Hervé Pagès
| Snapshot Date: 2025-11-13 13:40 -0500 (Thu, 13 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/Biostrings |
| git_branch: devel |
| git_last_commit: b15bffb |
| git_last_commit_date: 2025-11-04 14:49:55 -0500 (Tue, 04 Nov 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-14 11:35 -0500 (Fri, 14 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4825 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4547 |
| 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 220/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Biostrings 2.79.2 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
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. |
| Package: Biostrings |
| Version: 2.79.2 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Biostrings_2.79.2.tar.gz |
| StartedAt: 2025-11-13 21:31:41 -0500 (Thu, 13 Nov 2025) |
| EndedAt: 2025-11-13 21:40:54 -0500 (Thu, 13 Nov 2025) |
| EllapsedTime: 552.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Biostrings.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Biostrings_2.79.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/Biostrings.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Biostrings/DESCRIPTION’ ... OK
* this is package ‘Biostrings’ version ‘2.79.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Biostrings’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
installed size is 13.3Mb
sub-directories of 1Mb or more:
R 1.1Mb
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 loading without being on the library search path ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
MultipleAlignment-class.Rd: NormalIRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 'parallel_slot_names' and siglist 'ByPos_MIndex'
generic 'parallel_slot_names' and siglist 'MIndex'
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'
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
File ‘Biostrings/libs/Biostrings.so’:
Found non-API calls to R: ‘NAMED’, ‘R_lsInternal’, ‘SET_NAMED’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
matchPDict-exact 258.447 1.942 260.399
matchPDict-inexact 51.602 0.513 52.133
findPalindromes 45.585 0.118 45.817
XStringSet-class 9.317 0.485 9.815
XStringSet-io 7.013 0.251 7.266
matchPattern 5.019 0.156 5.175
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/Biostrings.Rcheck/00check.log’
for details.
Biostrings.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL Biostrings
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘Biostrings’ ...
** this is package ‘Biostrings’ version ‘2.79.2’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c BAB_class.c -o BAB_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c XStringSetList_class.c -o XStringSetList_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c XString_class.c -o XString_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c find_palindromes.c -o find_palindromes.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c gtestsim.c -o gtestsim.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c inject_code.c -o inject_code.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c lcsuffix.c -o lcsuffix.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c lowlevel_matching.c -o lowlevel_matching.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c match_PWM.c -o match_PWM.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c match_pattern.c -o match_pattern.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c match_pdict_Twobit.c -o match_pdict_Twobit.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/include/Rdefines.h:41,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include/S4Vectors_defines.h:18,
from /home/biocbuild/bbs-3.23-bioc/R/site-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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
388 | #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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c match_reporting.c -o match_reporting.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c read_fasta_files.c -o read_fasta_files.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c replaceAt.c -o replaceAt.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c replace_letter_at.c -o replace_letter_at.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c strutils.c -o strutils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c translate.c -o translate.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c xscat.c -o xscat.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/include/Rdefines.h:41,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include/S4Vectors_defines.h:18,
from /home/biocbuild/bbs-3.23-bioc/R/site-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-3.23-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)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
388 | #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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
388 | #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’:
/home/biocbuild/bbs-3.23-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)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
388 | #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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
388 | #define PROTECT(s) Rf_protect(s)
| ^
xscat.c:68:21: note: ‘ans_element_type’ was declared here
68 | const char *ans_element_type;
| ^~~~~~~~~~~~~~~~
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-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 find_palindromes.o gtestsim.o inject_code.o lcsuffix.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 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-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-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)
Biostrings.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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> library(testthat)
> library(Biostrings)
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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
Loading required package: XVector
Loading required package: Seqinfo
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
>
> test_check("Biostrings")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2865 ]
>
> proc.time()
user system elapsed
27.986 0.578 28.574
Biostrings.Rcheck/Biostrings-Ex.timings
| name | user | system | elapsed | |
| AAString-class | 0.003 | 0.000 | 0.003 | |
| AMINO_ACID_CODE | 0.076 | 0.001 | 0.076 | |
| DNAString-class | 0.004 | 0.000 | 0.004 | |
| GENETIC_CODE | 0.009 | 0.004 | 0.013 | |
| HNF4alpha | 0.028 | 0.001 | 0.030 | |
| IUPAC_CODE_MAP | 0.316 | 0.000 | 0.316 | |
| MIndex-class | 0 | 0 | 0 | |
| MaskedXString-class | 0.176 | 0.026 | 0.203 | |
| MultipleAlignment-class | 1.097 | 0.058 | 1.157 | |
| PDict-class | 3.133 | 0.136 | 3.270 | |
| QualityScaledXStringSet-class | 0.159 | 0.005 | 0.165 | |
| RNAString-class | 0.025 | 0.000 | 0.025 | |
| XString-class | 0.031 | 0.002 | 0.033 | |
| XStringQuality-class | 0.131 | 0.003 | 0.133 | |
| XStringSet-class | 9.317 | 0.485 | 9.815 | |
| XStringSet-comparison | 2.148 | 0.062 | 2.210 | |
| XStringSet-io | 7.013 | 0.251 | 7.266 | |
| XStringSetList-class | 0.206 | 0.003 | 0.208 | |
| XStringViews-class | 0.193 | 0.006 | 0.198 | |
| chartr | 0.489 | 0.008 | 0.496 | |
| coloring | 0.038 | 0.002 | 0.041 | |
| detail | 0.234 | 0.044 | 0.278 | |
| dinucleotideFrequencyTest | 0.010 | 0.002 | 0.011 | |
| findPalindromes | 45.585 | 0.118 | 45.817 | |
| getSeq | 0.058 | 0.011 | 0.070 | |
| gregexpr2 | 0.001 | 0.001 | 0.001 | |
| injectHardMask | 0.042 | 0.005 | 0.048 | |
| letter | 0.021 | 0.003 | 0.023 | |
| letterFrequency | 0.675 | 0.090 | 0.764 | |
| longestConsecutive | 0.000 | 0.000 | 0.001 | |
| lowlevel-matching | 0.350 | 0.029 | 0.380 | |
| maskMotif | 1.012 | 0.073 | 1.088 | |
| match-utils | 0.017 | 0.002 | 0.019 | |
| matchLRPatterns | 0.402 | 0.030 | 0.440 | |
| matchPDict-exact | 258.447 | 1.942 | 260.399 | |
| matchPDict-inexact | 51.602 | 0.513 | 52.133 | |
| matchPWM | 2.022 | 0.009 | 2.032 | |
| matchPattern | 5.019 | 0.156 | 5.175 | |
| matchProbePair | 1.078 | 0.025 | 1.102 | |
| misc | 0.015 | 0.000 | 0.016 | |
| nucleotideFrequency | 0.572 | 0.027 | 0.600 | |
| padAndClip | 0.375 | 0.012 | 0.388 | |
| predefined_scoring_matrices | 0.000 | 0.001 | 0.000 | |
| replaceAt | 2.100 | 0.159 | 2.259 | |
| replaceLetterAt | 0.315 | 0.092 | 0.407 | |
| reverseComplement | 0.969 | 0.051 | 1.019 | |
| seqinfo-methods | 0.448 | 0.002 | 0.450 | |
| toComplex | 0.001 | 0.000 | 0.001 | |
| translate | 0.978 | 0.008 | 0.986 | |
| trimLRPatterns | 0.051 | 0.003 | 0.056 | |
| xscat | 1.845 | 0.014 | 1.860 | |
| yeastSEQCHR1 | 0.002 | 0.001 | 0.003 | |