| Back to Rapid builds (Linux only) of a subset of BioC 3.21 Report updated every 6 hours |
This page was generated on 2025-03-25 07:58 -0400 (Tue, 25 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 870 |
| 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 41/217 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| Biostrings 2.75.4 (landing page) Hervé Pagès
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||
|
To the developers/maintainers of the Biostrings package: - 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: 2.75.4 |
| Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings Biostrings_2.75.4.tar.gz |
| StartedAt: 2025-03-25 07:16:06 -0400 (Tue, 25 Mar 2025) |
| EndedAt: 2025-03-25 07:18:10 -0400 (Tue, 25 Mar 2025) |
| EllapsedTime: 124.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: Biostrings.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings Biostrings_2.75.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Biostrings.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Biostrings/DESCRIPTION’ ... OK
* this is package ‘Biostrings’ version ‘2.75.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Biostrings’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
installed size is 14.2Mb
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 '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'
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
File ‘Biostrings/libs/Biostrings.so’:
Found non-API calls to R: ‘NAMED’, ‘SET_NAMED’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* 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-io
> ### Title: Read/write an XStringSet object from/to a file
> ### Aliases: XStringSet-io readBStringSet readDNAStringSet readRNAStringSet
> ### readAAStringSet fasta.seqlengths fasta.index fastq.seqlengths
> ### fastq.geometry writeXStringSet saveXStringSet
> ### Keywords: utilities manip
>
> ### ** Examples
>
> ## ---------------------------------------------------------------------
> ## A. READ/WRITE FASTA FILES
> ## ---------------------------------------------------------------------
>
> ## Read a non-compressed FASTA files:
> filepath1 <- system.file("extdata", "someORF.fa", package="Biostrings")
> fasta.seqlengths(filepath1, seqtype="DNA")
YAL001C TFC3 SGDID:S0000001, Chr I from 152168-146596, reverse complement, Verified ORF
5573
YAL002W VPS8 SGDID:S0000002, Chr I from 142709-148533, Verified ORF
5825
YAL003W EFB1 SGDID:S0000003, Chr I from 141176-144162, Verified ORF
2987
YAL005C SSA1 SGDID:S0000004, Chr I from 142433-138505, reverse complement, Verified ORF
3929
YAL007C ERP2 SGDID:S0000005, Chr I from 139347-136700, reverse complement, Verified ORF
2648
YAL008W FUN14 SGDID:S0000006, Chr I from 135916-138512, Verified ORF
2597
YAL009W SPO7 SGDID:S0000007, Chr I from 134856-137635, Verified ORF
2780
> x1 <- readDNAStringSet(filepath1)
> x1
DNAStringSet object of length 7:
width seq names
[1] 5573 ACTTGTAAATATATCTTTTATTT...CTTATCGACCTTATTGTTGATAT YAL001C TFC3 SGDI...
[2] 5825 TTCCAAGGCCGATGAATTCGACT...AGTAAATTTTTTTCTATTCTCTT YAL002W VPS8 SGDI...
[3] 2987 CTTCATGTCAGCCTGCACTTCTG...TGGTACTCATGTAGCTGCCTCAT YAL003W EFB1 SGDI...
[4] 3929 CACTCATATCGGGGGTCTTACTT...TGTCCCGAAACACGAAAAAGTAC YAL005C SSA1 SGDI...
[5] 2648 AGAGAAAGAGTTTCACTTCTTGA...ATATAATTTATGTGTGAACATAG YAL007C ERP2 SGDI...
[6] 2597 GTGTCCGGGCCTCGCAGGCGTTC...AAGTTTTGGCAGAATGTACTTTT YAL008W FUN14 SGD...
[7] 2780 CAAGATAATGTCAAAGTTAGTGG...GCTAAGGAAGAAAAAAAAATCAC YAL009W SPO7 SGDI...
