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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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

Package 215/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biostrings 2.73.1  (landing page)
Hervé Pagès
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/Biostrings
git_branch: devel
git_last_commit: a1fae35
git_last_commit_date: 2024-06-07 13:02:07 -0400 (Fri, 07 Jun 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  


CHECK results for Biostrings on palomino6

To the developers/maintainers of the Biostrings package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Biostrings
Version: 2.73.1
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Biostrings.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Biostrings_2.73.1.tar.gz
StartedAt: 2024-07-15 22:11:45 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 22:20:38 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 532.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Biostrings.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Biostrings.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Biostrings_2.73.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/Biostrings.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.73.1'
* 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 whether package 'Biostrings' can be installed ... WARNING
Found the following significant warnings:
  strutils.c:50:73: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/Biostrings.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... NOTE
  installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    extdata  11.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* 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 'hasOnlyBaseLetters' and siglist 'AAString'
  generic 'hasOnlyBaseLetters' and siglist 'AAStringSet'
  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 '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'
  generic 'updateObject' and siglist 'AAString'
  generic 'updateObject' and siglist 'AAStringSet'
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 for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/libs/x64/Biostrings.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
matchPDict-exact   242.00   3.13  246.08
matchPDict-inexact  68.40   1.16   70.28
findPalindromes     29.31   0.03   29.79
XStringSet-class     9.83   0.61   10.54
PDict-class          4.55   4.07    9.31
XStringSet-io        7.99   0.50    8.82
matchPattern         7.31   0.16    7.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'run_unitTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/Biostrings.Rcheck/00check.log'
for details.


