CRAN Package Check Results for Package MLPA

Last updated on 2021-10-14 13:52:54 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	1.10.0	4.27	38.14	42.41	ERROR
r-devel-linux-x86_64-debian-gcc	1.10.0	3.32	29.40	32.72	ERROR
r-devel-linux-x86_64-fedora-clang	1.10.0			63.37	ERROR
r-devel-linux-x86_64-fedora-gcc	1.10.0			53.53	ERROR
r-devel-windows-x86_64	1.10.0	7.00	41.00	48.00	ERROR
r-devel-windows-x86_64-gcc10-UCRT	1.10.0				ERROR
r-patched-linux-x86_64	1.10.0	4.64	39.95	44.59	OK
r-patched-solaris-x86	1.10.0			78.60	OK
r-release-linux-x86_64	1.10.0	3.97	39.45	43.42	OK
r-release-macos-arm64	1.10.0				OK
r-release-macos-x86_64	1.10.0				OK
r-release-windows-ix86+x86_64	1.10.0	9.00	57.00	66.00	OK
r-oldrel-macos-x86_64	1.10.0				OK
r-oldrel-windows-ix86+x86_64	1.10.0	11.00	55.00	66.00	OK

Check Details

Version: 1.10.0
Check: examples
Result: ERROR
    Running examples in 'MLPA-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: GEP.process
    > ### Title: MLPA peak detection
    > ### Aliases: GEP.process GEP.interface
    >
    > ### ** Examples
    >
    > # Working in temporary directory
    > output <- sprintf("%s/test.log", tempdir())
    >
    > # See files before analysis
    > dir(system.file("extdata", package="MLPA"))
    [1] "ab1" "design.conf" "fsa" "rescue.conf"
    >
    > # Launch analysis in package directory
    > GEP.process(
    + input = system.file("extdata/fsa", package="MLPA"),
    + design = system.file("extdata/design.conf", package="MLPA"),
    + output = output
    + )
    Tue Oct 12 16:10:40 2021
    MLPA 1.10.0
    
    Design file : /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/MLPA/extdata/design.conf [c3ede9beca2291307483391447ba9be1]
    Design setting set to default for function GEP.process : overwrite, gene.cex, file.line, mar, progressBar, disable
    Design setting set to default for function read.fsa : applyLowess, processed, meta.extra, disable
    Design setting set to default for function align.fsa : channel, fullLadder, useLadder, outThreshold, noiseLevel, surePeaks, trim, maskOffScale, rMin, rescue, ylim, disable
    Design setting set to default for function peaks.fsa : logTransform, lowThreshold, channels, noiseRange, primerRange, disable
    Design setting set to default for function plot.fsa : units, ladder, offScaleCol, offScalePch, offScaleCex, bg, fg, title, xlab, ylab, ylim, xaxt, yaxt, bty, xaxp, nticks, all.bp, disable
    Design setting set to default for function model : groupColors, threshold, disable
    Design setting set to default for function classify : plot, disable
    Processing /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/MLPA/extdata/fsa/A1270.fsa
    FSA metadata : user="VR", machine="3130-18321022", runModule.name="TCTM2", runModule.version="15", runProtocole.name="TCTM2", runProtocole.version="1", runStart="2013-04-24 10:41:42", runStop="2013-04-24 11:05:10", collectionStart="2013-04-24 10:52:06", collectionStop="2013-04-24 11:05:06", injectionTime="3"
    Error in rect(xleft = sapply(design$PEAKS$ranges, "[", 1), xright = sapply(design$PEAKS$ranges, :
     invalid RGB specification
    Calls: GEP.process -> rect
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.10.0
Check: examples
Result: ERROR
    Running examples in ‘MLPA-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: GEP.process
    > ### Title: MLPA peak detection
    > ### Aliases: GEP.process GEP.interface
    >
    > ### ** Examples
    >
    > # Working in temporary directory
    > output <- sprintf("%s/test.log", tempdir())
    >
    > # See files before analysis
    > dir(system.file("extdata", package="MLPA"))
    [1] "ab1" "design.conf" "fsa" "rescue.conf"
    >
    > # Launch analysis in package directory
    > GEP.process(
    + input = system.file("extdata/fsa", package="MLPA"),
    + design = system.file("extdata/design.conf", package="MLPA"),
    + output = output
    + )
    Wed Oct 13 19:11:20 2021
    MLPA 1.10.0
    