>
> ## Read a gzip-compressed FASTA file:
> filepath2 <- system.file("extdata", "someORF.fa.gz", package="Biostrings")
> fasta.seqlengths(filepath2, seqtype="DNA")
YAL001C TFC3 SGDID:S0000001, Chr I from 152168-146596, reverse complement, Verified ORF
5573
YAL002W VPS8 SGDID:S0000002, Chr I from 142709-148533, Verified ORF
5825
YAL003W EFB1 SGDID:S0000003, Chr I from 141176-144162, Verified ORF
2987
YAL005C SSA1 SGDID:S0000004, Chr I from 142433-138505, reverse complement, Verified ORF
3929
YAL007C ERP2 SGDID:S0000005, Chr I from 139347-136700, reverse complement, Verified ORF
2648
YAL008W FUN14 SGDID:S0000006, Chr I from 135916-138512, Verified ORF
2597
YAL009W SPO7 SGDID:S0000007, Chr I from 134856-137635, Verified ORF
2780
> x2 <- readDNAStringSet(filepath2)
> x2
DNAStringSet object of length 7:
width seq names
[1] 5573 ACTTGTAAATATATCTTTTATTT...CTTATCGACCTTATTGTTGATAT YAL001C TFC3 SGDI...
[2] 5825 TTCCAAGGCCGATGAATTCGACT...AGTAAATTTTTTTCTATTCTCTT YAL002W VPS8 SGDI...
[3] 2987 CTTCATGTCAGCCTGCACTTCTG...TGGTACTCATGTAGCTGCCTCAT YAL003W EFB1 SGDI...
[4] 3929 CACTCATATCGGGGGTCTTACTT...TGTCCCGAAACACGAAAAAGTAC YAL005C SSA1 SGDI...
[5] 2648 AGAGAAAGAGTTTCACTTCTTGA...ATATAATTTATGTGTGAACATAG YAL007C ERP2 SGDI...
[6] 2597 GTGTCCGGGCCTCGCAGGCGTTC...AAGTTTTGGCAGAATGTACTTTT YAL008W FUN14 SGD...
[7] 2780 CAAGATAATGTCAAAGTTAGTGG...GCTAAGGAAGAAAAAAAAATCAC YAL009W SPO7 SGDI...
>
> ## Sanity check:
> stopifnot(identical(as.character(x1), as.character(x2)))
>
> ## Read 2 FASTA files at once:
> filepath3 <- system.file("extdata", "fastaEx.fa", package="Biostrings")
> fasta.seqlengths(c(filepath2, filepath3), seqtype="DNA")
YAL001C TFC3 SGDID:S0000001, Chr I from 152168-146596, reverse complement, Verified ORF
5573
YAL002W VPS8 SGDID:S0000002, Chr I from 142709-148533, Verified ORF
5825
YAL003W EFB1 SGDID:S0000003, Chr I from 141176-144162, Verified ORF
2987
YAL005C SSA1 SGDID:S0000004, Chr I from 142433-138505, reverse complement, Verified ORF
3929
YAL007C ERP2 SGDID:S0000005, Chr I from 139347-136700, reverse complement, Verified ORF
2648
YAL008W FUN14 SGDID:S0000006, Chr I from 135916-138512, Verified ORF
2597
YAL009W SPO7 SGDID:S0000007, Chr I from 134856-137635, Verified ORF
2780
sequence1
72
sequence2
70
> x23 <- readDNAStringSet(c(filepath2, filepath3))
> x23
DNAStringSet object of length 9:
width seq names
[1] 5573 ACTTGTAAATATATCTTTTATTT...CTTATCGACCTTATTGTTGATAT YAL001C TFC3 SGDI...
[2] 5825 TTCCAAGGCCGATGAATTCGACT...AGTAAATTTTTTTCTATTCTCTT YAL002W VPS8 SGDI...
[3] 2987 CTTCATGTCAGCCTGCACTTCTG...TGGTACTCATGTAGCTGCCTCAT YAL003W EFB1 SGDI...
[4] 3929 CACTCATATCGGGGGTCTTACTT...TGTCCCGAAACACGAAAAAGTAC YAL005C SSA1 SGDI...
[5] 2648 AGAGAAAGAGTTTCACTTCTTGA...ATATAATTTATGTGTGAACATAG YAL007C ERP2 SGDI...
[6] 2597 GTGTCCGGGCCTCGCAGGCGTTC...AAGTTTTGGCAGAATGTACTTTT YAL008W FUN14 SGD...
[7] 2780 CAAGATAATGTCAAAGTTAGTGG...GCTAAGGAAGAAAAAAAAATCAC YAL009W SPO7 SGDI...
