Hervé Pagès
| Snapshot Date: 2024-06-02 14:00:17 -0400 (Sun, 02 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/Biostrings |
| git_branch: RELEASE_3_19 |
| git_last_commit: 959b3ba |
| git_last_commit_date: 2024-05-31 00:43:13 -0400 (Fri, 31 May 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-04 11:35:04 -0400 (Tue, 04 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4487 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
| 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 219/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Biostrings 2.72.1 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | 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: 2.72.1 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Biostrings_2.72.1.tar.gz |
| StartedAt: 2024-06-03 04:13:13 -0400 (Mon, 03 Jun 2024) |
| EndedAt: 2024-06-03 04:21:58 -0400 (Mon, 03 Jun 2024) |
| EllapsedTime: 525.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Biostrings.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Biostrings_2.72.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Biostrings.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Biostrings/DESCRIPTION’ ... OK
* this is package ‘Biostrings’ version ‘2.72.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Biostrings’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
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 ... 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 265.592 2.426 268.025
matchPDict-inexact 51.961 0.424 52.387
findPalindromes 42.792 0.024 42.823
XStringSet-class 8.561 0.436 8.999
XStringSet-io 7.560 0.319 7.882
matchPattern 5.368 0.112 5.480
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/Biostrings.Rcheck/00check.log’
for details.
Biostrings.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL Biostrings
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘Biostrings’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c BAB_class.c -o BAB_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XStringSetList_class.c -o XStringSetList_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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 in this function [-Wmaybe-uninitialized]
124 | _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
125 | INTEGER(start)[i], lkup0, lkup_len);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XString_class.c -o XString_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_palindromes.c -o find_palindromes.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c gtestsim.c -o gtestsim.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c inject_code.c -o inject_code.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c lowlevel_matching.c -o lowlevel_matching.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_PWM.c -o match_PWM.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pattern.c -o match_pattern.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pdict.c -o match_pdict.o
match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’:
match_pdict.c:419:33: warning: ‘ans_col’ may be used uninitialized in this function [-Wmaybe-uninitialized]
419 | ans_col += tb_length;
| ~~~~~~~~^~~~~~~~~~~~
match_pdict.c:392:65: note: ‘ans_col’ was declared here
392 | int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
| ^~~~~~~
match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’:
match_pdict.c:470:41: warning: ‘ans_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
470 | ans_elt += P_length;
| ~~~~~~~~^~~~~~~~~~~
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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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;
| ^~~~~
At top level:
match_pdict_ACtree2.c:602:21: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used [-Wunused-function]
602 | static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
match_pdict_ACtree2.c:139:13: warning: ‘debug_node_counting_functions’ defined but not used [-Wunused-function]
139 | static void debug_node_counting_functions(int maxdepth)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function ‘build_Twobit’:
match_pdict_Twobit.c:75:27: warning: ‘twobit_sign2pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
75 | PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos));
| ^~~~~~~~~~~~~~~~~~~~~
match_pdict_Twobit.c:110:19: note: ‘twobit_sign2pos’ was declared here
110 | SEXP ans, twobit_sign2pos;
| ^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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
| ^~~~
At top level:
match_pdict_utils.c:820:34: warning: ‘total_NFC’ defined but not used [-Wunused-variable]
820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
| ^~~~~~~~~
match_pdict_utils.c:820:51: warning: ‘subtotal_NFC’ defined but not used [-Wunused-variable]
820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
| ^~~~~~~~~~~~
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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_reporting.c -o match_reporting.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c matchprobes.c -o matchprobes.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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:394:28: warning: ‘dont_load’ may be used uninitialized in this function [-Wmaybe-uninitialized]
