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### Running command:
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### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:methVisual.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings methVisual_1.42.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/methVisual.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methVisual/DESCRIPTION’ ... OK
* this is package ‘methVisual’ version ‘1.42.0’
* 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 ‘methVisual’ can be installed ... WARNING
Found the following significant warnings:
Note: possible error in 'windows(n, lengthData, ': unused argument (rescale = "fixed")
Warning: Package 'methVisual' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.12-bioc/meat/methVisual.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biostrings’ ‘grid’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘gsubfn’ ‘plotrix’ ‘sqldf’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MethylQC: no visible global function definition for ‘score’
makeDataMethGFF: no visible binding for global variable ‘fn’
plotMatrixSNP: no visible global function definition for ‘color.legend’
Undefined global functions or variables:
color.legend fn score
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘methVisual-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MethAlignNW
> ### Title: Summary of methylation states
> ### Aliases: MethAlignNW
> ### Keywords: graphs
>
> ### ** Examples
>
> ## In order to use the following example
> ## make sure that you have writing permission under R.home()
> ## directory. If you do not have permission choose your own path.
> #dir.create(file.path(R.home(component="home"),"/BiqAnalyzer"))
> BiqAnalyzer_path <- file.path(tempdir(), "BiqAnalyzer")
> dir.create(BiqAnalyzer_path)
Warning in dir.create(BiqAnalyzer_path) :
'/tmp/RtmpfKcy6R/BiqAnalyzer' already exists
> makeLocalExpDir(dataPath="/examples/BiqAnalyzer", localDir=BiqAnalyzer_path)
[1] "seq_A.fasta"
[1] "seq_B.fasta"
[1] "seq_C.fasta"
[1] "seq_D.fasta"
[1] "seq_E.fasta"
[1] "seq_F.fasta"
[1] "seq_G.fasta"
[1] "seq_H.fasta"
[1] "seq_I.fasta"
[1] "seq_J.fasta"
FILE PATH
1 seq_A.fasta /tmp/RtmpfKcy6R/BiqAnalyzer
2 seq_B.fasta /tmp/RtmpfKcy6R/BiqAnalyzer
3 seq_C.fasta /tmp/RtmpfKcy6R/BiqAnalyzer
4 seq_D.fasta /tmp/RtmpfKcy6R/BiqAnalyzer
5 seq_E.fasta /tmp/RtmpfKcy6R/BiqAnalyzer
6 seq_F.fasta /tmp/RtmpfKcy6R/BiqAnalyzer
7 seq_G.fasta /tmp/RtmpfKcy6R/BiqAnalyzer
8 seq_H.fasta /tmp/RtmpfKcy6R/BiqAnalyzer
9 seq_I.fasta /tmp/RtmpfKcy6R/BiqAnalyzer
10 seq_J.fasta /tmp/RtmpfKcy6R/BiqAnalyzer
> datameth <- MethDataInput(file.path(BiqAnalyzer_path, "PathFileTab.txt"))
> refseq <- selectRefSeq(file.path(BiqAnalyzer_path, "Master_Sequence.txt"))
Read 1 item
> QCdata <- MethylQC(refseq, datameth)
checking seq_A.fasta
seq_A.fasta BAD SEQUENCE IDENTITY: 67.98246 % !!!
checking seq_B.fasta
checking seq_C.fasta
checking seq_D.fasta
seq_D.fasta BAD CONVERSION RATE: 89.85507 % !!!
checking seq_E.fasta
checking seq_F.fasta
seq_F.fasta BAD CONVERSION RATE: 88.4058 % !!!
checking seq_G.fasta
checking seq_H.fasta
checking seq_I.fasta
checking seq_J.fasta
seq_J.fasta BAD SEQUENCE IDENTITY: 47.80702 % !!!
The new experiment data files after QC (QC_*) and the QCINFO.Rdata are under /tmp/RtmpfKcy6R/BiqAnalyzer
please use load("/tmp/RtmpfKcy6R/BiqAnalyzer/QCINFO.Rdata") in order to view QC information
> methData <- MethAlignNW( refseq , QCdata)
Alignment with QC_seq_B.fasta done
Alignment with QC_seq_C.fasta done
Alignment with QC_seq_E.fasta done
Alignment with QC_seq_G.fasta done
Alignment with QC_seq_H.fasta done
Alignment with QC_seq_I.fasta done
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
methVisual
--- call from context ---
MethAlignNW(refseq, QCdata)
--- call from argument ---
missing(alignment) || alignment == FALSE
--- R stacktrace ---
where 1: MethAlignNW(refseq, QCdata)
--- value of length: 6 type: logical ---
[1] FALSE FALSE FALSE FALSE FALSE FALSE
--- function from context ---
function (refSeq, QCdata, alignment)
{
seqName <- c()
alignment <- c()
files <- paste(QCdata$FILE)
paths <- QCdata$PATH
mat <- matrix(0, length(DNA_ALPHABET), length(DNA_ALPHABET))
mat[1:4, 1:4] <- c(1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0,
0, 0, 1)
rownames(mat) <- colnames(mat) <- DNA_ALPHABET[1:length(DNA_ALPHABET)]
lengthRef <- nchar(refSeq)
cg_ref <- gregexpr("CG", refSeq)
positionCGIRef <- sort(cg_ref[[1]][1:length(cg_ref[[1]])])
methPos <- matrix(nrow = length(QCdata$PATH), ncol = length(cg_ref[[1]]))
startEnd <- matrix(nrow = length(QCdata$PATH), ncol = 2)
for (i in 1:length(paths)) {
seqFileTemp <- paste(paths[i], "/", files[i], sep = "")
seqTemp <- toupper(scan(seqFileTemp, what = "character",
sep = "", quiet = TRUE))
align <- pairwiseAlignment(refSeq, seqTemp, substitutionMatrix = mat,
type = "local-global")
startRef <- start(pattern(align))
endRef <- end(pattern(align))
startEnd_temp <- c(startRef, endRef)
startEnd[i, ] <- startEnd_temp
newRef <- paste(substr(refSeq, 1, startRef - 1), pattern(align),
substr(refSeq, endRef + 1, lengthRef), sep = "")
newSeq <- paste(paste(rep("-", startRef - 1), collapse = ""),
subject(align), paste(rep("-", lengthRef - endRef)),
sep = "")
alignment[i] <- paste(subject(align))
methPos_Temp <- cgMethFinder(newRef, newSeq)
methPos[i, ] <- methPos_Temp
seqName[i] <- files[i]
cat("Alignment with ", seqName[i], " done", "\n")
}
if (missing(alignment) || alignment == FALSE) {
mathylAlign <- list(seqName = seqName, methPos = methPos,
positionCGIRef = positionCGIRef, startEnd = startEnd,
lengthRef = nchar(refSeq))
}
else {
mathylAlign <- list(seqName = seqName, alignment = alignment,
methPos = methPos, positionCGIRef = positionCGIRef,
startEnd = startEnd, lengthRef = nchar(refSeq))
}
return(mathylAlign)
}
<bytecode: 0x562f07178490>
<environment: namespace:methVisual>
--- function search by body ---
Function MethAlignNW in namespace methVisual has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: length > 1 in coercion to logical
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.12-bioc/meat/methVisual.Rcheck/00check.log’
for details.