[8] 72 AGTACGTAGTCGCTGCTGCTACG...GATGCTAGCTGACTAAACGATGC sequence1
[9] 70 AAACGATCGATCGTACTCGACTG...CATCGTCAGTTACTGCATGCGGG sequence2
>
> ## Sanity check:
> x3 <- readDNAStringSet(filepath3)
> stopifnot(identical(as.character(x23), as.character(c(x2, x3))))
>
> ## Use a FASTA index to load only an arbitrary subset of sequences:
> filepath4 <- system.file("extdata", "dm3_upstream2000.fa.gz",
+ package="Biostrings")
> fai <- fasta.index(filepath4, seqtype="DNA")
> head(fai)
recno fileno offset
1 1 1 0
2 2 1 2100
3 3 1 4200
4 4 1 6300
5 5 1 8400
6 6 1 10500
desc seqlength
1 NM_078863_up_2000_chr2L_16764737_f chr2L:16764737-16766736 2000
2 NM_001201794_up_2000_chr2L_8382455_f chr2L:8382455-8384454 2000
3 NM_001201795_up_2000_chr2L_8382455_f chr2L:8382455-8384454 2000
4 NM_001201796_up_2000_chr2L_8382455_f chr2L:8382455-8384454 2000
5 NM_001201797_up_2000_chr2L_8382455_f chr2L:8382455-8384454 2000
6 NM_164812_up_2000_chr2L_8382455_f chr2L:8382455-8384454 2000
filepath
1 /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/extdata/dm3_upstream2000.fa.gz
2 /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/extdata/dm3_upstream2000.fa.gz
3 /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/extdata/dm3_upstream2000.fa.gz
4 /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/extdata/dm3_upstream2000.fa.gz
5 /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/extdata/dm3_upstream2000.fa.gz
6 /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/extdata/dm3_upstream2000.fa.gz
> head(fai$desc)
[1] "NM_078863_up_2000_chr2L_16764737_f chr2L:16764737-16766736"
[2] "NM_001201794_up_2000_chr2L_8382455_f chr2L:8382455-8384454"
[3] "NM_001201795_up_2000_chr2L_8382455_f chr2L:8382455-8384454"
[4] "NM_001201796_up_2000_chr2L_8382455_f chr2L:8382455-8384454"
[5] "NM_001201797_up_2000_chr2L_8382455_f chr2L:8382455-8384454"
[6] "NM_164812_up_2000_chr2L_8382455_f chr2L:8382455-8384454"
> i <- sample(nrow(fai), 10) # randomly pick up 10 sequences
> x4 <- readDNAStringSet(fai[i, ])
>
> ## Sanity check:
> stopifnot(identical(as.character(readDNAStringSet(filepath4)[i]),
+ as.character(x4)))
>
> ## Write FASTA files:
> out23a <- tempfile()
> writeXStringSet(x23, out23a)
> out23b <- tempfile()
> writeXStringSet(x23, out23b, compress=TRUE)
> file.info(c(out23a, out23b))$size
[1] 27382 7941
>
> ## Sanity checks:
> stopifnot(identical(as.character(readDNAStringSet(out23a)),
+ as.character(x23)))
> stopifnot(identical(readLines(out23a), readLines(out23b)))
>
> ## ---------------------------------------------------------------------
> ## B. READ/WRITE FASTQ FILES
> ## ---------------------------------------------------------------------
>
> filepath5 <- system.file("extdata", "s_1_sequence.txt",
+ package="Biostrings")
>
> fastq.geometry(filepath5)
[1] 256 36
>
> ## The quality strings are ignored by default:
> reads <- readDNAStringSet(filepath5, format="fastq")
> reads
DNAStringSet object of length 256:
width seq names
[1] 36 GGACTTTGTAGGATACCCTCGCTTTCCTTCTCCTGT HWI-EAS88_1_1_1_1...
[2] 36 GATTTCTTACCTATTAGTGGTTGAACAGCATCGGAC HWI-EAS88_1_1_1_8...
[3] 36 GCGGTGGTCTATAGTGTTATTAATATCAATTTGGGT HWI-EAS88_1_1_1_9...
[4] 36 GTTACCATGATGTTATTTCTTCATTTGGAGGTAAAA HWI-EAS88_1_1_1_8...
[5] 36 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT HWI-EAS88_1_1_1_9...
... ... ...
[252] 36 GTTTAGATATGAGTCACATTTTGTTCATGGTAGAGT HWI-EAS88_1_1_1_6...
