H. Pagès
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/Biostrings |
| git_branch: RELEASE_3_13 |
| git_last_commit: 2024073 |
| git_last_commit_date: 2021-08-04 00:39:03 -0400 (Wed, 04 Aug 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:29 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the Biostrings package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 190/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Biostrings 2.60.2 (landing page) H. Pagès
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: Biostrings |
| Version: 2.60.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Biostrings_2.60.2.tar.gz |
| StartedAt: 2021-10-14 16:49:49 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 17:00:57 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 668.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Biostrings.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Biostrings_2.60.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/Biostrings.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biostrings/DESCRIPTION’ ... OK
* this is package ‘Biostrings’ version ‘2.60.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Biostrings’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 14.3Mb
sub-directories of 1Mb or more:
R 2.0Mb
extdata 11.1Mb
* 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 R 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘BiocGenerics:::testPackage’ ‘IRanges:::.showAtomicList’
‘IRanges:::new_Views’ ‘IRanges:::regroupBySupergroup’
‘IRanges:::show_IntegerRangesList’ ‘IRanges:::unlist_as_integer’
‘S4Vectors:::anyMissingOrOutside’ ‘XVector:::close_filexp’
‘XVector:::extract_character_from_XRaw_by_positions’
‘XVector:::extract_character_from_XRaw_by_ranges’
‘XVector:::new_XVectorList_from_list_of_XVector’
‘XVector:::open_output_file’
See the note in ?`:::` about the use of this operator.
* 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 '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 'relistToClass' and siglist 'XStringSet'
generic 'showAsCell' and siglist 'XStringSetList'
generic 'strsplit' and siglist 'XStringSet'
generic 'twoWayAlphabetFrequency' and siglist 'XString,XString'
generic 'twoWayAlphabetFrequency' and siglist 'XString,XStringSet'
generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XString'
generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XStringSet'
generic 'unstrsplit' and siglist 'XStringSet'
generic 'unstrsplit' and siglist 'XStringSetList'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
matchPDict-exact 311.360 2.859 314.515
matchPDict-inexact 54.021 0.678 54.761
findPalindromes 46.631 0.130 46.821
XStringSet-class 13.557 0.429 14.005
XStringSet-io 9.025 0.503 9.600
matchPattern 6.007 0.131 6.145
stringDist 6.083 0.034 6.122
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.13-bioc/meat/Biostrings.Rcheck/00check.log’
for details.
Biostrings.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Biostrings
###
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##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘Biostrings’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c BAB_class.c -o BAB_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c BitMatrix.c -o BitMatrix.o
BitMatrix.c:299:13: warning: unused function 'BitMatrix_print' [-Wunused-function]
static void BitMatrix_print(BitMatrix *bitmat)
^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c MIndex_class.c -o MIndex_class.o
MIndex_class.c:184:20: warning: unused variable 'poffsets_order' [-Wunused-variable]
IntAE *poffsets, *poffsets_order;
^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_Biostrings.c -o R_init_Biostrings.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RoSeqs_utils.c -o RoSeqs_utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c SparseList_utils.c -o SparseList_utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c XStringSetList_class.c -o XStringSetList_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c XStringSet_class.c -o XStringSet_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c XString_class.c -o XString_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c align_needwunsQS.c -o align_needwunsQS.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c align_utils.c -o align_utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c find_palindromes.c -o find_palindromes.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c gtestsim.c -o gtestsim.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c inject_code.c -o inject_code.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c letter_frequency.c -o letter_frequency.o
letter_frequency.c:956:13: warning: unused variable 'ans_dimnames' [-Wunused-variable]
SEXP ans, ans_dimnames;
^
letter_frequency.c:957:48: warning: unused variable 'x_pos' [-Wunused-variable]
int x_width, y_width, x_length, *ans_mat, i, x_pos;
^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c lowlevel_matching.c -o lowlevel_matching.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c match_PWM.c -o match_PWM.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c match_pattern.c -o match_pattern.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c match_pattern_indels.c -o match_pattern_indels.o
match_pattern_indels.c:7:13: warning: unused function 'test_match_pattern_indels' [-Wunused-function]
static void test_match_pattern_indels(const char *p, const char *s,
^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c match_pdict.c -o match_pdict.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c:139:13: warning: unused function 'debug_node_counting_functions' [-Wunused-function]
static void debug_node_counting_functions(int maxdepth)
