Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:07 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for Biostrings on nebbiolo2


To the developers/maintainers of the Biostrings package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Biostrings.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 193/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biostrings 2.62.0  (landing page)
H. Pagès
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/Biostrings
git_branch: RELEASE_3_14
git_last_commit: 53ed287
git_last_commit_date: 2021-10-26 11:46:31 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Biostrings
Version: 2.62.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings Biostrings_2.62.0.tar.gz
StartedAt: 2022-04-12 06:35:47 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 06:44:44 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 537.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Biostrings.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings Biostrings_2.62.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/Biostrings.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘2.62.0’
* 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-3.14-bioc/meat/Biostrings.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 14.9Mb
  sub-directories of 1Mb or more:
    R         1.8Mb
    extdata  11.1Mb
    libs      1.1Mb
* 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   269.399  1.652 271.051
matchPDict-inexact  60.652  0.428  61.081
findPalindromes     47.302  0.064  47.373
XStringSet-class     8.380  0.477   8.858
XStringSet-io        8.056  0.305   8.361
matchPattern         5.047  0.088   5.135
* 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-3.14-bioc/meat/Biostrings.Rcheck/00check.log’
for details.



Installation output

Biostrings.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL Biostrings
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘Biostrings’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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]
  299 | static void BitMatrix_print(BitMatrix *bitmat)
      |             ^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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]
  184 |  IntAE *poffsets, *poffsets_order;
      |                    ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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]
  124 |   _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  125 |     INTEGER(start)[i], lkup0, lkup_len);
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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]
  155 |  INTEGER(ans_elt)[0] = score;
      |  ~~~~~~~~~~~~~~~~~~~~^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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:250:14: warning: ‘indelWidthSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  250 |     jPattern += indelWidthSubject;
      |     ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:231:42: warning: ‘indelStartSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  231 |    if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
      |                                       ~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:221:26: warning: ‘indelWidthPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  221 |   int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
      |                          ^~~~~~~~~~~~~~~~~
align_utils.c:232:50: warning: ‘indelStartPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  232 |     if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
      |                                        ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c gtestsim.c -o gtestsim.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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]
  957 |   int x_width, y_width, x_length, *ans_mat, i, x_pos;
      |                                                ^~~~~
letter_frequency.c:956:13: warning: unused variable ‘ans_dimnames’ [-Wunused-variable]
  956 |   SEXP ans, ans_dimnames;
      |             ^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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]
    7 | static void test_match_pattern_indels(const char *p, const char *s,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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]
  419 |    ans_col += tb_length;
      |    ~~~~~~~~^~~~~~~~~~~~
match_pdict.c:392:58: note: ‘ans_col’ was declared here
  392 |  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]
  470 |     ans_elt += P_length;
      |     ~~~~~~~~^~~~~~~~~~~
match_pdict.c:441:57: note: ‘ans_elt’ was declared here
  441 |  int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
      |                                                         ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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]
 1031 |  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]
 1076 |  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]
  602 | 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]
  139 | static void debug_node_counting_functions(int maxdepth)
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function ‘build_Twobit’:
match_pdict_Twobit.c:75:20: warning: ‘twobit_sign2pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   75 |  PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos));
      |                    ^~~~~~~~~~~~~~~~~~~~~
match_pdict_Twobit.c:110:12: note: ‘twobit_sign2pos’ was declared here
  110 |  SEXP ans, twobit_sign2pos;
      |            ^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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]
  652 |  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]
  712 |  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]
  819 |  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                            ^~~~~~~~~~~~
match_pdict_utils.c:819:27: warning: unused variable ‘total_NFC’ [-Wunused-variable]
  819 |  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                           ^~~~~~~~~
match_pdict_utils.c:818:33: warning: unused variable ‘NFC’ [-Wunused-variable]
  818 |  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                                 ^~~
match_pdict_utils.c:818:26: warning: unused variable ‘nloci’ [-Wunused-variable]
  818 |  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                          ^~~~~
match_pdict_utils.c:818:20: warning: unused variable ‘ndup’ [-Wunused-variable]
  818 |  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]
  819 |  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]
  819 |  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]
  260 | static void match_headtail_by_loc(const HeadTail *headtail,
      |             ^~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c matchprobes.c -o matchprobes.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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]
  186 |  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]
  186 |  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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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]
  392 |    if (dont_load || loader->new_empty_seq_hook == NULL)
      |       ^
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c replaceAt.c -o replaceAt.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c strutils.c -o strutils.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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]
  110 |     if (if_ambig == TRANSLATE_ERROR) {
      |        ^
translate.c:136:29: note: ‘if_ambig0’ was declared here
  136 |  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]
  106 |     if (if_non_ambig == TRANSLATE_TO_X)
      |        ^
translate.c:136:14: note: ‘if_non_ambig0’ was declared here
  136 |  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
      |              ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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]
  157 |  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]
  164 |  int i, j, twobit_sign;
      |            ^~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.14-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-3.14-bioc/R/include/Rdefines.h:100:21: warning: ‘ans_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  100 | #define NEW_RAW(n)  Rf_allocVector(RAWSXP,n)
      |                     ^~~~~~~~~~~~~~
xscat.c:18:13: note: ‘ans_length’ was declared here
   18 |  int nargs, ans_length, tag_offset, j;
      |             ^~~~~~~~~~
xscat.c:52:16: warning: ‘ans_classname’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   52 |  PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag));
      |                ^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.14-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-3.14-bioc/R/include/Rdefines.h:94:25: warning: ‘ans_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   94 | #define NEW_INTEGER(n)  Rf_allocVector(INTSXP,n)
      |                         ^~~~~~~~~~~~~~
xscat.c:66:32: note: ‘ans_length’ was declared here
   66 |  int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
      |                                ^~~~~~~~~~
xscat.c:108:16: warning: ‘ans_element_type’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  108 |  PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width));
      |                ^~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.14-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-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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 ‘pattern’ 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)

