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WISH: Add URL and BugReports to DESCRIPTION
Please consider adding:
URL: https://github.com/Bioconductor/ShortRead
BugReports: https://github.com/Bioconductor/ShortRead/issues
to the DESCRIPTION file, so this repo can be found from the package page https://bioconductor.org/packages/release/bioc/html/ShortRead.html.
Error in example: invalid 'nrow' value (too large or NA)
This is Bioconductor ShortRead 1.56.1:
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: powerpc-apple-darwin10.8.0 (32-bit)
. . .
> ### Name: Utilites
> ### Title: Utilities for common, simple operations
> ### Aliases: polyn
> ### Keywords: manip
>
> ### ** Examples
>
> polyn(c("A", "N"), 35)
A N
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
>
>
>
> cleanEx()
> nameEx("qa")
> ### * qa
>
> flush(stderr()); flush(stdout())
>
> ### Name: qa
> ### Title: Perform quality assessment on short reads
> ### Aliases: qa qa,character-method qa,list-method
> ### Keywords: manip
>
> ### ** Examples
>
> dirPath <- system.file(package="ShortRead", "extdata", "E-MTAB-1147")
> ## sample 1M reads / file
> qa <- qa(dirPath, "fastq.gz", BPPARAM=SerialParam())
> if (interactive())
+ browseURL(report(qa))
>
> showMethods("qa", where=getNamespace("ShortRead"))
Function: qa (package ShortRead)
dirPath="ShortReadQ"
dirPath="SolexaPath"
dirPath="character"
dirPath="list"
>
>
>
> cleanEx()
> nameEx("qa2")
> ### * qa2
>
> flush(stderr()); flush(stdout())
>
> ### Name: qa2
> ### Title: (Updated) quality assessment reports on short reads
> ### Aliases: QAFastqSource QACollate QA QAFlagged QAFiltered
> ### QAAdapterContamination QAData QAFrequentSequence QANucleotideByCycle
> ### QANucleotideUse QAQualityByCycle QAQualityUse QAReadQuality
> ### QASequenceUse QACollate,QAFastqSource-method QACollate,missing-method
> ### qa2 qa2,FastqSampler-method qa2,QAAdapterContamination-method
> ### qa2,QACollate-method qa2,QAFastqSource-method
> ### qa2,QAFrequentSequence-method qa2,QANucleotideByCycle-method
> ### qa2,QANucleotideUse-method qa2,QAQualityByCycle-method
> ### qa2,QAQualityUse-method qa2,QAReadQuality-method
> ### qa2,QASequenceUse-method flag flag,.QA2-method
> ### flag,QAFrequentSequence-method flag,QAReadQuality-method
> ### flag,QASource-method report,QA-method
> ### report,QAAdapterContamination-method report,QAFiltered-method
> ### report,QAFlagged-method report,QAFrequentSequence-method
> ### report,QANucleotideByCycle-method report,QANucleotideUse-method
> ### report,QAQualityByCycle-method report,QAQualityUse-method
> ### report,QAReadQuality-method report,QASequenceUse-method
> ### report,QASource-method rbind,QASummary-method
> ### show,QAAdapterContamination-method show,QACollate-method
> ### show,QAFastqSource-method show,QAFrequentSequence-method
> ### show,QAReadQuality-method show,QASummary-method
> ### Keywords: manip
>
> ### ** Examples
>
> dirPath <- system.file(package="ShortRead", "extdata", "E-MTAB-1147")
> fls <- dir(dirPath, "fastq.gz", full=TRUE)
>
> coll <- QACollate(QAFastqSource(fls), QAReadQuality(),
+ QAAdapterContamination(), QANucleotideUse(),
+ QAQualityUse(), QASequenceUse(),
+ QAFrequentSequence(n=10), QANucleotideByCycle(),
+ QAQualityByCycle())
> x <- qa2(coll, BPPARAM=SerialParam(), verbose=TRUE)
qa2,QACollate-method
qa2,QACollate1-method
qa2,QAFastqSource-method
qa2,FastqSampler-method
qa2,QAReadQuality-method
qa2,QAAdapterContamination-method
qa2,QANucleotideUse-method
qa2,QAQualityUse-method
qa2,QASequenceUse-method
qa2,QAFrequentSequence-method
qa2,QANucleotideByCycle-method
qa2,QAQualityByCycle-method
qa2,QACollate1-method
qa2,QAFastqSource-method
qa2,FastqSampler-method
qa2,QAReadQuality-method
qa2,QAAdapterContamination-method
qa2,QANucleotideUse-method
qa2,QAQualityUse-method
qa2,QASequenceUse-method
qa2,QAFrequentSequence-method
qa2,QANucleotideByCycle-method
qa2,QAQualityByCycle-method
flag,QASource-method
flag,QAReadQuality-method
flag,ANY-method
flag,ANY-method
flag,ANY-method
flag,ANY-method
flag,ANY-method
flag,ANY-method
>
> res <- report(x)
Error in matrix(0, rows.per.page, cols.per.page) :
invalid 'nrow' value (too large or NA)
Calls: report ... .html_img -> print -> print.trellis -> printFunction -> matrix
Execution halted
Tests pass fine, only one example fails.