    Design file : /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MLPA/extdata/design.conf [c3ede9beca2291307483391447ba9be1]
    Design setting set to default for function GEP.process : overwrite, gene.cex, file.line, mar, progressBar, disable
    Design setting set to default for function read.fsa : applyLowess, processed, meta.extra, disable
    Design setting set to default for function align.fsa : channel, fullLadder, useLadder, outThreshold, noiseLevel, surePeaks, trim, maskOffScale, rMin, rescue, ylim, disable
    Design setting set to default for function peaks.fsa : logTransform, lowThreshold, channels, noiseRange, primerRange, disable
    Design setting set to default for function plot.fsa : units, ladder, offScaleCol, offScalePch, offScaleCex, bg, fg, title, xlab, ylab, ylim, xaxt, yaxt, bty, xaxp, nticks, all.bp, disable
    Design setting set to default for function model : groupColors, threshold, disable
    Design setting set to default for function classify : plot, disable
    Processing /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MLPA/extdata/fsa/A1270.fsa
    FSA metadata : user="VR", machine="3130-18321022", runModule.name="TCTM2", runModule.version="15", runProtocole.name="TCTM2", runProtocole.version="1", runStart="2013-04-24 10:41:42", runStop="2013-04-24 11:05:10", collectionStart="2013-04-24 10:52:06", collectionStop="2013-04-24 11:05:06", injectionTime="3"
    Error in rect(xleft = sapply(design$PEAKS$ranges, "[", 1), xright = sapply(design$PEAKS$ranges, :
     invalid RGB specification
    Calls: GEP.process -> rect
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.10.0
Check: examples
Result: ERROR
    Running examples in ‘MLPA-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: GEP.process
    > ### Title: MLPA peak detection
    > ### Aliases: GEP.process GEP.interface
    >
    > ### ** Examples
    >
    > # Working in temporary directory
    > output <- sprintf("%s/test.log", tempdir())
    >
    > # See files before analysis
    > dir(system.file("extdata", package="MLPA"))
    [1] "ab1" "design.conf" "fsa" "rescue.conf"
    >
    > # Launch analysis in package directory
    > GEP.process(
    + input = system.file("extdata/fsa", package="MLPA"),
    + design = system.file("extdata/design.conf", package="MLPA"),
    + output = output
    + )
    Fri Oct 8 20:36:04 2021
    MLPA 1.10.0
    
    Design file : /data/gannet/ripley/R/packages/tests-clang/MLPA.Rcheck/MLPA/extdata/design.conf [c3ede9beca2291307483391447ba9be1]
    Design setting set to default for function GEP.process : overwrite, gene.cex, file.line, mar, progressBar, disable
    Design setting set to default for function read.fsa : applyLowess, processed, meta.extra, disable
    Design setting set to default for function align.fsa : channel, fullLadder, useLadder, outThreshold, noiseLevel, surePeaks, trim, maskOffScale, rMin, rescue, ylim, disable
    Design setting set to default for function peaks.fsa : logTransform, lowThreshold, channels, noiseRange, primerRange, disable
    Design setting set to default for function plot.fsa : units, ladder, offScaleCol, offScalePch, offScaleCex, bg, fg, title, xlab, ylab, ylim, xaxt, yaxt, bty, xaxp, nticks, all.bp, disable
    Design setting set to default for function model : groupColors, threshold, disable
    Design setting set to default for function classify : plot, disable
    Processing /data/gannet/ripley/R/packages/tests-clang/MLPA.Rcheck/MLPA/extdata/fsa/A1270.fsa
    FSA metadata : user="VR", machine="3130-18321022", runModule.name="TCTM2", runModule.version="15", runProtocole.name="TCTM2", runProtocole.version="1", runStart="2013-04-24 10:41:42", runStop="2013-04-24 11:05:10", collectionStart="2013-04-24 10:52:06", collectionStop="2013-04-24 11:05:06", injectionTime="3"
    Error in rect(xleft = sapply(design$PEAKS$ranges, "[", 1), xright = sapply(design$PEAKS$ranges, :
     invalid RGB specification
    Calls: GEP.process -> rect
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.10.0
Check: examples
Result: ERROR
    Running examples in ‘MLPA-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: GEP.process
    > ### Title: MLPA peak detection
    > ### Aliases: GEP.process GEP.interface
    >
    > ### ** Examples
    >
    > # Working in temporary directory
    > output <- sprintf("%s/test.log", tempdir())
    >
    > # See files before analysis
    > dir(system.file("extdata", package="MLPA"))
    [1] "ab1" "design.conf" "fsa" "rescue.conf"
    >
    > # Launch analysis in package directory
    > GEP.process(
    + input = system.file("extdata/fsa", package="MLPA"),
    + design = system.file("extdata/design.conf", package="MLPA"),
    + output = output
    + )
    Sun Oct 10 06:27:22 2021
    MLPA 1.10.0
    