[253] 36 GTTTTACAGACACCTAAAGCTACATCGTCAACGTTA HWI-EAS88_1_1_1_1...
[254] 36 GATGAACTAAGTCAACCTCAGCACTAACCTTGCGAG HWI-EAS88_1_1_1_3...
[255] 36 GTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTA HWI-EAS88_1_1_1_8...
[256] 36 GCAATCTGCCGACCACTCGCGATTCAATCATGACTT HWI-EAS88_1_1_1_8...
> mcols(reads)
NULL
>
> ## Use 'with.qualities=TRUE' to load them:
> reads <- readDNAStringSet(filepath5, format="fastq", with.qualities=TRUE)
> reads
DNAStringSet object of length 256:
width seq names
[1] 36 GGACTTTGTAGGATACCCTCGCTTTCCTTCTCCTGT HWI-EAS88_1_1_1_1...
[2] 36 GATTTCTTACCTATTAGTGGTTGAACAGCATCGGAC HWI-EAS88_1_1_1_8...
[3] 36 GCGGTGGTCTATAGTGTTATTAATATCAATTTGGGT HWI-EAS88_1_1_1_9...
[4] 36 GTTACCATGATGTTATTTCTTCATTTGGAGGTAAAA HWI-EAS88_1_1_1_8...
[5] 36 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT HWI-EAS88_1_1_1_9...
... ... ...
[252] 36 GTTTAGATATGAGTCACATTTTGTTCATGGTAGAGT HWI-EAS88_1_1_1_6...
[253] 36 GTTTTACAGACACCTAAAGCTACATCGTCAACGTTA HWI-EAS88_1_1_1_1...
[254] 36 GATGAACTAAGTCAACCTCAGCACTAACCTTGCGAG HWI-EAS88_1_1_1_3...
[255] 36 GTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTA HWI-EAS88_1_1_1_8...
[256] 36 GCAATCTGCCGACCACTCGCGATTCAATCATGACTT HWI-EAS88_1_1_1_8...
> mcols(reads)
DataFrame with 256 rows and 1 column
qualities
<BStringSet>
HWI-EAS88_1_1_1_1001_499 ]]]]]]]]]]...]VCHVMPLAS
HWI-EAS88_1_1_1_898_392 ]]]]]]]]]]...T][PZPICCK
HWI-EAS88_1_1_1_922_465 ]]]]Y]]]]]...TMJEUXEFLA
HWI-EAS88_1_1_1_895_493 ]]]]]]]]]]...]RJRZTQLOA
HWI-EAS88_1_1_1_953_493 ]]]]]]]]]]...]]MJUJVLSS
... ...
HWI-EAS88_1_1_1_693_898 ]]]]]]]]]]...R]MJQNSAOC
HWI-EAS88_1_1_1_183_559 ]]]]]]]]]]...]VTVVRVMSM
HWI-EAS88_1_1_1_314_891 ]]]]Y]Y]]]...VVTSZUOOHH
HWI-EAS88_1_1_1_884_867 ]]]]]]]]]]...]T[OVXEJSJ
HWI-EAS88_1_1_1_878_444 ]]]]]]]]]]...EVVRSRHHNH
> mcols(reads)$qualities
BStringSet object of length 256:
width seq
[1] 36 ]]]]]]]]]]]]Y]Y]]]]]]]]]]]]VCHVMPLAS
[2] 36 ]]]]]]]]]]]]Y]]]]]]]]]YPV]T][PZPICCK
[3] 36 ]]]]Y]]]]]V]T]]]]]T]]]]]V]TMJEUXEFLA
[4] 36 ]]]]]]]]]]]]]]]]]]]]]]T]]]]RJRZTQLOA
[5] 36 ]]]]]]]]]]]]]]]]]T]]]]]]]]]]MJUJVLSS
... ... ...