ShortRead_Ex_out.txt
FastqSampler/FastqStreamer: Seeking clarification for OpenMP threads issues
In ?FastqStreamer, there's:
ShortRead/man/Sampler-class.Rd
Lines 166 to 179 in cca7724
I'm trying to figure out when the error happens. What does "running on multiple threads" in "... create problems when a process is already running on multiple threads ..." exactly mean here? Is the term "thread" here used in the classical way, where a process can have multiple threads? Could it be that this happens in forked parallel worker, e.g. parallel::mclapply() and BiocParallel::MulticoreParam()? That is, is it that this OpenMP implementation, which in itself is multi-threaded, is not fork safe? But it works just fine if one parallelize in separate processes, e.g. a PSOCK cluster.
Was a reproducible example identified? If so, that could be a great example of illustrating issues with OpenMP and R parallelization. I'm looking for such examples.
ghost files?
delete
Contribution of Sweave2Rmd
Hi,
I'm volunteering with Sweave2Rmd
and we're trying to replace all Bioconductor Sweave vignettes R Markdown
vignettes for the second contribution in Outreachy.
Thanks for your time.
Cant read fasta file with long line.
Hello,
while trying to import sequences from a .fasta file I encounter the following error :
cannot read line 14348, line is too long (and indeed it is long: 25157 character)
In encounter the same error while trying to use Biostrings packages.
Do you have any suggestions on how I could resolve this issue?
The error occurs in the getSequences function from dada2 that is using ShortRead to read .fasta for taxonomic assignment.
Here is my sessioninfo:
Let me know if you need anything more to address this issue.
Thanks for your work and have a nice day!
ShortRead can segfault
Issue
ShortRead may segfault. See below for a minimal reproducible example. This may for instance happen when someone try to parallelize using some of the ShortRead helper objects, which then often result in a "silent" crash with little information to go by.
Wish
I understand why the following is not meant to work, but I'd argue an R package should never be able to core dump R. Instead, it should detect the problem and produce an informative run-time error.
Reproducible example
library(ShortRead)
sp <- SolexaPath(system.file("extdata", package="ShortRead"))
fl <- file.path(analysisPath(sp), "s_1_sequence.txt")
f <- FastqStreamer(fl, 50)
print(f)
close(f)library(ShortRead)
f2 <- readRDS("f.rds")
print(f2)results in a segfault:
class: FastqStreamer
file: closed
*** caught segfault ***
address 0x8, cause 'memory not mapped'
Traceback:
1: .Call(.streamer_status, sampler)
2: .self$status()
3: object$show()
4: (new("standardGeneric", .Data = function (object) standardGeneric("show"), generic = "show", package = "methods", group = list(), valueClass = character(0), signature = "object", default = new("derivedDefaultMethod", .Data = function (object) showDefault(object), target = new("signature", .Data = "ANY", names = "object", package = "methods"), defined = new("signature", .Data = "ANY", names = "object", package = "methods"), generic = "show"), skeleton = (new("derivedDefaultMethod", .Data = function (object) showDefault(object), target = new("signature", .Data = "ANY", names = "object", package = "methods"), defined = new("signature", .Data = "ANY", names = "object", package = "methods"), generic = "show"))(object)))(new("FastqStreamer", .xData = <environment>))
5: (new("standardGeneric", .Data = function (object) standardGeneric("show"), generic = "show", package = "methods", group = list(), valueClass = character(0), signature = "object", default = new("derivedDefaultMethod", .Data = function (object) showDefault(object), target = new("signature", .Data = "ANY", names = "object", package = "methods"), defined = new("signature", .Data = "ANY", names = "object", package = "methods"), generic = "show"), skeleton = (new("derivedDefaultMethod", .Data = function (object) showDefault(object), target = new("signature", .Data = "ANY", names = "object", package = "methods"), defined = new("signature", .Data = "ANY", names = "object", package = "methods"), generic = "show"))(object)))(new("FastqStreamer", .xData = <environment>))
