Hervé Pagès
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/Biostrings |
| git_branch: devel |
| git_last_commit: d13154e |
| git_last_commit_date: 2024-03-23 15:57:19 -0400 (Sat, 23 Mar 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:22 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 218/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Biostrings 2.71.5 (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 | | ||||||||
| 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: 2.71.5 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings Biostrings_2.71.5.tar.gz |
| StartedAt: 2024-03-28 03:20:22 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:31:10 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 647.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Biostrings.Rcheck |
| Warnings: 2 |
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### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings Biostrings_2.71.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Biostrings.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
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 ‘2.71.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘Rmpi’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Biostrings’ can be installed ... WARNING
Found the following significant warnings:
letter_frequency.c:536:10: warning: too many arguments for format [-Wformat-extra-args]
letter_frequency.c:589:10: warning: too many arguments for format [-Wformat-extra-args]
match_pdict_ACtree2.c:732:31: warning: unknown conversion type character ‘)’ in format [-Wformat=]
match_reporting.c:49:9: warning: too many arguments for format [-Wformat-extra-args]
strutils.c:50:72: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/biocbuild/bbs-3.19-bioc/meat/Biostrings.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 14.8Mb
sub-directories of 1Mb or more:
R 1.7Mb
extdata 11.1Mb
libs 1.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 357.028 1.166 358.911
matchPDict-inexact 45.708 0.127 45.934
findPalindromes 38.517 0.019 38.582
XStringSet-class 14.064 0.299 14.415
XStringSet-io 7.571 0.128 7.716
matchPattern 5.983 0.048 6.044
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 4 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/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL Biostrings
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘Biostrings’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:184:20: warning: unused variable ‘poffsets_order’ [-Wunused-variable]
184 | IntAE *poffsets, *poffsets_order;
| ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:124:3: warning: ‘lkup_len’ may be used uninitialized in this function [-Wmaybe-uninitialized]
124 | _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
125 | INTEGER(start)[i], lkup0, lkup_len);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function ‘align_needwunsQS’:
align_needwunsQS.c:155:22: warning: ‘sc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
155 | INTEGER(ans_elt)[0] = score;
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c align_utils.c -o align_utils.o
align_utils.c: In function ‘PairwiseAlignmentsSingleSubject_align_aligned’:
align_utils.c:250:14: warning: ‘indelWidthSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized]
250 | jPattern += indelWidthSubject;
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:231:42: warning: ‘indelStartSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized]
231 | if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
| ~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:239:30: warning: ‘indelWidthPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
239 | mappedStringPtr[index] = gapCodeValue;
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
align_utils.c:232:50: warning: ‘indelStartPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
232 | if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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 ‘XString_letterFrequencyInSlidingView’:
letter_frequency.c:536:10: warning: too many arguments for format [-Wformat-extra-args]
536 | error("Biostrings internal error in "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
letter_frequency.c: In function ‘XStringSet_letterFrequency’:
letter_frequency.c:589:10: warning: too many arguments for format [-Wformat-extra-args]
589 | error("Biostrings internal error in "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
letter_frequency.c: In function ‘XStringSet_two_way_letter_frequency’:
letter_frequency.c:957:48: warning: unused variable ‘x_pos’ [-Wunused-variable]
