##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methVisual.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings methVisual_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/methVisual.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methVisual/DESCRIPTION' ... OK
* this is package 'methVisual' version '1.40.0'
* 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 whether package 'methVisual' can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'windows(n, lengthData, ': unused argument (rescale = "fixed") 
See 'C:/Users/biocbuild/bbs-3.11-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Cooccurrence: no visible global function definition for 'windows'
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 windows
Consider adding
  importFrom("grDevices", "windows")
to your NAMESPACE file.
* 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 ...
** running examples for arch 'i386' ... 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) :
  'C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\Rtmpgd8b87\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
1  seq_A.fasta
2  seq_B.fasta
3  seq_C.fasta
4  seq_D.fasta
5  seq_E.fasta
6  seq_F.fasta
7  seq_G.fasta
8  seq_H.fasta
9  seq_I.fasta
10 seq_J.fasta
                                                                  PATH
1  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\Rtmpgd8b87/BiqAnalyzer
2  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\Rtmpgd8b87/BiqAnalyzer
3  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\Rtmpgd8b87/BiqAnalyzer
4  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\Rtmpgd8b87/BiqAnalyzer
5  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\Rtmpgd8b87/BiqAnalyzer
6  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\Rtmpgd8b87/BiqAnalyzer
7  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\Rtmpgd8b87/BiqAnalyzer
8  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\Rtmpgd8b87/BiqAnalyzer
9  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\Rtmpgd8b87/BiqAnalyzer
10 C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\Rtmpgd8b87/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 C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\Rtmpgd8b87/BiqAnalyzer 
 please use  load("C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\Rtmpgd8b87/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: 0x1285a868>
<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

** running examples for arch 'x64' ... 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) :
  'C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\RtmpGERoai\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
1  seq_A.fasta
2  seq_B.fasta
3  seq_C.fasta
4  seq_D.fasta
5  seq_E.fasta
6  seq_F.fasta
7  seq_G.fasta
8  seq_H.fasta
9  seq_I.fasta
10 seq_J.fasta
                                                                  PATH
1  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\RtmpGERoai/BiqAnalyzer
2  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\RtmpGERoai/BiqAnalyzer
3  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\RtmpGERoai/BiqAnalyzer
4  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\RtmpGERoai/BiqAnalyzer
5  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\RtmpGERoai/BiqAnalyzer
6  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\RtmpGERoai/BiqAnalyzer
7  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\RtmpGERoai/BiqAnalyzer
8  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\RtmpGERoai/BiqAnalyzer
9  C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\RtmpGERoai/BiqAnalyzer
10 C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\RtmpGERoai/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 C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\RtmpGERoai/BiqAnalyzer 
 please use  load("C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\RtmpGERoai/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: 0x000000001f85a100>
<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: 2 ERRORs, 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/methVisual.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/methVisual_1.40.0.tar.gz && rm -rf methVisual.buildbin-libdir && mkdir methVisual.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methVisual.buildbin-libdir methVisual_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL methVisual_1.40.0.zip && rm methVisual_1.40.0.tar.gz methVisual_1.40.0.zip
###
##############################################################################
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                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 24255  100 24255    0     0   151k      0 --:--:-- --:--:-- --:--:--  158k

install for i386

* installing *source* package 'methVisual' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for request: 'score' when loading 'methVisual'
Note: possible error in 'windows(n, lengthData, ': unused argument (rescale = "fixed") 
** help
*** installing help indices
  converting help for package 'methVisual'
    finding HTML links ... done
    Cooccurrence                            html  
    MethAlignNW                             html  
    MethDataInput                           html  
    MethLollipops                           html  
    MethylQC                                html  
    cgInAlign                               html  
    cgMethFinder                            html  
    coversionGenom                          html  
    findNonAligned                          html  
    heatMapMeth                             html  
    makeDataMethGFF                         html  
    makeLocalExpDir                         html  
    makeTabFilePath                         html  
    matrixSNP                               html  
    methCA                                  html  
    methData                                html  
    methFisherTest                          html  
    methWhitneyUTest                        html  
    plotAbsMethyl                           html  
    plotMatrixSNP                           html  
    readBisulfFASTA                         html  
    selectRefSeq                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'IRanges' for request: 'score' when loading 'methVisual'
** testing if installed package can be loaded from final location
No methods found in package 'IRanges' for request: 'score' when loading 'methVisual'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'methVisual' ...
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'score' when loading 'methVisual'
* MD5 sums
packaged installation of 'methVisual' as methVisual_1.40.0.zip
* DONE (methVisual)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'methVisual' successfully unpacked and MD5 sums checked