[252] 36 ]]]]]]]]]]]Y]]]]]NY]]]]Y]VR]MJQNSAOC
[253] 36 ]]]]]]]]]]]]]]]]]]]]]]]Y]]]VTVVRVMSM
[254] 36 ]]]]Y]Y]]]]]]]OYY]]]Y]]]YYVVTSZUOOHH
[255] 36 ]]]]]]]]]]]]]]]T]]]]]]]]]V]T[OVXEJSJ
[256] 36 ]]]]]]]]]]]Y]]T]T]]]]TRYVMEVVRSRHHNH
>
> ## Each quality string contains one letter per nucleotide in the
> ## corresponding read:
> stopifnot(identical(width(mcols(reads)$qualities), width(reads)))
>
> ## Write the reads to a FASTQ file:
> outfile <- tempfile()
> writeXStringSet(reads, outfile, format="fastq")
> outfile2 <- tempfile()
> writeXStringSet(reads, outfile2, compress=TRUE, format="fastq")
>
> ## Sanity checks:
> stopifnot(identical(readLines(outfile), readLines(filepath5)))
> stopifnot(identical(readLines(outfile), readLines(outfile2)))
>
> ## ---------------------------------------------------------------------
> ## C. READ FILES BY CHUNK
> ## ---------------------------------------------------------------------
> ## readDNAStringSet() supports reading an arbitrary number of FASTA or
> ## FASTQ records at a time in a loop. This can be useful to process
> ## big FASTA or FASTQ files by chunk and thus avoids loading the entire
> ## file in memory. To achieve this the files to read from need to be
> ## opened with open_input_files() first. Note that open_input_files()
> ## accepts a vector of file paths and/or URLs.
>
> ## With FASTA files:
> files <- open_input_files(filepath4)
> i <- 0
> while (TRUE) {
+ i <- i + 1
+ ## Load 4000 records at a time. Each new call to readDNAStringSet()
+ ## picks up where the previous call left.
+ dna <- readDNAStringSet(files, nrec=4000)
+ if (length(dna) == 0L)
+ break
+ cat("processing chunk", i, "...\n")
+ ## do something with 'dna' ...
+ }
processing chunk 1 ...
processing chunk 2 ...
processing chunk 3 ...
processing chunk 4 ...
processing chunk 5 ...
processing chunk 6 ...
processing chunk 7 ...
>
> ## With FASTQ files:
> files <- open_input_files(filepath5)
> i <- 0
> while (TRUE) {
+ i <- i + 1
+ ## Load 75 records at a time.
+ reads <- readDNAStringSet(files, format="fastq", nrec=75)
+ if (length(reads) == 0L)
+ break
+ cat("processing chunk", i, "...\n")
+ ## do something with 'reads' ...
+ }
processing chunk 1 ...
processing chunk 2 ...
processing chunk 3 ...
processing chunk 4 ...
>
> ## IMPORTANT NOTE: Like connections, the object returned by
> ## open_input_files() can NOT be shared across workers in the
> ## context of parallelization!
>
> ## ---------------------------------------------------------------------
> ## D. READ A FASTQ FILE AS A QualityScaledDNAStringSet OBJECT
> ## ---------------------------------------------------------------------
>
> ## Use readQualityScaledDNAStringSet() if you want the object to be
> ## returned as a QualityScaledDNAStringSet instead of a DNAStringSet
> ## object. See ?readQualityScaledDNAStringSet for more information.
>
> ## Note that readQualityScaledDNAStringSet() is a simple wrapper around
> ## readDNAStringSet() that does the following if the file contains
> ## "Phred quality scores" (which is the standard Sanger variant to
> ## assess reliability of a base call):
> reads <- readDNAStringSet(filepath5, format="fastq", with.qualities=TRUE)
> quals <- PhredQuality(mcols(reads)$qualities)
> QualityScaledDNAStringSet(reads, quals)
Warning in XStringSet("DNA", x, start = start, end = end, width = width, :
metadata columns on input DNAStringSet object were dropped
A QualityScaledDNAStringSet instance containing:
DNAStringSet object of length 256:
width seq names
[1] 36 GGACTTTGTAGGATACCCTCGCTTTCCTTCTCCTGT HWI-EAS88_1_1_1_1...
[2] 36 GATTTCTTACCTATTAGTGGTTGAACAGCATCGGAC HWI-EAS88_1_1_1_8...
[3] 36 GCGGTGGTCTATAGTGTTATTAATATCAATTTGGGT HWI-EAS88_1_1_1_9...
[4] 36 GTTACCATGATGTTATTTCTTCATTTGGAGGTAAAA HWI-EAS88_1_1_1_8...
[5] 36 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT HWI-EAS88_1_1_1_9...
... ... ...
[252] 36 GTTTAGATATGAGTCACATTTTGTTCATGGTAGAGT HWI-EAS88_1_1_1_6...
[253] 36 GTTTTACAGACACCTAAAGCTACATCGTCAACGTTA HWI-EAS88_1_1_1_1...