6: print.default(f2)
7: print(f2)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: Session info
> sessionInfo()
R version 4.1.0 RC (2021-05-10 r80282)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS
Matrix products: default
BLAS: /home/hb/software/R-devel/R-4-1-branch/lib/R/lib/libRblas.so
LAPACK: /home/hb/software/R-devel/R-4-1-branch/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] ShortRead_1.49.2 GenomicAlignments_1.27.2
[3] SummarizedExperiment_1.21.3 Biobase_2.51.0
[5] MatrixGenerics_1.3.1 matrixStats_0.58.0
[7] Rsamtools_2.7.2 GenomicRanges_1.43.4
[9] Biostrings_2.59.4 GenomeInfoDb_1.27.13
[11] XVector_0.31.1 IRanges_2.25.11
[13] S4Vectors_0.29.19 BiocParallel_1.25.5
[15] BiocGenerics_0.37.6
loaded via a namespace (and not attached):
[1] rstudioapi_0.13 zlibbioc_1.37.0 lattice_0.20-44
[4] jpeg_0.1-8.1 hwriter_1.3.2 tools_4.1.0
[7] grid_4.1.0 png_0.1-7 latticeExtra_0.6-29
[10] crayon_1.4.1 Matrix_1.3-3 GenomeInfoDbData_1.2.6
[13] RColorBrewer_1.1-2 bitops_1.0-7 RCurl_1.98-1.3
[16] DelayedArray_0.17.13 compiler_4.1.0 ShortRead/libs/ShortRead.so: undefined symbol: bioc_gzread
When install ShortRead by BiocManager::install(), and R version is 4.2.1, this package is not successful installed, and detail is as follow:
`installing to /home/xinzhepang/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-ShortRead/00new/ShortRead/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘ShortRead’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/xxx/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-ShortRead/00new/ShortRead/libs/ShortRead.so':
/home/xxx/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-ShortRead/00new/ShortRead/libs/ShortRead.so: undefined symbol: bioc_gzread
Error: loading failed
Execution halted
ERROR: loading failed
- removing ‘/home/xxx/R/x86_64-pc-linux-gnu-library/4.2/ShortRead’
The downloaded source packages are in
‘/tmp/RtmpteFAiR/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
foreign, MASS, mgcv, rpart, spatial
Warning message:
In install.packages(...) :
installation of package ‘ShortRead’ had non-zero exit status`
ShortRead fails test test_readPrb.R for non-Intel architectures
[the below was sent to Bioconductor Package Maintainer [email protected] by @tillea but I didn't see any response, so I thought I'd try here]
Hi,
the Debian packaged ShortRead is tested in CI test on different hardware
architectures. On the debci page[1] you can see the matrix for success
and failure which shows that amd64 and i386 are passing the complete
test suite while other architectures are failing. In those failing cases
the test log says something like
Timing stopped at: 1.012 0.02 1.031
Error in checkIdentical(exp, as(readPrb(sp, ".*prb.txt", as = "FastqEncoding"), :
FALSE
In addition: Warning messages:
1: In .class1(object) :
closing unused connection 6 (/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
2: In .class1(object) :
closing unused connection 5 (/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
Timing stopped at: 0.028 0.001 0.031
Error in checkIdentical(36L, unique(width(obj))) : FALSE
RUNIT TEST PROTOCOL -- Sun Jan 24 21:54:15 2021
***********************************************
Number of test functions: 104
Number of errors: 0
Number of failures: 2
1 Test Suite :
ShortRead RUnit Tests - 104 test functions, 0 errors, 2 failures
FAILURE in test_readPrb_consistent: Error in checkIdentical(exp, as(readPrb(sp, ".*prb.txt", as = "FastqEncoding"), :
FALSE
FAILURE in test_readPrb_input: Error in checkIdentical(36L, unique(width(obj))) : FALSE
Test files with failing tests
test_readPrb.R
test_readPrb_consistent
test_readPrb_input
Error in BiocGenerics:::testPackage("ShortRead") :
unit tests failed for package ShortRead
In addition: Warning message:
In is.factor(x) :
closing unused connection 3 (/tmp/RtmpEinleR/file1d7b55bbcf1b)
Execution halted
When removing the file test_readPrb.R from the installation the tests
are passing but before I do such nasty things I'd like to clarify the
situation with you.