957 | int x_width, y_width, x_length, *ans_mat, i, x_pos;
| ^~~~~
letter_frequency.c:956:13: warning: unused variable ‘ans_dimnames’ [-Wunused-variable]
956 | SEXP ans, ans_dimnames;
| ^~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:419:12: warning: ‘ans_col’ may be used uninitialized in this function [-Wmaybe-uninitialized]
419 | ans_col += tb_length;
| ~~~~~~~~^~~~~~~~~~~~
match_pdict.c:392:58: note: ‘ans_col’ was declared here
392 | int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
| ^~~~~~~
match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’:
match_pdict.c:470:13: warning: ‘ans_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
470 | ans_elt += P_length;
| ~~~~~~~~^~~~~~~~~~~
match_pdict.c:441:57: note: ‘ans_elt’ was declared here
441 | int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
| ^~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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 ‘ACtree2_summary’:
match_pdict_ACtree2.c:732:31: warning: unknown conversion type character ‘)’ in format [-Wformat=]
732 | Rprintf("| - %u nodes (%.2f%) with %d links\n",
| ^
match_pdict_ACtree2.c: In function ‘split_and_move_pointers’:
match_pdict_ACtree2.c:1031:10: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable]
1031 | ACnode *node0, *node1, *node2;
| ^~~~~
match_pdict_ACtree2.c: In function ‘merge_pointers’:
match_pdict_ACtree2.c:1076:10: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable]
1076 | ACnode *node0, *node1, *node2;
| ^~~~~
At top level:
match_pdict_ACtree2.c:602:21: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used [-Wunused-function]
602 | static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
match_pdict_ACtree2.c:139:13: warning: ‘debug_node_counting_functions’ defined but not used [-Wunused-function]
139 | static void debug_node_counting_functions(int maxdepth)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:75:20: warning: ‘twobit_sign2pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
75 | PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos));
| ^~~~~~~~~~~~~~~~~~~~~
match_pdict_Twobit.c:110:12: note: ‘twobit_sign2pos’ was declared here
110 | SEXP ans, twobit_sign2pos;
| ^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:653:49: 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:713:6: 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:820:44: warning: unused variable ‘subtotal_NFC’ [-Wunused-variable]
820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
| ^~~~~~~~~~~~
match_pdict_utils.c:820:27: warning: unused variable ‘total_NFC’ [-Wunused-variable]
820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
| ^~~~~~~~~
match_pdict_utils.c:819:33: warning: unused variable ‘NFC’ [-Wunused-variable]
819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
| ^~~
match_pdict_utils.c:819:26: warning: unused variable ‘nloci’ [-Wunused-variable]
819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
| ^~~~~
match_pdict_utils.c:819:20: 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:820:27: warning: ‘total_NFC’ defined but not used [-Wunused-variable]
820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
| ^~~~~~~~~
match_pdict_utils.c:820:44: 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/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c match_reporting.c -o match_reporting.o
match_reporting.c: In function ‘_new_MatchBuf’:
match_reporting.c:49:9: warning: too many arguments for format [-Wformat-extra-args]
49 | error("Biostrings internal error in _new_MatchBuf(): ",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:394:7: 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/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c strutils.c -o strutils.o
strutils.c: In function ‘MP_longestConsecutive’:
strutils.c:50:72: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
50 | error("'letter' must contain exactly one character but contains %d.",
| ~^
| |
| int
| %ld
51 | strlen(pc));
| ~~~~~~~~~~
| |
| size_t {aka long unsigned int}
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:110:8: warning: ‘if_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
110 | if (if_ambig == TRANSLATE_ERROR) {
| ^
translate.c:136:29: note: ‘if_ambig0’ was declared here
136 | int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
| ^~~~~~~~~
translate.c:106:8: warning: ‘if_non_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
106 | if (if_non_ambig == TRANSLATE_TO_X)
| ^
translate.c:136:14: note: ‘if_non_ambig0’ was declared here
136 | int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
| ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:157:9: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