[254] 36 GATGAACTAAGTCAACCTCAGCACTAACCTTGCGAG HWI-EAS88_1_1_1_3...
[255] 36 GTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTA HWI-EAS88_1_1_1_8...
[256] 36 GCAATCTGCCGACCACTCGCGATTCAATCATGACTT HWI-EAS88_1_1_1_8...
PhredQuality object of length 256:
width seq
[1] 36 ]]]]]]]]]]]]Y]Y]]]]]]]]]]]]VCHVMPLAS
[2] 36 ]]]]]]]]]]]]Y]]]]]]]]]YPV]T][PZPICCK
[3] 36 ]]]]Y]]]]]V]T]]]]]T]]]]]V]TMJEUXEFLA
[4] 36 ]]]]]]]]]]]]]]]]]]]]]]T]]]]RJRZTQLOA
[5] 36 ]]]]]]]]]]]]]]]]]T]]]]]]]]]]MJUJVLSS
... ... ...
[252] 36 ]]]]]]]]]]]Y]]]]]NY]]]]Y]VR]MJQNSAOC
[253] 36 ]]]]]]]]]]]]]]]]]]]]]]]Y]]]VTVVRVMSM
[254] 36 ]]]]Y]Y]]]]]]]OYY]]]Y]]]YYVVTSZUOOHH
[255] 36 ]]]]]]]]]]]]]]]T]]]]]]]]]V]T[OVXEJSJ
[256] 36 ]]]]]]]]]]]Y]]T]T]]]]TRYVMEVVRSRHHNH
>
> ## The call to PhredQuality() is replaced with a call to SolexaQuality()
> ## or IlluminaQuality() if the quality scores are Solexa quality scores.
>
> ## ---------------------------------------------------------------------
> ## E. GENERATE FAKE READS AND WRITE THEM TO A FASTQ FILE
> ## ---------------------------------------------------------------------
>
> library(BSgenome.Celegans.UCSC.ce2)
Loading required package: BSgenome
Loading required package: GenomicRanges
Loading required package: BiocIO
Loading required package: rtracklayer
>
> ## Create a "sliding window" on chr I:
> sw_start <- seq.int(1, length(Celegans$chrI)-50, by=50)
> sw <- Views(Celegans$chrI, start=sw_start, width=10)
> my_fake_reads <- as(sw, "XStringSet")
> my_fake_ids <- sprintf("ID%06d", seq_len(length(my_fake_reads)))
> names(my_fake_reads) <- my_fake_ids
> my_fake_reads
DNAStringSet object of length 301609:
width seq names
[1] 10 GCCTAAGCCT ID000001
[2] 10 CTAAGCCTAA ID000002
[3] 10 AAGCCTAAGC ID000003
[4] 10 GCCTAAGCCT ID000004
[5] 10 CTAAGCCTAA ID000005
... ... ...
[301605] 10 GCCGATCCAT ID301605
[301606] 10 AGCTTTGGAA ID301606
[301607] 10 GTTGCGGTAT ID301607
[301608] 10 CTTAGGCTTA ID301608
[301609] 10 TAGGCTTAGG ID301609
>
> ## Fake quality ';' will be assigned to each base in 'my_fake_reads':
> out2 <- tempfile()
> writeXStringSet(my_fake_reads, out2, format="fastq")
>
> ## Passing qualities thru the 'qualities' argument:
> my_fake_quals <- rep.int(BStringSet("DCBA@?>=<;"), length(my_fake_reads))
> my_fake_quals
BStringSet object of length 301609:
width seq
[1] 10 DCBA@?>=<;
[2] 10 DCBA@?>=<;
[3] 10 DCBA@?>=<;
[4] 10 DCBA@?>=<;
[5] 10 DCBA@?>=<;
... ... ...
[301605] 10 DCBA@?>=<;
[301606] 10 DCBA@?>=<;
[301607] 10 DCBA@?>=<;
[301608] 10 DCBA@?>=<;
[301609] 10 DCBA@?>=<;
> out3 <- tempfile()
> writeXStringSet(my_fake_reads, out3, format="fastq",
+ qualities=my_fake_quals)
>
> ## ---------------------------------------------------------------------
> ## F. SERIALIZATION
> ## ---------------------------------------------------------------------
> saveXStringSet(my_fake_reads, "my_fake_reads", dirpath=tempdir())
Saving /tmp/RtmpnCoevk/my_fake_reads.rda ... Error in save(list = objname, file = filepath) :
error writing to connection
Calls: saveXStringSet -> save
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
XStringSet-class 7.518 0.634 8.153
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Biostrings.Rcheck/00check.log’
for details.
