_utils.c:819:27: warning: ‘total_NFC’ defined but not used [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                           ^~~~~~~~~
match_pdict_utils.c:819:44: warning: ‘subtotal_NFC’ defined but not used [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                                            ^~~~~~~~~~~~
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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c matchprobes.c -o matchprobes.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c read_fasta_files.c -o read_fasta_files.o
read_fasta_files.c: In function ‘read_fasta_files’:
read_fasta_files.c:186:9: warning: ‘*((void *)&loader_ext+64)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  return loader_ext;
         ^~~~~~~~~~
read_fasta_files.c:186:9: warning: ‘*((void *)&loader_ext+72)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
read_fasta_files.c: In function ‘read_fasta_blocks’:
read_fasta_files.c:186:9: warning: ‘*((void *)&loader_ext+64)’ is used uninitialized in this function [-Wuninitialized]
  return loader_ext;
         ^~~~~~~~~~
read_fasta_files.c:186:9: warning: ‘*((void *)&loader_ext+72)’ is used uninitialized in this function [-Wuninitialized]
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c read_fastq_files.c -o read_fastq_files.o
read_fastq_files.c: In function ‘parse_FASTQ_file’:
read_fastq_files.c:392:7: warning: ‘dont_load’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (dont_load || loader->new_empty_seq_hook == NULL)
       ^
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c replaceAt.c -o replaceAt.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c strutils.c -o strutils.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from /home/biocbuild/bbs-3.10-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-3.10-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-3.10-bioc/R/include/Rdefines.h:40:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.10-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-3.10-bioc/R/include/Rinternals.h:852:20: 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-3.10-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from /home/biocbuild/bbs-3.10-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-3.10-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;
                                ^~~~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/include/Rdefines.h:40:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.10-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-3.10-bioc/R/include/Rinternals.h:852:20: warning: ‘ans_element_type’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^~~~~~~~~~
xscat.c:68:14: note: ‘ans_element_type’ was declared here
  const char *ans_element_type;
              ^~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.10-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 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 -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-Biostrings/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Biostrings)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 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, 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 -- Wed Apr 15 00:21:03 2020 
*********************************************** 
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 
 10.792   0.324  11.248 

name	user	system	elapsed
AAString-class	0.004	0.000	0.005
AMINO_ACID_CODE	0.004	0.000	0.003
AlignedXStringSet-class	0.312	0.000	0.312
DNAString-class	0.004	0.000	0.003
GENETIC_CODE	0.016	0.000	0.018
HNF4alpha	0.024	0.000	0.024
IUPAC_CODE_MAP	0.176	0.004	0.178
MIndex-class	0	0	0
MaskedXString-class	0.208	0.012	0.219
MultipleAlignment-class	1.604	0.020	1.659
PDict-class	4.356	0.064	4.481
PairwiseAlignments-class	0.576	0.004	0.579
PairwiseAlignments-io	2.524	0.084	2.616
QualityScaledXStringSet-class	0.228	0.008	0.484
RNAString-class	0.004	0.004	0.010
XString-class	0.008	0.000	0.010
XStringQuality-class	0.204	0.004	0.214
XStringSet-class	12.800	0.364	13.315
XStringSet-comparison	2.892	0.108	3.007
XStringSet-io	9.424	0.112	9.613
XStringSetList-class	0.328	0.004	0.334
XStringViews-class	0.152	0.004	0.155
align-utils	0.052	0.000	0.049
chartr	0.592	0.008	0.615
detail	0.328	0.108	0.444
dinucleotideFrequencyTest	0.012	0.008	0.019
findPalindromes	31.876	0.064	32.192
getSeq	0.092	0.000	0.094
gregexpr2	0.000	0.004	0.002
injectHardMask	0.052	0.000	0.053
letter	0.028	0.000	0.026
letterFrequency	1.108	0.060	1.174
longestConsecutive	0	0	0
lowlevel-matching	0.388	0.024	0.414
maskMotif	1.016	0.020	1.038
match-utils	0.012	0.004	0.017
matchLRPatterns	0.544	0.032	0.666
matchPDict-exact	341.176	0.736	342.751
matchPDict-inexact	56.704	0.108	56.926
matchPWM	2.848	0.000	2.858
matchPattern	6.948	0.044	6.997
matchProbePair	1.608	0.004	1.616
matchprobes	0.468	0.004	0.475
misc	0.028	0.000	0.029
needwunsQS	0.000	0.000	0.001
nucleotideFrequency	1.060	0.032	1.098
padAndClip	0.476	0.000	0.477
pairwiseAlignment	0.684	0.004	0.691
phiX174Phage	0.416	0.000	0.417
pid	0.488	0.008	0.505
replaceAt	2.516	0.008	2.527
replaceLetterAt	0.704	0.020	0.723
reverseComplement	1.640	0.012	1.672
stringDist	5.168	0.000	5.193
substitution_matrices	0.624	0.000	0.626
toComplex	0.004	0.000	0.001
translate	1.104	0.008	1.114
trimLRPatterns	0.052	0.000	0.053
xscat	0.880	0.000	0.883
yeastSEQCHR1	0.000	0.000	0.003