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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Biostrings_2.79.5.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/Biostrings.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biostrings/DESCRIPTION’ ... OK
* this is package ‘Biostrings’ version ‘2.79.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Biostrings’ can be installed ... OK
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* checking installed package size ... INFO
  installed size is 14.1Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    extdata  11.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MultipleAlignment-class.Rd: NormalIRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 'parallel_slot_names' and siglist 'ByPos_MIndex'
  generic 'parallel_slot_names' and siglist 'MIndex'
  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'
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 ... ERROR
Running examples in ‘Biostrings-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: XStringSet-class
> ### Title: XStringSet objects
> ### Aliases: class:XStringSet XStringSet-class XStringSet class:BStringSet
> ###   BStringSet-class BStringSet class:DNAStringSet DNAStringSet-class
> ###   DNAStringSet class:RNAStringSet RNAStringSet-class RNAStringSet
> ###   class:AAStringSet AAStringSet-class AAStringSet
> ###   width,character-method nchar,XStringSet-method
> ###   is.na,XStringSet-method anyNA,XStringSet-method
> ###   windows,character-method narrow,character-method
> ###   subseq,character-method subseq<-,character-method
> ###   subseq<-,XStringSet-method threebands,character-method
> ###   seqtype,XStringSet-method seqtype<-,XStringSet-method
> ###   coerce,ANY,BStringSet-method coerce,ANY,DNAStringSet-method
> ###   coerce,ANY,RNAStringSet-method coerce,ANY,AAStringSet-method
> ###   coerce,ANY,XStringSet-method show,XStringSet-method
> ###   showAsCell,XStringSet-method unlist,XStringSet-method
> ###   as.character,XStringSet-method as.factor,XStringSet-method
> ###   as.data.frame,XStringSet-method as.vector,XStringSet-method
> ###   toString,XStringSet-method as.matrix,XStringSet-method
> ###   updateObject,XStringSet-method updateObject,AAStringSet-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## A. USING THE XStringSet CONSTRUCTORS ON A CHARACTER VECTOR OR FACTOR
> ## ---------------------------------------------------------------------
> ## Note that there is no XStringSet() constructor, but an XStringSet
> ## family of constructors: BStringSet(), DNAStringSet(), RNAStringSet(),
> ## etc...
> x0 <- c("#CTC-NACCAGTAT", "#TTGA", "TACCTAGAG")
> width(x0)
[1] 14  5  9
> x1 <- BStringSet(x0)
> x1
BStringSet object of length 3:
    width seq
[1]    14 #CTC-NACCAGTAT
[2]     5 #TTGA
[3]     9 TACCTAGAG
> 
> ## 3 equivalent ways to obtain the same BStringSet object:
> BStringSet(x0, start=4, end=-3)
BStringSet object of length 3:
    width seq
[1]     9 C-NACCAGT
[2]     0 
[3]     4 CTAG
> subseq(x1, start=4, end=-3)
BStringSet object of length 3:
    width seq
[1]     9 C-NACCAGT
[2]     0 
[3]     4 CTAG
> BStringSet(subseq(x0, start=4, end=-3))
BStringSet object of length 3:
    width seq
[1]     9 C-NACCAGT
[2]     0 
[3]     4 CTAG
> 
> dna0 <- DNAStringSet(x0, start=4, end=-3)
> dna0  # 'options(Biostrings.coloring=FALSE)' to turn off coloring
DNAStringSet object of length 3:
    width seq
[1]     9 C-NACCAGT
[2]     0 
[3]     4 CTAG
> 
> names(dna0)
NULL
> names(dna0)[2] <- "seqB"
> dna0
DNAStringSet object of length 3:
    width seq                                               names               
[1]     9 C-NACCAGT                                         <NA>
[2]     0                                                   seqB
[3]     4 CTAG                                              <NA>
> 
> ## When the input vector contains a lot of duplicates, turning it into
> ## a factor first before passing it to the constructor will produce an
> ## XStringSet object that is more compact in memory:
> library(hgu95av2probe)
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> x2 <- sample(hgu95av2probe$sequence, 999000, replace=TRUE)
> dna2a <- DNAStringSet(x2)
> dna2b <- DNAStringSet(factor(x2))  # slower but result is more compact
> object.size(dna2a)
36967032 bytes
> object.size(dna2b)
16959232 bytes
> 
> ## ---------------------------------------------------------------------
> ## B. USING THE XStringSet CONSTRUCTORS ON A SINGLE SEQUENCE (XString
> ##    OBJECT OR CHARACTER STRING)
> ## ---------------------------------------------------------------------
> x3 <- "abcdefghij"
> BStringSet(x3, start=2, end=6:2)  # behaves like 'substring(x3, 2, 6:2)'
BStringSet object of length 5:
    width seq
[1]     5 bcdef
[2]     4 bcde
[3]     3 bcd
[4]     2 bc
[5]     1 b
> BStringSet(x3, start=-(1:6))
BStringSet object of length 6:
    width seq
[1]     1 j
[2]     2 ij
[3]     3 hij
[4]     4 ghij
[5]     5 fghij
[6]     6 efghij
> x4 <- BString(x3)
> BStringSet(x4, end=-(1:6), width=3)
BStringSet object of length 6:
    width seq
[1]     3 hij
[2]     3 ghi
[3]     3 fgh
[4]     3 efg
[5]     3 def
[6]     3 cde
> 
> ## Randomly extract 1 million 40-mers from C. elegans chrI:
> extractRandomReads <- function(subject, nread, readlength)
+ {
+     if (!is.integer(readlength))
+         readlength <- as.integer(readlength)
+     start <- sample(length(subject) - readlength + 1L, nread,
+                     replace=TRUE)
+     DNAStringSet(subject, start=start, width=readlength)
+ }
> library(BSgenome.Celegans.UCSC.ce2)
Loading required package: BSgenome
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: BiocIO
Loading required package: rtracklayer
Error: package or namespace load failed for ‘rtracklayer’:
 class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'
Error: package ‘rtracklayer’ could not be loaded
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
PDict-class             5.316  5.239  40.058
MultipleAlignment-class 1.929  0.373   5.785
XStringQuality-class    0.198  0.649   6.636
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/Biostrings.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL Biostrings
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘Biostrings’ ...
** this is package ‘Biostrings’ version ‘2.79.5’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c BAB_class.c -o BAB_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -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)
      |             ^~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c MIndex_class.c -o MIndex_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c PreprocessedTB_class.c -o PreprocessedTB_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c R_init_Biostrings.c -o R_init_Biostrings.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c RoSeqs_utils.c -o RoSeqs_utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c XStringSetList_class.c -o XStringSetList_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -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;
      |                      ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c XString_class.c -o XString_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c find_palindromes.c -o find_palindromes.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c gtestsim.c -o gtestsim.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c inject_code.c -o inject_code.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c lcsuffix.c -o lcsuffix.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -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;
      |                                                ^~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c lowlevel_matching.c -o lowlevel_matching.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c match_PWM.c -o match_PWM.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c match_pattern.c -o match_pattern.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -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,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c match_pattern_shiftor.c -o match_pattern_shiftor.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -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;
      |                                                                ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -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)
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c match_pdict_Twobit.c -o match_pdict_Twobit.o
In file included from /home/biocbuild/R/R/include/Rdefines.h:41,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from match_pdict_Twobit.c:10:
In function ‘Twobit_asLIST’,
    inlined from ‘build_Twobit’ at match_pdict_Twobit.c:145:2:
match_pdict_Twobit.c:75:27: warning: ‘twobit_sign2pos’ may be used uninitialized [-Wmaybe-uninitialized]
   75 |         PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos));
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
  388 | #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;
      |                   ^~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -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,
      |             ^~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c match_reporting.c -o match_reporting.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c read_fasta_files.c -o read_fasta_files.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -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;
      |                          ^~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c replaceAt.c -o replaceAt.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c replace_letter_at.c -o replace_letter_at.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c strutils.c -o strutils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c translate.c -o translate.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c unstrsplit_methods.c -o unstrsplit_methods.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -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;
      |                   ^~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c xscat.c -o xscat.o
In file included from /home/biocbuild/R/R/include/Rdefines.h:41,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/R/R-devel_2025-02-19/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/include/Rdefines.h:91:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized]
   91 | #define NEW_RAW(n)              Rf_allocVector(RAWSXP,n)
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
xscat.c:38:27: note: in expansion of macro ‘NEW_RAW’
   38 |         PROTECT(ans_tag = NEW_RAW(ans_length));
      |                           ^~~~~~~
xscat.c:18:20: note: ‘ans_length’ was declared here
   18 |         int nargs, ans_length, tag_offset, j;
      |                    ^~~~~~~~~~
xscat.c:52:23: warning: ‘ans_classname’ may be used uninitialized [-Wmaybe-uninitialized]
   52 |         PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag));
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
xscat.c:20:21: note: ‘ans_classname’ was declared here
   20 |         const char *ans_classname;
      |                     ^~~~~~~~~~~~~
xscat.c: In function ‘XStringSet_xscat’:
/home/biocbuild/R/R/include/Rdefines.h:85:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized]
   85 | #define NEW_INTEGER(n)          Rf_allocVector(INTSXP,n)
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
xscat.c:91:29: note: in expansion of macro ‘NEW_INTEGER’
   91 |         PROTECT(ans_width = NEW_INTEGER(ans_length));
      |                             ^~~~~~~~~~~
xscat.c:66:39: note: ‘ans_length’ was declared here
   66 |         int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
      |                                       ^~~~~~~~~~
xscat.c:108:23: warning: ‘ans_element_type’ may be used uninitialized [-Wmaybe-uninitialized]
  108 |         PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width));
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
xscat.c:68:21: note: ‘ans_element_type’ was declared here
   68 |         const char *ans_element_type;
      |                     ^~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o find_palindromes.o gtestsim.o inject_code.o lcsuffix.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 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/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/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 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)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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> library(testthat)
> library(Biostrings)
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

> 
> test_check("Biostrings")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2866 ]
> 
> proc.time()
   user  system elapsed 
 41.777   1.272  43.252