^
match_pdict_ACtree2.c:602:21: warning: unused function 'a_nice_max_nodeextbuf_nelt' [-Wunused-function]
static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c match_pdict_Twobit.c -o match_pdict_Twobit.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c:652:49: warning: unused variable 'ncol' [-Wunused-variable]
int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
^
match_pdict_utils.c:712:6: warning: unused variable 'nelt' [-Wunused-variable]
int nelt, nkey0, nkey1, nkey2, i, key;
^
match_pdict_utils.c:819:27: warning: unused variable 'total_NFC' [-Wunused-variable]
static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
^
match_pdict_utils.c:819:44: warning: unused variable 'subtotal_NFC' [-Wunused-variable]
static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
^
match_pdict_utils.c:818:26: warning: unused variable 'nloci' [-Wunused-variable]
unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
^
match_pdict_utils.c:818:20: warning: unused variable 'ndup' [-Wunused-variable]
unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
^
match_pdict_utils.c:818:33: warning: unused variable 'NFC' [-Wunused-variable]
unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
^
match_pdict_utils.c:260:13: warning: unused function 'match_headtail_by_loc' [-Wunused-function]
static void match_headtail_by_loc(const HeadTail *headtail,
^
8 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c match_reporting.c -o match_reporting.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c matchprobes.c -o matchprobes.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pmatchPattern.c -o pmatchPattern.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c read_fasta_files.c -o read_fasta_files.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c read_fastq_files.c -o read_fastq_files.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c replaceAt.c -o replaceAt.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c replace_letter_at.c -o replace_letter_at.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c strutils.c -o strutils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c translate.c -o translate.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c unstrsplit_methods.c -o unstrsplit_methods.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utils.c -o utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -fPIC -Wall -g -O2 -c xscat.c -o xscat.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
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 Oct 14 17:00:43 2021
***********************************************
Number of test functions: 40
Number of errors: 0
Number of failures: 0
1 Test Suite :
Biostrings RUnit Tests - 40 test functions, 0 errors, 0 failures
Number of test functions: 40
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
12.985 1.335 14.309
Biostrings.Rcheck/Biostrings-Ex.timings
| name | user | system | elapsed | |
| AAString-class | 0.005 | 0.001 | 0.006 | |
| AMINO_ACID_CODE | 0.003 | 0.001 | 0.004 | |
| AlignedXStringSet-class | 0.090 | 0.005 | 0.094 | |
| DNAString-class | 0.004 | 0.001 | 0.005 | |
| GENETIC_CODE | 0.012 | 0.006 | 0.018 | |
| HNF4alpha | 0.023 | 0.004 | 0.029 | |
| IUPAC_CODE_MAP | 0.183 | 0.017 | 0.200 | |
| MIndex-class | 0.000 | 0.001 | 0.001 | |
| MaskedXString-class | 0.300 | 0.039 | 0.340 | |
| MultipleAlignment-class | 2.012 | 0.046 | 2.061 | |
| PDict-class | 4.158 | 0.143 | 4.306 | |
| PairwiseAlignments-class | 0.943 | 0.012 | 0.957 | |
| PairwiseAlignments-io | 3.018 | 0.227 | 3.247 | |
| QualityScaledXStringSet-class | 0.261 | 0.010 | 0.272 | |
| RNAString-class | 0.009 | 0.001 | 0.009 | |
| XString-class | 0.012 | 0.002 | 0.014 | |
| XStringQuality-class | 0.232 | 0.004 | 0.237 | |
| XStringSet-class | 13.557 | 0.429 | 14.005 | |
| XStringSet-comparison | 2.921 | 0.160 | 3.083 | |
| XStringSet-io | 9.025 | 0.503 | 9.600 | |
| XStringSetList-class | 0.333 | 0.013 | 0.346 | |
| XStringViews-class | 0.168 | 0.015 | 0.183 | |
| align-utils | 0.055 | 0.009 | 0.066 | |
| chartr | 0.666 | 0.033 | 0.700 | |
| detail | 0.489 | 0.076 | 0.569 | |
| dinucleotideFrequencyTest | 0.015 | 0.004 | 0.018 | |
| findPalindromes | 46.631 | 0.130 | 46.821 | |
| getSeq | 0.183 | 0.028 | 0.209 | |
| gregexpr2 | 0.001 | 0.001 | 0.002 | |
| injectHardMask | 0.066 | 0.003 | 0.071 | |
| letter | 0.030 | 0.001 | 0.032 | |
| letterFrequency | 1.084 | 0.036 | 1.121 | |
| longestConsecutive | 0.000 | 0.000 | 0.001 | |
| lowlevel-matching | 0.488 | 0.047 | 0.536 | |
| maskMotif | 2.026 | 0.104 | 2.131 | |
| match-utils | 0.023 | 0.001 | 0.024 | |
| matchLRPatterns | 0.619 | 0.017 | 0.637 | |
| matchPDict-exact | 311.360 | 2.859 | 314.515 | |
| matchPDict-inexact | 54.021 | 0.678 | 54.761 | |
| matchPWM | 2.881 | 0.013 | 2.895 | |
| matchPattern | 6.007 | 0.131 | 6.145 | |
| matchProbePair | 1.326 | 0.016 | 1.342 | |
| matchprobes | 0.390 | 0.007 | 0.399 | |
| misc | 0.029 | 0.000 | 0.030 | |
| needwunsQS | 0.000 | 0.001 | 0.001 | |
| nucleotideFrequency | 0.940 | 0.077 | 1.017 | |
| padAndClip | 0.648 | 0.015 | 0.663 | |
| pairwiseAlignment | 0.922 | 0.018 | 0.940 | |
| phiX174Phage | 0.496 | 0.031 | 0.527 | |
| pid | 0.45 | 0.01 | 0.46 | |
| replaceAt | 2.806 | 0.399 | 3.206 | |
| replaceLetterAt | 0.494 | 0.006 | 0.500 | |
| reverseComplement | 1.338 | 0.054 | 1.393 | |
| seqinfo | 0.756 | 0.012 | 0.769 | |
| stringDist | 6.083 | 0.034 | 6.122 | |
| substitution_matrices | 1.024 | 0.375 | 1.400 | |
| toComplex | 0.001 | 0.001 | 0.002 | |
| translate | 1.619 | 0.019 | 1.638 | |
| trimLRPatterns | 0.107 | 0.003 | 0.110 | |
| xscat | 1.573 | 0.080 | 1.652 | |
| yeastSEQCHR1 | 0.003 | 0.002 | 0.005 | |