157 | return twobit_sign;
| ^~~~~~~~~~~
utils.c: In function ‘_get_twobit_signature_at’:
utils.c:164:12: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
164 | int i, j, twobit_sign;
| ^~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/S4Vectors/include/S4Vectors_defines.h:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include/Rdefines.h:91:21: warning: ‘ans_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
91 | #define NEW_RAW(n) Rf_allocVector(RAWSXP,n)
| ^~~~~~~~~~~~~~
xscat.c:18:13: note: ‘ans_length’ was declared here
18 | int nargs, ans_length, tag_offset, j;
| ^~~~~~~~~~
xscat.c:52:16: warning: ‘ans_classname’ may be used uninitialized in this function [-Wmaybe-uninitialized]
52 | PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag));
| ^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include/S4Vectors_defines.h:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/include/Rdefines.h:85:25: warning: ‘ans_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
85 | #define NEW_INTEGER(n) Rf_allocVector(INTSXP,n)
| ^~~~~~~~~~~~~~
xscat.c:66:32: note: ‘ans_length’ was declared here
66 | int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
| ^~~~~~~~~~
xscat.c:108:16: warning: ‘ans_element_type’ may be used uninitialized in this function [-Wmaybe-uninitialized]
108 | PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width));
| ^~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/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 Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
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> require("Biostrings") || stop("unable to load Biostrings package")
Loading required package: Biostrings
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
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 -- Thu Mar 28 03:31:01 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
7.071 0.142 7.218
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 | |
| AlignedXStringSet-class | 0.318 | 0.004 | 0.323 | |
| DNAString-class | 0.004 | 0.000 | 0.004 | |
| GENETIC_CODE | 0.006 | 0.003 | 0.010 | |
| HNF4alpha | 0.024 | 0.000 | 0.024 | |
| IUPAC_CODE_MAP | 0.152 | 0.016 | 0.168 | |
| MIndex-class | 0 | 0 | 0 | |
| MaskedXString-class | 0.247 | 0.016 | 0.271 | |
| MultipleAlignment-class | 1.542 | 0.024 | 1.572 | |
| PDict-class | 4.124 | 0.088 | 4.225 | |
| PairwiseAlignments-class | 0.719 | 0.004 | 0.724 | |
| PairwiseAlignments-io | 2.860 | 0.116 | 2.982 | |
| QualityScaledXStringSet-class | 0.176 | 0.008 | 0.186 | |
| RNAString-class | 0.011 | 0.000 | 0.012 | |
| XString-class | 0.010 | 0.000 | 0.011 | |
| XStringQuality-class | 0.230 | 0.004 | 0.235 | |
| XStringSet-class | 14.064 | 0.299 | 14.415 | |
| XStringSet-comparison | 3.366 | 0.092 | 3.464 | |
| XStringSet-io | 7.571 | 0.128 | 7.716 | |
| XStringSetList-class | 0.310 | 0.000 | 0.311 | |
| XStringViews-class | 0.149 | 0.000 | 0.150 | |
| align-utils | 0.048 | 0.000 | 0.049 | |
| chartr | 0.747 | 0.008 | 0.761 | |
| detail | 0.344 | 0.010 | 0.363 | |
| dinucleotideFrequencyTest | 0.011 | 0.000 | 0.011 | |
| findPalindromes | 38.517 | 0.019 | 38.582 | |
| getSeq | 0.071 | 0.011 | 0.083 | |
| gregexpr2 | 0.001 | 0.000 | 0.001 | |
| injectHardMask | 0.038 | 0.011 | 0.050 | |
| letter | 0.021 | 0.004 | 0.026 | |
| letterFrequency | 0.933 | 0.020 | 0.954 | |
| longestConsecutive | 0 | 0 | 0 | |
| lowlevel-matching | 0.601 | 0.020 | 0.622 | |
| maskMotif | 1.469 | 0.028 | 1.503 | |
| match-utils | 0.026 | 0.000 | 0.026 | |
| matchLRPatterns | 0.566 | 0.020 | 0.600 | |
| matchPDict-exact | 357.028 | 1.166 | 358.911 | |
| matchPDict-inexact | 45.708 | 0.127 | 45.934 | |
| matchPWM | 3.907 | 0.072 | 3.987 | |
| matchPattern | 5.983 | 0.048 | 6.044 | |
| matchProbePair | 1.658 | 0.000 | 1.660 | |
| matchprobes | 0.000 | 0.000 | 0.001 | |
| misc | 0.019 | 0.000 | 0.020 | |
| needwunsQS | 0 | 0 | 0 | |
| nucleotideFrequency | 0.801 | 0.008 | 0.811 | |
| padAndClip | 0.625 | 0.016 | 0.642 | |
| pairwiseAlignment | 0.863 | 0.026 | 0.891 | |
| phiX174Phage | 0.534 | 0.008 | 0.543 | |
| pid | 0.424 | 0.000 | 0.424 | |
| replaceAt | 2.932 | 0.084 | 3.023 | |
| replaceLetterAt | 0.878 | 0.004 | 0.883 | |
| reverseComplement | 1.388 | 0.028 | 1.418 | |
| seqinfo-methods | 0.695 | 0.036 | 0.732 | |
| stringDist | 4.072 | 0.008 | 4.088 | |
| substitution_matrices | 1.027 | 0.008 | 1.037 | |
| toComplex | 0.002 | 0.000 | 0.001 | |
| translate | 1.551 | 0.012 | 1.567 | |
| trimLRPatterns | 0.08 | 0.00 | 0.08 | |
| xscat | 1.393 | 0.004 | 1.399 | |
| yeastSEQCHR1 | 0.003 | 0.000 | 0.003 | |