Tests output

Biostrings.Rcheck/tests/run_unitTests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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

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

Attaching package: 'BiocGenerics'

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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

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

    strsplit

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


RUNIT TEST PROTOCOL -- Tue Apr 12 06:44:36 2022 
*********************************************** 
Number of test functions: 40 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Biostrings RUnit Tests - 40 test functions, 0 errors, 0 failures
Number of test functions: 40 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  9.050   0.342   9.381 

Example timings

Biostrings.Rcheck/Biostrings-Ex.timings

nameusersystemelapsed
AAString-class0.0030.0000.003
AMINO_ACID_CODE0.0020.0000.002
AlignedXStringSet-class0.0560.0000.056
DNAString-class0.0040.0000.003
GENETIC_CODE0.0090.0000.009
HNF4alpha0.0150.0020.018
IUPAC_CODE_MAP0.1220.0030.126
MIndex-class000
MaskedXString-class0.1710.0200.193
MultipleAlignment-class0.9230.0280.951
PDict-class4.2380.1804.419
PairwiseAlignments-class0.5390.0040.542
PairwiseAlignments-io2.1240.2642.388
QualityScaledXStringSet-class0.1500.0000.151
RNAString-class0.0070.0000.007
XString-class0.0070.0000.007
XStringQuality-class0.1310.0000.132
XStringSet-class8.3800.4778.858
XStringSet-comparison2.6140.1152.729
XStringSet-io8.0560.3058.361
XStringSetList-class0.1960.0080.204
XStringViews-class0.1120.0000.113
align-utils0.030.000.03
chartr0.4720.0200.492
detail0.2430.0160.258
dinucleotideFrequencyTest0.0140.0000.013
findPalindromes47.302 0.06447.373
getSeq0.0480.0160.064
gregexpr20.0010.0000.001
injectHardMask0.0430.0000.043
letter0.0230.0000.023
letterFrequency1.6590.1281.787
longestConsecutive000
lowlevel-matching0.2810.0240.305
maskMotif0.9250.0120.940
match-utils0.0180.0000.018
matchLRPatterns0.4890.0120.534
matchPDict-exact269.399 1.652271.051
matchPDict-inexact60.652 0.42861.081
matchPWM2.3610.0082.369
matchPattern5.0470.0885.135
matchProbePair1.1440.0041.148
matchprobes0.2580.0000.257
misc0.0170.0000.016
needwunsQS000
nucleotideFrequency0.5290.0040.533
padAndClip0.3830.0080.391
pairwiseAlignment0.5970.0200.616
phiX174Phage0.3970.0360.432
pid0.3040.0400.344
replaceAt2.0160.0002.016
replaceLetterAt0.3160.0240.340
reverseComplement0.9680.0641.033
seqinfo0.5160.0360.552
stringDist3.3290.0243.352
substitution_matrices0.6790.0360.715
toComplex0.0020.0000.002
translate1.070.001.07
trimLRPatterns0.0560.0000.056
xscat0.8590.0000.858
yeastSEQCHR10.0030.0000.003