Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 215/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Biostrings 2.73.1 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | 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: 2.73.1 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Biostrings.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Biostrings_2.73.1.tar.gz |
StartedAt: 2024-07-15 22:11:45 -0400 (Mon, 15 Jul 2024) |
EndedAt: 2024-07-15 22:20:38 -0400 (Mon, 15 Jul 2024) |
EllapsedTime: 532.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: Biostrings.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Biostrings.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Biostrings_2.73.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/Biostrings.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'Biostrings/DESCRIPTION' ... OK * this is package 'Biostrings' version '2.73.1' * 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 whether package 'Biostrings' can be installed ... WARNING Found the following significant warnings: strutils.c:50:73: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/Biostrings.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.2.0' * checking installed package size ... NOTE installed size is 13.6Mb sub-directories of 1Mb or more: R 1.5Mb extdata 11.1Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking 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 for x64 is not available File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/libs/x64/Biostrings.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * 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 242.00 3.13 246.08 matchPDict-inexact 68.40 1.16 70.28 findPalindromes 29.31 0.03 29.79 XStringSet-class 9.83 0.61 10.54 PDict-class 4.55 4.07 9.31 XStringSet-io 7.99 0.50 8.82 matchPattern 7.31 0.16 7.47 * 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, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/Biostrings.Rcheck/00check.log' for details.
Biostrings.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Biostrings ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'Biostrings' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BAB_class.c -o BAB_class.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PreprocessedTB_class.c -o PreprocessedTB_class.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_Biostrings.c -o R_init_Biostrings.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RoSeqs_utils.c -o RoSeqs_utils.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SparseList_utils.c -o SparseList_utils.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XStringSetList_class.c -o XStringSetList_class.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XStringSet_class.c -o XStringSet_class.o XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER': XStringSet_class.c:124:17: warning: 'lkup_len' may be used uninitialized [-Wmaybe-uninitialized] 124 | _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 | INTEGER(start)[i], lkup0, lkup_len); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ XStringSet_class.c:103:22: note: 'lkup_len' was declared here 103 | int ans_len, lkup_len, i; | ^~~~~~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XString_class.c -o XString_class.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c find_palindromes.c -o find_palindromes.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gtestsim.c -o gtestsim.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c inject_code.c -o inject_code.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c lowlevel_matching.c -o lowlevel_matching.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c match_PWM.c -o match_PWM.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c match_pattern.c -o match_pattern.