Hervé Pagès
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/Biostrings |
| git_branch: RELEASE_3_20 |
| git_last_commit: fcfc37a |
| git_last_commit_date: 2024-10-29 09:22:23 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 220/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Biostrings 2.74.0 (landing page) Hervé Pagès
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Biostrings |
| Version: 2.74.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Biostrings_2.74.0.tar.gz |
| StartedAt: 2024-11-20 05:41:32 -0000 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 05:52:12 -0000 (Wed, 20 Nov 2024) |
| EllapsedTime: 640.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Biostrings.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Biostrings_2.74.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Biostrings.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biostrings/DESCRIPTION’ ... OK
* this is package ‘Biostrings’ version ‘2.74.0’
* 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 ... OK
* used C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... NOTE
installed size is 14.2Mb
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 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 ... 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 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 320.813 1.289 322.850
matchPDict-inexact 56.800 0.315 57.230
findPalindromes 36.849 0.024 36.916
XStringSet-class 12.368 0.447 12.857
XStringSet-io 6.954 0.148 7.117
matchPattern 6.169 0.084 6.267
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/Biostrings.Rcheck/00check.log’
for details.
Biostrings.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL Biostrings
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘Biostrings’ ...
** using staged installation
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c BAB_class.c -o BAB_class.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-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:184:27: warning: unused variable 'poffsets_order' [-Wunused-variable]
184 | IntAE *poffsets, *poffsets_order;
| ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c XStringSetList_class.c -o XStringSetList_class.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-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:124:17: 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"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c XString_class.c -o XString_class.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c find_palindromes.c -o find_palindromes.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c gtestsim.c -o gtestsim.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c inject_code.c -o inject_code.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-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;
| ^~~~~
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c lowlevel_matching.c -o lowlevel_matching.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c match_PWM.c -o match_PWM.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c match_pattern.c -o match_pattern.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -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"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-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:1031:17: 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"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
In file included from /home/biocbuild/R/R-4.4.1/include/Rdefines.h:41,
from /home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include/S4Vectors_defines.h:18,
from /home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/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"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-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: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"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c match_reporting.c -o match_reporting.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c matchprobes.c -o matchprobes.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c read_fasta_files.c -o read_fasta_files.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-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: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"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c replaceAt.c -o replaceAt.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c strutils.c -o strutils.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -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"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-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:157:16: 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"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c xscat.c -o xscat.o
In file included from /home/biocbuild/R/R-4.4.1/include/Rdefines.h:41,
from /home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include/S4Vectors_defines.h:18,
from /home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/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/R/R-4.4.1/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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/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':
/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/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 -L/home/biocbuild/R/R-4.4.1/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 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/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/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 ‘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)
Biostrings.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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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
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> library(testthat)
> library(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, saveRDS, 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
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
>
> test_check("Biostrings")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1333 ]
>
> proc.time()
user system elapsed
22.447 0.526 22.933
Biostrings.Rcheck/Biostrings-Ex.timings
| name | user | system | elapsed | |
| AAString-class | 0.004 | 0.000 | 0.004 | |
| AMINO_ACID_CODE | 0.002 | 0.000 | 0.002 | |
| DNAString-class | 0.005 | 0.000 | 0.005 | |
| GENETIC_CODE | 0.012 | 0.000 | 0.012 | |
| HNF4alpha | 0.309 | 0.000 | 0.310 | |
| IUPAC_CODE_MAP | 0.166 | 0.000 | 0.167 | |
| MIndex-class | 0 | 0 | 0 | |
| MaskedXString-class | 0.225 | 0.032 | 0.261 | |
| MultipleAlignment-class | 1.729 | 0.064 | 1.807 | |
| PDict-class | 4.207 | 0.080 | 4.300 | |
| QualityScaledXStringSet-class | 0.236 | 0.008 | 0.246 | |
| RNAString-class | 0.011 | 0.000 | 0.011 | |
| XString-class | 0.011 | 0.000 | 0.011 | |
| XStringQuality-class | 0.202 | 0.003 | 0.206 | |
| XStringSet-class | 12.368 | 0.447 | 12.857 | |
| XStringSet-comparison | 3.257 | 0.028 | 3.290 | |
| XStringSet-io | 6.954 | 0.148 | 7.117 | |
| XStringSetList-class | 0.299 | 0.004 | 0.303 | |
| XStringViews-class | 0.148 | 0.000 | 0.148 | |
| chartr | 1.807 | 0.048 | 1.863 | |
| detail | 0.348 | 0.006 | 0.363 | |
| dinucleotideFrequencyTest | 0.012 | 0.000 | 0.012 | |
| findPalindromes | 36.849 | 0.024 | 36.916 | |
| getSeq | 0.074 | 0.009 | 0.082 | |
| gregexpr2 | 0.001 | 0.000 | 0.001 | |
| injectHardMask | 0.049 | 0.004 | 0.053 | |
| letter | 0.027 | 0.000 | 0.027 | |
| letterFrequency | 0.904 | 0.016 | 0.921 | |
| longestConsecutive | 0 | 0 | 0 | |
| lowlevel-matching | 0.552 | 0.034 | 0.587 | |
| maskMotif | 1.347 | 0.032 | 1.386 | |
| match-utils | 0.028 | 0.000 | 0.028 | |
| matchLRPatterns | 0.548 | 0.016 | 0.577 | |
| matchPDict-exact | 320.813 | 1.289 | 322.850 | |
| matchPDict-inexact | 56.800 | 0.315 | 57.230 | |
| matchPWM | 2.583 | 0.016 | 2.604 | |
| matchPattern | 6.169 | 0.084 | 6.267 | |
| matchProbePair | 1.365 | 0.012 | 1.379 | |
| matchprobes | 0 | 0 | 0 | |
| misc | 0.019 | 0.000 | 0.019 | |
| needwunsQS | 0 | 0 | 0 | |
| nucleotideFrequency | 0.762 | 0.012 | 0.776 | |
| padAndClip | 0.615 | 0.009 | 0.625 | |
| replaceAt | 2.809 | 0.040 | 2.856 | |
| replaceLetterAt | 0.800 | 0.056 | 0.859 | |
| reverseComplement | 1.434 | 0.008 | 1.444 | |
| seqinfo-methods | 0.818 | 0.012 | 0.832 | |
| toComplex | 0.002 | 0.000 | 0.001 | |
| translate | 1.490 | 0.036 | 1.529 | |
| trimLRPatterns | 0.070 | 0.004 | 0.075 | |
| xscat | 1.451 | 0.004 | 1.458 | |
| yeastSEQCHR1 | 0.003 | 0.000 | 0.003 | |