Kind regards
Andreas.
countFastq can overflow
countFastq can overflow and return a negative number of bases.
It looks like the count_records C function returns results as 32 bit integers. Maybe better to return them as doubles, which can represent up to 52 bit integers accurately.
Example:
n <- 3000000 #Reads
m <- 1000 #Read length
dna <- paste(rep("A",m),collapse="")
qual <- paste(rep("J",m),collapse="")
sink("example.fastq")
for(i in 1:n)
cat(paste0("@read",i,"\n",dna,"\n+\n",qual,"\n"))
sink()
library(ShortRead)
countFastq("example.fastq")
#Result:
# records nucleotides scores
# example.fastq 3e+06 -1294967296 -1294967296
P.S. This is a very handy function, thank you! Much better than needing a command line tool to get fastq statistics.
Converting from a ShortRead object to a QualityScaledDNAStringSet discards names
If we have a look at this example:
library(ShortRead)
sp <- SolexaPath(system.file('extdata', package='ShortRead'))
fl <- file.path(analysisPath(sp), "s_1_sequence.txt")
f <- FastqSampler(fl, 50)
out <- yield(f)
out
## class: ShortReadQ
## length: 50 reads; width: 36 cyclesThis does okay:
as(out, "QualityScaledDNAStringSet")
## A QualityScaledDNAStringSet instance containing:
##
## DNAStringSet object of length 50:
## width seq
## [1] 36 GGTAAAGGACTTCTTGACGGTACGTTGCATGCTTGG
## [2] 36 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA
## [3] 36 GACATTATGGGTCTGCAAGCTGCTTATGCTACTTTG
## [4] 36 GTTACCATGATGTTATTTCTTCATTTGGAGGTAAAA
## [5] 36 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT
## ... ... ...
## [46] 36 GTTAATGCTGGTAATGGTGGTTTTCTTCTTTTCCTT
## [47] 36 GGGGGAGCACATTGTAGCATTGTGCCAATTCATCCA
## [48] 36 GCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAG
## [49] 36 GGGTGATAAGCAGGAGAAACATACGAAGGCGCATAA
## [50] 36 GTTTTCATGCCTCCCAATCTTGGAGGCTTTTTTATG
##
## SolexaQuality object of length 50:
## width seq
## [1] 36 ]]]]]]]]]]T]]]]]RC]Y]R]]]]WPCTVCQCMA
## [2] 36 ]]]]]]]]]]]]]]]]]V]]]]]O]]]]MQZXEAOK
## [3] 36 ]]]]]]]]]]]]]]]]YR]]]]]]]T]VWZSEVSSJ
## [4] 36 ]]]]]]]]]]]]]]]]]]]]]]T]]]]RJRZTQLOA
## [5] 36 ]]]]]]]]]]]]]]]]]T]]]]]]]]]]MJUJVLSS
## ... ... ...
## [46] 36 ]]]]]]]]]]]Y]]]]]]]]J]]]OR]MCUZEKAOO
## [47] 36 ]]]]]Y]]Y]Y]Y]HTRVVT]MRY]VCEVVZJQKHF
## [48] 36 ]]]]]]]]]]]]]]]]]VYR]]]]]]O][ZSXVSHJ
## [49] 36 ]]]]]]]]]]]Y]]V]YVTYHYJ]VJTVWPZOHJHF
## [50] 36 ]]]]]]]]]]]]]]HT]]]]]]]C]]V][ZZXVASSBut it doesn't pass on the names of each sequence in id(out), which makes it difficult to write back to FASTQ.
Plus it would also be nice for as(out, "DNAStringSet") to work, whereas it currently gives:
## Error in h(simpleError(msg, call)) :
## error in evaluating the argument 'x' in selecting a method for function 'XStringSet': no method for coercing this S4 class to a vector
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