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o match_pattern_boyermoore.c: In function '_match_pattern_boyermoore': match_pattern_boyermoore.c:417:32: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized] 417 | for (i = i1-1, j = j1-1; j >= 0; i--, j--) | ~~^~~~~~ match_pattern_boyermoore.c:383:42: note: 'i1' was declared here 383 | int nmatches, last_match_end, n, i1, i2, j1, j2, shift, shift1, | ^~ match_pattern_boyermoore.c:417:42: warning: 'j1' may be used uninitialized [-Wmaybe-uninitialized] 417 | for (i = i1-1, j = j1-1; j >= 0; i--, j--) | ~~^~~~~~ match_pattern_boyermoore.c:383:50: note: 'j1' was declared here 383 | int nmatches, last_match_end, n, i1, i2, j1, j2, shift, shift1, | ^~ match_pattern_boyermoore.c:383:46: warning: 'i2' may be used uninitialized [-Wmaybe-uninitialized] 383 | int nmatches, last_match_end, n, i1, i2, j1, j2, shift, shift1, | ^~ match_pattern_boyermoore.c:385:23: warning: 'c' may be used uninitialized [-Wmaybe-uninitialized] 385 | char ppP_rmc, c; /* ppP_rmc is 'ppP.seq' right-most char */ | ^ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c match_pattern_shiftor.c -o match_pattern_shiftor.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c match_pdict.c -o match_pdict.o In function 'vcount_PDict3Parts_XStringSet', inlined from 'vmatch_PDict3Parts_XStringSet' at match_pdict.c:508:10: match_pdict.c:419:33: warning: 'ans_col' may be used uninitialized [-Wmaybe-uninitialized] 419 | ans_col += tb_length; | ~~~~~~~~^~~~~~~~~~~~ match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet': match_pdict.c:392:65: note: 'ans_col' was declared here 392 | int tb_length, S_length, collapse0, i, j, match_count, *ans_col; | ^~~~~~~ In function 'vcount_XStringSet_XStringSet', inlined from 'vmatch_XStringSet_XStringSet' at match_pdict.c:542:10: match_pdict.c:470:41: warning: 'ans_elt' may be used uninitialized [-Wmaybe-uninitialized] 470 | ans_elt += P_length; | ~~~~~~~~^~~~~~~~~~~ match_pdict.c: In function 'vmatch_XStringSet_XStringSet': match_pdict.c:441:64: note: 'ans_elt' was declared here 441 | int P_length, S_length, collapse0, i, j, match_count, *ans_elt; | ^~~~~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o match_pdict_ACtree2.c: In function 'split_and_move_pointers': match_pdict_ACtree2.c:1031:17: warning: variable 'node0' set but not used [-Wunused-but-set-variable] 1031 | ACnode *node0, *node1, *node2; | ^~~~~ match_pdict_ACtree2.c: In function 'merge_pointers': match_pdict_ACtree2.c:1076:17: warning: variable 'node0' set but not used [-Wunused-but-set-variable] 1076 | ACnode *node0, *node1, *node2; | ^~~~~ match_pdict_ACtree2.c: At top level: match_pdict_ACtree2.c:602:21: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used [-Wunused-function] 602 | static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ match_pdict_ACtree2.c:139:13: warning: 'debug_node_counting_functions' defined but not used [-Wunused-function] 139 | static void debug_node_counting_functions(int maxdepth) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c match_pdict_Twobit.c -o match_pdict_Twobit.o In file included from C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41, from C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18, from C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include/IRanges_defines.h:18, from ../inst/include/Biostrings_defines.h:18, from Biostrings.h:1, from match_pdict_Twobit.c:10: In function 'Twobit_asLIST', inlined from 'build_Twobit' at match_pdict_Twobit.c:145:2: match_pdict_Twobit.c:75:27: warning: 'twobit_sign2pos' may be used uninitialized [-Wmaybe-uninitialized] 75 | PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ match_pdict_Twobit.c: In function 'build_Twobit': match_pdict_Twobit.c:110:19: note: 'twobit_sign2pos' was declared here 110 | SEXP ans, twobit_sign2pos; | ^~~~~~~~~~~~~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c match_pdict_utils.c -o match_pdict_utils.o match_pdict_utils.c: In function 'match_ppheadtail0': match_pdict_utils.c:653:56: warning: unused variable 'ncol' [-Wunused-variable] 653 | int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol; | ^~~~ match_pdict_utils.c: In function 'match_ppheadtail': match_pdict_utils.c:713:13: warning: unused variable 'nelt' [-Wunused-variable] 713 | int nelt, nkey0, nkey1, nkey2, i, key; | ^~~~ match_pdict_utils.c: In function '_match_pdict_all_flanks': match_pdict_utils.c:820:51: warning: unused variable 'subtotal_NFC' [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~~~~ match_pdict_utils.c:820:34: warning: unused variable 'total_NFC' [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~ match_pdict_utils.c:819:40: warning: unused variable 'NFC' [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~ match_pdict_utils.c:819:33: warning: unused variable 'nloci' [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~~~ match_pdict_utils.c:819:27: warning: unused variable 'ndup' [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~~ match_pdict_utils.c: At top level: match_pdict_utils.c:261:13: warning: 'match_headtail_by_loc' defined but not used [-Wunused-function] 261 | static void match_headtail_by_loc(const HeadTail *headtail, | ^~~~~~~~~~~~~~~~~~~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c match_reporting.c -o match_reporting.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matchprobes.c -o matchprobes.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pmatchPattern.c -o pmatchPattern.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_fasta_files.c -o read_fasta_files.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_fastq_files.c -o read_fastq_files.o read_fastq_files.c: In function 'parse_FASTQ_file': read_fastq_files.c:408:28: warning: 'dont_load' may be used uninitialized [-Wmaybe-uninitialized] 408 | if (dont_load || loader->new_qualid_hook == NULL) | ^ read_fastq_files.c:311:26: note: 'dont_load' was declared here 311 | lineinrecno, dont_load; | ^~~~~~~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c replaceAt.c -o replaceAt.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c replace_letter_at.c -o replace_letter_at.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c strutils.c -o strutils.o strutils.c: In function 'MP_longestConsecutive': strutils.c:50:73: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 50 | error("'letter' must contain exactly one character but contains %lu.", | ~~^ | | | long unsigned int | %llu 51 | strlen(pc)); | ~~~~~~~~~~ | | | size_t {aka long long unsigned int} gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c translate.c -o translate.o In function 'translate', inlined from 'DNAStringSet_translate' at translate.c:195:4: translate.c:99:36: warning: 'if_non_ambig0' may be used uninitialized [-Wmaybe-uninitialized] 99 | if (if_non_ambig == TRANSLATE_ERROR) { | ^ translate.c: In function 'DNAStringSet_translate': translate.c:136:21: note: 'if_non_ambig0' was declared here 136 | int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode; | ^~~~~~~~~~~~~ In function 'translate', inlined from 'DNAStringSet_translate' at translate.c:195:4: translate.c:110:36: warning: 'if_ambig0' may be used uninitialized [-Wmaybe-uninitialized] 110 | if (if_ambig == TRANSLATE_ERROR) { | ^ translate.c: In function 'DNAStringSet_translate': translate.c:136:36: note: 'if_ambig0' was declared here 136 | int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode; | ^~~~~~~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c unstrsplit_methods.c -o unstrsplit_methods.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o utils.c: In function '_get_twobit_signature': utils.c:157:16: warning: 'twobit_sign' may be used uninitialized [-Wmaybe-uninitialized] 157 | return twobit_sign; | ^~~~~~~~~~~ utils.c:150:16: note: 'twobit_sign' was declared here 150 | int i, twobit_sign; | ^~~~~~~~~~~ utils.c: In function '_get_twobit_signature_at': utils.c:174:16: warning: 'twobit_sign' may be used uninitialized [-Wmaybe-uninitialized] 174 | return twobit_sign; | ^~~~~~~~~~~ utils.c:164:19: note: 'twobit_sign' was declared here 164 | int i, j, twobit_sign; | ^~~~~~~~~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c xscat.c -o xscat.o In file included from