Installation output

Biostrings.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Biostrings
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'Biostrings' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c BAB_class.c -o BAB_class.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function 'SparseMIndex_endIndex':
MIndex_class.c:184:27: warning: unused variable 'poffsets_order' [-Wunused-variable]
  184 |         IntAE *poffsets, *poffsets_order;
      |                           ^~~~~~~~~~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SparseList_utils.c -o SparseList_utils.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XStringSetList_class.c -o XStringSetList_class.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
XStringSet_class.c:124:17: warning: 'lkup_len' may be used uninitialized [-Wmaybe-uninitialized]
  124 |                 _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  125 |                                 INTEGER(start)[i], lkup0, lkup_len);
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
XStringSet_class.c:103:22: note: 'lkup_len' was declared here
  103 |         int ans_len, lkup_len, i;
      |                      ^~~~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XString_class.c -o XString_class.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c find_palindromes.c -o find_palindromes.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gtestsim.c -o gtestsim.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c inject_code.c -o inject_code.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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;
      |                                                ^~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c lowlevel_matching.c -o lowlevel_matching.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_PWM.c -o match_PWM.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_pattern.c -o match_pattern.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
match_pattern_boyermoore.c: In function '_match_pattern_boyermoore':
match_pattern_boyermoore.c:417:32: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized]
  417 |                         for (i = i1-1, j = j1-1; j >= 0; i--, j--)
      |                              ~~^~~~~~
match_pattern_boyermoore.c:383:42: note: 'i1' was declared here
  383 |         int nmatches, last_match_end, n, i1, i2, j1, j2, shift, shift1,
      |                                          ^~
match_pattern_boyermoore.c:417:42: warning: 'j1' may be used uninitialized [-Wmaybe-uninitialized]
  417 |                         for (i = i1-1, j = j1-1; j >= 0; i--, j--)
      |                                        ~~^~~~~~
match_pattern_boyermoore.c:383:50: note: 'j1' was declared here
  383 |         int nmatches, last_match_end, n, i1, i2, j1, j2, shift, shift1,
      |                                                  ^~
match_pattern_boyermoore.c:383:46: warning: 'i2' may be used uninitialized [-Wmaybe-uninitialized]
  383 |         int nmatches, last_match_end, n, i1, i2, j1, j2, shift, shift1,
      |                                              ^~
match_pattern_boyermoore.c:385:23: warning: 'c' may be used uninitialized [-Wmaybe-uninitialized]
  385 |         char ppP_rmc, c; /* ppP_rmc is 'ppP.seq' right-most char */
      |                       ^
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_pdict.c -o match_pdict.o
In function 'vcount_PDict3Parts_XStringSet',
    inlined from 'vmatch_PDict3Parts_XStringSet' at match_pdict.c:508:10:
match_pdict.c:419:33: warning: 'ans_col' may be used uninitialized [-Wmaybe-uninitialized]
  419 |                         ans_col += tb_length;
      |                         ~~~~~~~~^~~~~~~~~~~~
match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet':
match_pdict.c:392:65: note: 'ans_col' was declared here
  392 |         int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
      |                                                                 ^~~~~~~
In function 'vcount_XStringSet_XStringSet',
    inlined from 'vmatch_XStringSet_XStringSet' at match_pdict.c:542:10:
match_pdict.c:470:41: warning: 'ans_elt' may be used uninitialized [-Wmaybe-uninitialized]
  470 |                                 ans_elt += P_length;
      |                                 ~~~~~~~~^~~~~~~~~~~
match_pdict.c: In function 'vmatch_XStringSet_XStringSet':
match_pdict.c:441:64: note: 'ans_elt' was declared here
  441 |         int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
      |                                                                ^~~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c: In function 'split_and_move_pointers':
match_pdict_ACtree2.c:1031:17: 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:1076:17: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
 1076 |         ACnode *node0, *node1, *node2;
      |                 ^~~~~
match_pdict_ACtree2.c: 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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_pdict_Twobit.c -o match_pdict_Twobit.o
In file included from C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41,
                 from C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from C:/Users/biocbuild/bbs-3.20-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:
In function 'Twobit_asLIST',
    inlined from 'build_Twobit' at match_pdict_Twobit.c:145:2:
match_pdict_Twobit.c:75:27: warning: 'twobit_sign2pos' may be used uninitialized [-Wmaybe-uninitialized]
   75 |         PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos));
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT'
  371 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
match_pdict_Twobit.c: In function 'build_Twobit':
match_pdict_Twobit.c:110:19: note: 'twobit_sign2pos' was declared here
  110 |         SEXP ans, twobit_sign2pos;
      |                   ^~~~~~~~~~~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function 'match_ppheadtail0':
match_pdict_utils.c:653:56: warning: unused variable 'ncol' [-Wunused-variable]
  653 |         int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
      |                                                        ^~~~
match_pdict_utils.c: In function 'match_ppheadtail':
match_pdict_utils.c:713:13: warning: unused variable 'nelt' [-Wunused-variable]
  713 |         int nelt, nkey0, nkey1, nkey2, i, key;
      |             ^~~~
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:820:51: warning: unused variable 'subtotal_NFC' [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                                   ^~~~~~~~~~~~
match_pdict_utils.c:820:34: warning: unused variable 'total_NFC' [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                  ^~~~~~~~~
match_pdict_utils.c:819:40: warning: unused variable 'NFC' [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                                        ^~~
match_pdict_utils.c:819:33: warning: unused variable 'nloci' [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                                 ^~~~~
match_pdict_utils.c:819:27: warning: unused variable 'ndup' [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                           ^~~~
match_pdict_utils.c: At top level:
match_pdict_utils.c:261:13: warning: 'match_headtail_by_loc' defined but not used [-Wunused-function]
  261 | static void match_headtail_by_loc(const HeadTail *headtail,
      |             ^~~~~~~~~~~~~~~~~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_reporting.c -o match_reporting.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matchprobes.c -o matchprobes.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pmatchPattern.c -o pmatchPattern.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_fasta_files.c -o read_fasta_files.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_fastq_files.c -o read_fastq_files.o
read_fastq_files.c: In function 'parse_FASTQ_file':
read_fastq_files.c:408:28: warning: 'dont_load' may be used uninitialized [-Wmaybe-uninitialized]
  408 |                         if (dont_load || loader->new_qualid_hook == NULL)
      |                            ^
read_fastq_files.c:311:26: note: 'dont_load' was declared here
  311 |             lineinrecno, dont_load;
      |                          ^~~~~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c replaceAt.c -o replaceAt.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c replace_letter_at.c -o replace_letter_at.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c strutils.c -o strutils.o
strutils.c: In function 'MP_longestConsecutive':
strutils.c:50:73: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
   50 |       error("'letter' must contain exactly one character but contains %lu.",
      |                                                                       ~~^
      |                                                                         |
      |                                                                         long unsigned int
      |                                                                       %llu
   51 |           strlen(pc));
      |           ~~~~~~~~~~                                                     
      |           |
      |           size_t {aka long long unsigned int}
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c translate.c -o translate.o
In function 'translate',
    inlined from 'DNAStringSet_translate' at translate.c:195:4:
translate.c:99:36: warning: 'if_non_ambig0' may be used uninitialized [-Wmaybe-uninitialized]
   99 |                                 if (if_non_ambig == TRANSLATE_ERROR) {
      |                                    ^
translate.c: In function 'DNAStringSet_translate':
translate.c:136:21: note: 'if_non_ambig0' was declared here
  136 |         int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
      |                     ^~~~~~~~~~~~~
In function 'translate',
    inlined from 'DNAStringSet_translate' at translate.c:195:4:
translate.c:110:36: warning: 'if_ambig0' may be used uninitialized [-Wmaybe-uninitialized]
  110 |                                 if (if_ambig == TRANSLATE_ERROR) {
      |                                    ^
translate.c: In function 'DNAStringSet_translate':
translate.c:136:36: note: 'if_ambig0' was declared here
  136 |         int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
      |                                    ^~~~~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature':
utils.c:157:16: warning: 'twobit_sign' may be used uninitialized [-Wmaybe-uninitialized]
  157 |         return twobit_sign;
      |                ^~~~~~~~~~~
utils.c:150:16: note: 'twobit_sign' was declared here
  150 |         int i, twobit_sign;
      |                ^~~~~~~~~~~
utils.c: In function '_get_twobit_signature_at':
utils.c:174:16: warning: 'twobit_sign' may be used uninitialized [-Wmaybe-uninitialized]
  174 |         return twobit_sign;
      |                ^~~~~~~~~~~
utils.c:164:19: note: 'twobit_sign' was declared here
  164 |         int i, j, twobit_sign;
      |                   ^~~~~~~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c xscat.c -o xscat.o
In file included from C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41,
                 from C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from C:/Users/biocbuild/bbs-3.20-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':
C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:91:33: warning: 'ans_length' may be used uninitialized [-Wmaybe-uninitialized]
   91 | #define NEW_RAW(n)              Rf_allocVector(RAWSXP,n)
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT'
  371 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
xscat.c:38:27: note: in expansion of macro 'NEW_RAW'
   38 |         PROTECT(ans_tag = NEW_RAW(ans_length));
      |                           ^~~~~~~
xscat.c:18:20: note: 'ans_length' was declared here
   18 |         int nargs, ans_length, tag_offset, j;
      |                    ^~~~~~~~~~
xscat.c:52:23: warning: 'ans_classname' may be used uninitialized [-Wmaybe-uninitialized]
   52 |         PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag));
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT'
  371 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
xscat.c:20:21: note: 'ans_classname' was declared here
   20 |         const char *ans_classname;
      |                     ^~~~~~~~~~~~~
xscat.c: In function 'XStringSet_xscat':
C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:85:33: warning: 'ans_length' may be used uninitialized [-Wmaybe-uninitialized]
   85 | #define NEW_INTEGER(n)          Rf_allocVector(INTSXP,n)
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT'
  371 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
xscat.c:91:29: note: in expansion of macro 'NEW_INTEGER'
   91 |         PROTECT(ans_width = NEW_INTEGER(ans_length));
      |                             ^~~~~~~~~~~
xscat.c:66:39: note: 'ans_length' was declared here
   66 |         int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
      |                                       ^~~~~~~~~~
xscat.c:108:23: warning: 'ans_element_type' may be used uninitialized [-Wmaybe-uninitialized]
  108 |         PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width));
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT'
  371 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
xscat.c:68:21: note: 'ans_element_type' was declared here
   68 |         const char *ans_element_type;
      |                     ^~~~~~~~~~~~~~~~
gcc -shared -s -static-libgcc -o Biostrings.dll tmp.def 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 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 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-Biostrings/00new/Biostrings/libs/x64
** 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
** 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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
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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, aperm, 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, 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:utils':