Biostrings.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL Biostrings
###
##############################################################################
##############################################################################
* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘Biostrings’ ...
** this is package ‘Biostrings’ version ‘2.75.4’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c BAB_class.c -o BAB_class.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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)
| ^~~~~~~~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function ‘SparseMIndex_endIndex’:
MIndex_class.c:184:27: warning: unused variable ‘poffsets_order’ [-Wunused-variable]
184 | IntAE *poffsets, *poffsets_order;
| ^~~~~~~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c SparseList_utils.c -o SparseList_utils.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c XStringSetList_class.c -o XStringSetList_class.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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;
| ^~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c XString_class.c -o XString_class.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c find_palindromes.c -o find_palindromes.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c gtestsim.c -o gtestsim.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c inject_code.c -o inject_code.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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;
| ^~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c lowlevel_matching.c -o lowlevel_matching.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c match_PWM.c -o match_PWM.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c match_pattern.c -o match_pattern.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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
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"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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;
| ^~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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/rapidbuild/bbs-3.21-bioc-rapid/R/include/Rdefines.h:41,
from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include/S4Vectors_defines.h:18,
from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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/rapidbuild/bbs-3.21-bioc-rapid/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;
| ^~~~~~~~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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,
| ^~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c match_reporting.c -o match_reporting.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c matchprobes.c -o matchprobes.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c pmatchPattern.c -o pmatchPattern.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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;
| ^~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c replaceAt.c -o replaceAt.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c strutils.c -o strutils.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c translate.c -o translate.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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;
| ^~~~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/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/rapidbuild/bbs-3.21-bioc-rapid/R/include/Rdefines.h:41,
from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include/S4Vectors_defines.h:18,
from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include/IRanges_defines.h:18,
from ../inst/include/Biostrings_defines.h:18,
from Biostrings.h:1,
from xscat.c:1:
xscat.c: In function ‘XString_xscat’:
/home/rapidbuild/bbs-3.21-bioc-rapid/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/rapidbuild/bbs-3.21-bioc-rapid/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/rapidbuild/bbs-3.21-bioc-rapid/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/rapidbuild/bbs-3.21-bioc-rapid/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/rapidbuild/bbs-3.21-bioc-rapid/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/rapidbuild/bbs-3.21-bioc-rapid/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;
| ^~~~~~~~~~~~~~~~
gcc -shared -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-Biostrings/00new/Biostrings/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet”
Creating a new generic function for ‘strsplit’ in package ‘Biostrings’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’
Creating a new generic function for ‘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/testthat.Rout
R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
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Platform: x86_64-pc-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: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
>
> test_check("Biostrings")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1349 ]
>
> proc.time()
user system elapsed
12.075 0.438 12.499
Biostrings.Rcheck/Biostrings-Ex.timings
| name | user | system | elapsed | |
| AAString-class | 0.003 | 0.000 | 0.003 | |
| AMINO_ACID_CODE | 0.001 | 0.001 | 0.002 | |
| DNAString-class | 0.003 | 0.000 | 0.003 | |
| GENETIC_CODE | 0.008 | 0.000 | 0.008 | |
| HNF4alpha | 0.020 | 0.002 | 0.022 | |
| IUPAC_CODE_MAP | 0.316 | 0.000 | 0.316 | |
| MIndex-class | 0 | 0 | 0 | |
| MaskedXString-class | 0.124 | 0.039 | 0.163 | |
| MultipleAlignment-class | 0.842 | 0.082 | 0.924 | |
| PDict-class | 2.790 | 0.135 | 2.937 | |
| QualityScaledXStringSet-class | 0.112 | 0.002 | 0.115 | |
| RNAString-class | 0.005 | 0.000 | 0.005 | |
| XString-class | 0.006 | 0.000 | 0.006 | |
| XStringQuality-class | 0.089 | 0.001 | 0.090 | |
| XStringSet-class | 7.518 | 0.634 | 8.153 | |
| XStringSet-comparison | 2.002 | 0.111 | 2.113 | |