394 | if (dont_load || loader->new_empty_seq_hook == NULL)
| ^
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c replaceAt.c -o replaceAt.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c strutils.c -o strutils.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c translate.c -o translate.o
translate.c: In function ‘DNAStringSet_translate’:
translate.c:110:36: warning: ‘if_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
110 | if (if_ambig == TRANSLATE_ERROR) {
| ^
translate.c:136:36: note: ‘if_ambig0’ was declared here
136 | int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
| ^~~~~~~~~
translate.c:106:36: warning: ‘if_non_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
106 | if (if_non_ambig == TRANSLATE_TO_X)
| ^
translate.c:136:21: note: ‘if_non_ambig0’ was declared here
136 | int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
| ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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 in this function [-Wmaybe-uninitialized]
157 | return twobit_sign;
| ^~~~~~~~~~~
utils.c: In function ‘_get_twobit_signature_at’:
utils.c:164:19: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
164 | int i, j, twobit_sign;
| ^~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c xscat.c -o xscat.o
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include/S4Vectors_defines.h:18,
from /home/biocbuild/bbs-3.19-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-3.19-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)
| ^~~~~~~~~~~~~~
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 in this function [-Wmaybe-uninitialized]
52 | PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag));
| ^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include/S4Vectors_defines.h:18,
from /home/biocbuild/bbs-3.19-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 ‘XStringSet_xscat’:
/home/biocbuild/bbs-3.19-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)
| ^~~~~~~~~~~~~~
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 in this function [-Wmaybe-uninitialized]
108 | PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width));
| ^~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.19-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 letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-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 ‘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/run_unitTests.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("Biostrings") || stop("unable to load Biostrings package")
Loading required package: Biostrings
Loading required package: BiocGenerics
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
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 Jun 3 04:21:24 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
5.532 0.160 5.702
Biostrings.Rcheck/Biostrings-Ex.timings
| name | user | system | elapsed | |
| AAString-class | 0.004 | 0.000 | 0.004 | |
| AMINO_ACID_CODE | 0.002 | 0.000 | 0.003 | |
| DNAString-class | 0.005 | 0.000 | 0.004 | |
| GENETIC_CODE | 0.014 | 0.000 | 0.015 | |
| HNF4alpha | 0.29 | 0.00 | 0.29 | |
| IUPAC_CODE_MAP | 0.119 | 0.000 | 0.118 | |
| MIndex-class | 0 | 0 | 0 | |
| MaskedXString-class | 0.188 | 0.011 | 0.202 | |
| MultipleAlignment-class | 1.095 | 0.177 | 1.273 | |
| PDict-class | 3.070 | 0.048 | 3.120 | |
| QualityScaledXStringSet-class | 0.128 | 0.016 | 0.144 | |
| RNAString-class | 0.007 | 0.000 | 0.007 | |
| XString-class | 0.008 | 0.000 | 0.008 | |
| XStringQuality-class | 0.126 | 0.008 | 0.134 | |
| XStringSet-class | 8.561 | 0.436 | 8.999 | |
| XStringSet-comparison | 1.642 | 0.078 | 1.719 | |
| XStringSet-io | 7.560 | 0.319 | 7.882 | |
| XStringSetList-class | 0.204 | 0.009 | 0.212 | |
| XStringViews-class | 0.097 | 0.000 | 0.098 | |
| chartr | 0.483 | 0.023 | 0.506 | |
| detail | 0.242 | 0.016 | 0.260 | |
| dinucleotideFrequencyTest | 0.01 | 0.00 | 0.01 | |
| findPalindromes | 42.792 | 0.024 | 42.823 | |
| getSeq | 0.052 | 0.009 | 0.060 | |
| gregexpr2 | 0.001 | 0.000 | 0.001 | |
| injectHardMask | 0.039 | 0.000 | 0.039 | |
| letter | 0.02 | 0.00 | 0.02 | |
| letterFrequency | 0.637 | 0.056 | 0.693 | |
| longestConsecutive | 0.001 | 0.000 | 0.001 | |
| lowlevel-matching | 0.288 | 0.012 | 0.300 | |
| maskMotif | 0.917 | 0.035 | 0.955 | |
| match-utils | 0.017 | 0.000 | 0.018 | |
| matchLRPatterns | 0.422 | 0.032 | 0.461 | |
| matchPDict-exact | 265.592 | 2.426 | 268.025 | |
| matchPDict-inexact | 51.961 | 0.424 | 52.387 | |
| matchPWM | 2.153 | 0.000 | 2.153 | |
| matchPattern | 5.368 | 0.112 | 5.480 | |
| matchProbePair | 1.156 | 0.016 | 1.172 | |
| matchprobes | 0.001 | 0.000 | 0.001 | |
| misc | 0.016 | 0.000 | 0.016 | |
| needwunsQS | 0 | 0 | 0 | |
| nucleotideFrequency | 0.514 | 0.032 | 0.546 | |
| padAndClip | 0.362 | 0.008 | 0.370 | |
| replaceAt | 2.098 | 0.060 | 2.158 | |
| replaceLetterAt | 0.317 | 0.080 | 0.396 | |
| reverseComplement | 0.959 | 0.024 | 0.983 | |
| seqinfo-methods | 0.496 | 0.008 | 0.504 | |
| toComplex | 0.000 | 0.002 | 0.002 | |
| translate | 0.918 | 0.010 | 0.928 | |
| trimLRPatterns | 0.052 | 0.000 | 0.052 | |
| xscat | 0.960 | 0.004 | 0.963 | |
| yeastSEQCHR1 | 0.003 | 0.000 | 0.003 | |