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

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 -- Mon Jul 15 22:20:23 2024 
*********************************************** 
Number of test functions: 34 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Biostrings RUnit Tests - 34 test functions, 0 errors, 0 failures
Number of test functions: 34 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In XStringSet("DNA", x, start = start, end = end, width = width,  :
  metadata columns on input DNAStringSet object were dropped
2: In XStringSet("DNA", x, start = start, end = end, width = width,  :
  metadata columns on input DNAStringSet object were dropped
3: In XStringSet("DNA", x, start = start, end = end, width = width,  :
  metadata columns on input DNAStringSet object were dropped
> 
> proc.time()
   user  system elapsed 
  11.03    0.23   11.26 

Example timings

Biostrings.Rcheck/Biostrings-Ex.timings

nameusersystemelapsed
AAString-class000
AMINO_ACID_CODE000
DNAString-class000
GENETIC_CODE0.000.010.01
HNF4alpha0.030.000.03
IUPAC_CODE_MAP0.080.040.11
MIndex-class000
MaskedXString-class0.140.090.28
MultipleAlignment-class1.080.011.10
PDict-class4.554.079.31
QualityScaledXStringSet-class0.140.010.16
RNAString-class0.010.000.01
XString-class000
XStringQuality-class0.110.000.11
XStringSet-class 9.83 0.6110.54
XStringSet-comparison4.150.214.42
XStringSet-io7.990.508.82
XStringSetList-class0.170.010.18
XStringViews-class0.110.000.11
chartr0.830.110.94
detail0.220.030.26
dinucleotideFrequencyTest0.000.020.02
findPalindromes29.31 0.0329.79
getSeq0.050.030.08
gregexpr2000
injectHardMask0.020.030.05
letter0.030.000.03
letterFrequency0.750.060.81
longestConsecutive000
lowlevel-matching0.230.080.31
maskMotif1.150.111.27
match-utils0.040.000.03
matchLRPatterns1.210.091.28
matchPDict-exact242.00 3.13246.08
matchPDict-inexact68.40 1.1670.28
matchPWM1.470.041.52
matchPattern7.310.167.47
matchProbePair1.800.091.89
matchprobes000
misc0.690.000.69
needwunsQS000
nucleotideFrequency0.450.080.53
padAndClip0.310.050.36
replaceAt1.520.241.75
replaceLetterAt0.280.150.44
reverseComplement0.750.070.81
seqinfo-methods0.340.060.44
toComplex000
translate0.720.160.87
trimLRPatterns0.030.010.04
xscat0.750.160.93
yeastSEQCHR1000