Multiple platform build/check report for BioC 3.12 - CHECK report for Biostrings on malbec1

Package: Biostrings

Version: 2.58.0

Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings Biostrings_2.58.0.tar.gz

StartedAt: 2021-05-05 23:30:59 -0400 (Wed, 05 May 2021)

EndedAt: 2021-05-05 23:41:49 -0400 (Wed, 05 May 2021)

EllapsedTime: 649.4 seconds

RetCode: 0

Status: WARNINGS

CheckDir: Biostrings.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings Biostrings_2.58.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/Biostrings.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘2.58.0’
* 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 ... OK
* 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-3.12-bioc/meat/Biostrings.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 14.8Mb
  sub-directories of 1Mb or more:
    R         1.8Mb
    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 'parallel_slot_names' and siglist 'ByPos_MIndex'
  generic 'parallel_slot_names' 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 (user + system) or elapsed time > 5s
                      user system elapsed
matchPDict-exact   342.840  0.604 344.063
matchPDict-inexact  56.176  0.104  56.382
findPalindromes     30.640  0.036  30.861
XStringSet-class    13.408  0.288  14.649
XStringSet-io       10.632  0.112  10.779
matchPattern         6.952  0.040   7.004
* 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, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/Biostrings.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL Biostrings
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘Biostrings’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c gtestsim.c -o gtestsim.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include/Rdefines.h:40:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.12-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-3.12-bioc/R/include/Rinternals.h:984:20: 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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c matchprobes.c -o matchprobes.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c replaceAt.c -o replaceAt.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c strutils.c -o strutils.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from /home/biocbuild/bbs-3.12-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-3.12-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-3.12-bioc/R/include/Rdefines.h:40:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.12-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-3.12-bioc/R/include/Rinternals.h:984:20: 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-3.12-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from /home/biocbuild/bbs-3.12-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-3.12-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-3.12-bioc/R/include/Rdefines.h:40:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.12-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-3.12-bioc/R/include/Rinternals.h:984:20: 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-3.12-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-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.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 May  5 23:41:40 2021 
*********************************************** 
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 
 12.012   0.448  12.541

name	user	system	elapsed
AAString-class	0.004	0.000	0.003
AMINO_ACID_CODE	0.004	0.000	0.003
AlignedXStringSet-class	0.132	0.000	0.132
DNAString-class	0.004	0.000	0.004
GENETIC_CODE	0.012	0.000	0.011
HNF4alpha	0.024	0.000	0.024
IUPAC_CODE_MAP	0.332	0.000	0.334
MIndex-class	0.000	0.000	0.001
MaskedXString-class	0.308	0.016	0.424
MultipleAlignment-class	1.476	0.048	1.540
PDict-class	3.816	0.060	3.938
PairwiseAlignments-class	0.908	0.000	0.908
PairwiseAlignments-io	3.096	0.088	3.189
QualityScaledXStringSet-class	0.200	0.000	0.245
RNAString-class	0.004	0.000	0.007
XString-class	0.008	0.000	0.008
XStringQuality-class	0.160	0.000	0.159
XStringSet-class	13.408	0.288	14.649
XStringSet-comparison	3.256	0.048	3.306
XStringSet-io	10.632	0.112	10.779
XStringSetList-class	0.396	0.004	0.400
XStringViews-class	0.184	0.004	0.188
align-utils	0.052	0.004	0.056
chartr	0.816	0.024	0.840
detail	0.368	0.032	0.407
dinucleotideFrequencyTest	0.024	0.000	0.021
findPalindromes	30.640	0.036	30.861
getSeq	0.064	0.000	0.066
gregexpr2	0.000	0.000	0.001
injectHardMask	0.044	0.000	0.044
letter	0.012	0.008	0.020
letterFrequency	1.936	0.092	2.032
longestConsecutive	0.000	0.000	0.001
lowlevel-matching	0.64	0.02	0.66
maskMotif	1.52	0.04	1.56
match-utils	0.032	0.000	0.032
matchLRPatterns	0.528	0.008	0.586
matchPDict-exact	342.840	0.604	344.063
matchPDict-inexact	56.176	0.104	56.382
matchPWM	2.812	0.004	2.822
matchPattern	6.952	0.040	7.004
matchProbePair	1.440	0.004	1.446
matchprobes	0.260	0.004	0.266
misc	0.016	0.000	0.016
needwunsQS	0	0	0
nucleotideFrequency	0.632	0.012	0.645
padAndClip	0.680	0.000	0.681
pairwiseAlignment	1.192	0.000	1.192
phiX174Phage	0.54	0.00	0.54
pid	0.596	0.000	0.595
replaceAt	2.484	0.056	2.547
replaceLetterAt	0.456	0.068	0.522
reverseComplement	1.432	0.076	1.511
stringDist	3.848	0.008	3.864
substitution_matrices	0.804	0.012	0.820
toComplex	0.000	0.000	0.002
translate	1.404	0.056	1.467
trimLRPatterns	0.064	0.000	0.065
xscat	1.272	0.000	1.271
yeastSEQCHR1	0.004	0.000	0.004

CHECK report for Biostrings on malbec1

Summary

Command output

Installation output

Tests output

Example timings