C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41, from C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18, from C:/Users/biocbuild/bbs-3.20-bioc/R/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': C:/Users/biocbuild/bbs-3.20-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) | ^~~~~~~~~~~~~~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:38:27: note: in expansion of macro 'NEW_RAW' 38 | PROTECT(ans_tag = NEW_RAW(ans_length)); | ^~~~~~~ xscat.c:18:20: note: 'ans_length' was declared here 18 | int nargs, ans_length, tag_offset, j; | ^~~~~~~~~~ xscat.c:52:23: warning: 'ans_classname' may be used uninitialized [-Wmaybe-uninitialized] 52 | PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:20:21: note: 'ans_classname' was declared here 20 | const char *ans_classname; | ^~~~~~~~~~~~~ xscat.c: In function 'XStringSet_xscat': C:/Users/biocbuild/bbs-3.20-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) | ^~~~~~~~~~~~~~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:91:29: note: in expansion of macro 'NEW_INTEGER' 91 | PROTECT(ans_width = NEW_INTEGER(ans_length)); | ^~~~~~~~~~~ xscat.c:66:39: note: 'ans_length' was declared here 66 | int nargs, *arg_lengths, *ii, ans_length, i, j, *width; | ^~~~~~~~~~ xscat.c:108:23: warning: 'ans_element_type' may be used uninitialized [-Wmaybe-uninitialized] 108 | PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:68:21: note: 'ans_element_type' was declared here 68 | const char *ans_element_type; | ^~~~~~~~~~~~~~~~ gcc -shared -s -static-libgcc -o Biostrings.dll tmp.def 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 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-Biostrings/00new/Biostrings/libs/x64 ** 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 ** 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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 Jul 15 22:20:23 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 11.03 0.23 11.26
Biostrings.Rcheck/Biostrings-Ex.timings
name | user | system | elapsed | |
AAString-class | 0 | 0 | 0 | |
AMINO_ACID_CODE | 0 | 0 | 0 | |
DNAString-class | 0 | 0 | 0 | |
GENETIC_CODE | 0.00 | 0.01 | 0.01 | |
HNF4alpha | 0.03 | 0.00 | 0.03 | |
IUPAC_CODE_MAP | 0.08 | 0.04 | 0.11 | |
MIndex-class | 0 | 0 | 0 | |
MaskedXString-class | 0.14 | 0.09 | 0.28 | |
MultipleAlignment-class | 1.08 | 0.01 | 1.10 | |
PDict-class | 4.55 | 4.07 | 9.31 | |
QualityScaledXStringSet-class | 0.14 | 0.01 | 0.16 | |
RNAString-class | 0.01 | 0.00 | 0.01 | |
XString-class | 0 | 0 | 0 | |
XStringQuality-class | 0.11 | 0.00 | 0.11 | |
XStringSet-class | 9.83 | 0.61 | 10.54 | |
XStringSet-comparison | 4.15 | 0.21 | 4.42 | |
XStringSet-io | 7.99 | 0.50 | 8.82 | |
XStringSetList-class | 0.17 | 0.01 | 0.18 | |
XStringViews-class | 0.11 | 0.00 | 0.11 | |
chartr | 0.83 | 0.11 | 0.94 | |
detail | 0.22 | 0.03 | 0.26 | |
dinucleotideFrequencyTest | 0.00 | 0.02 | 0.02 | |
findPalindromes | 29.31 | 0.03 | 29.79 | |
getSeq | 0.05 | 0.03 | 0.08 | |
gregexpr2 | 0 | 0 | 0 | |
injectHardMask | 0.02 | 0.03 | 0.05 | |
letter | 0.03 | 0.00 | 0.03 | |
letterFrequency | 0.75 | 0.06 | 0.81 | |
longestConsecutive | 0 | 0 | 0 | |
lowlevel-matching | 0.23 | 0.08 | 0.31 | |
maskMotif | 1.15 | 0.11 | 1.27 | |
match-utils | 0.04 | 0.00 | 0.03 | |
matchLRPatterns | 1.21 | 0.09 | 1.28 | |
matchPDict-exact | 242.00 | 3.13 | 246.08 | |
matchPDict-inexact | 68.40 | 1.16 | 70.28 | |
matchPWM | 1.47 | 0.04 | 1.52 | |
matchPattern | 7.31 | 0.16 | 7.47 | |
matchProbePair | 1.80 | 0.09 | 1.89 | |
matchprobes | 0 | 0 | 0 | |
misc | 0.69 | 0.00 | 0.69 | |
needwunsQS | 0 | 0 | 0 | |
nucleotideFrequency | 0.45 | 0.08 | 0.53 | |
padAndClip | 0.31 | 0.05 | 0.36 | |
replaceAt | 1.52 | 0.24 | 1.75 | |
replaceLetterAt | 0.28 | 0.15 | 0.44 | |
reverseComplement | 0.75 | 0.07 | 0.81 | |
seqinfo-methods | 0.34 | 0.06 | 0.44 | |
toComplex | 0 | 0 | 0 | |
translate | 0.72 | 0.16 | 0.87 | |
trimLRPatterns | 0.03 | 0.01 | 0.04 | |
xscat | 0.75 | 0.16 | 0.93 | |
yeastSEQCHR1 | 0 | 0 | 0 | |