    Design file : /data/gannet/ripley/R/packages/tests-devel/MLPA.Rcheck/MLPA/extdata/design.conf [c3ede9beca2291307483391447ba9be1]
    Design setting set to default for function GEP.process : overwrite, gene.cex, file.line, mar, progressBar, disable
    Design setting set to default for function read.fsa : applyLowess, processed, meta.extra, disable
    Design setting set to default for function align.fsa : channel, fullLadder, useLadder, outThreshold, noiseLevel, surePeaks, trim, maskOffScale, rMin, rescue, ylim, disable
    Design setting set to default for function peaks.fsa : logTransform, lowThreshold, channels, noiseRange, primerRange, disable
    Design setting set to default for function plot.fsa : units, ladder, offScaleCol, offScalePch, offScaleCex, bg, fg, title, xlab, ylab, ylim, xaxt, yaxt, bty, xaxp, nticks, all.bp, disable
    Design setting set to default for function model : groupColors, threshold, disable
    Design setting set to default for function classify : plot, disable
    Processing /data/gannet/ripley/R/packages/tests-devel/MLPA.Rcheck/MLPA/extdata/fsa/A1270.fsa
    FSA metadata : user="VR", machine="3130-18321022", runModule.name="TCTM2", runModule.version="15", runProtocole.name="TCTM2", runProtocole.version="1", runStart="2013-04-24 10:41:42", runStop="2013-04-24 11:05:10", collectionStart="2013-04-24 10:52:06", collectionStop="2013-04-24 11:05:06", injectionTime="3"
    Error in rect(xleft = sapply(design$PEAKS$ranges, "[", 1), xright = sapply(design$PEAKS$ranges, :
     invalid RGB specification
    Calls: GEP.process -> rect
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.10.0
Check: examples
Result: ERROR
    Running examples in 'MLPA-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: GEP.process
    > ### Title: MLPA peak detection
    > ### Aliases: GEP.process GEP.interface
    >
    > ### ** Examples
    >
    > # Working in temporary directory
    > output <- sprintf("%s/test.log", tempdir())
    >
    > # See files before analysis
    > dir(system.file("extdata", package="MLPA"))
    [1] "ab1" "design.conf" "fsa" "rescue.conf"
    >
    > # Launch analysis in package directory
    > GEP.process(
    + input = system.file("extdata/fsa", package="MLPA"),
    + design = system.file("extdata/design.conf", package="MLPA"),
    + output = output
    + )
    Fri Oct 08 19:42:06 2021
    MLPA 1.10.0
    
    Design file : d:\RCompile\CRANpkg\lib\4.2\MLPA\extdata\design.conf [c3ede9beca2291307483391447ba9be1]
    Design setting set to default for function GEP.process : overwrite, gene.cex, file.line, mar, progressBar, disable
    Design setting set to default for function read.fsa : applyLowess, processed, meta.extra, disable
    Design setting set to default for function align.fsa : channel, fullLadder, useLadder, outThreshold, noiseLevel, surePeaks, trim, maskOffScale, rMin, rescue, ylim, disable
    Design setting set to default for function peaks.fsa : logTransform, lowThreshold, channels, noiseRange, primerRange, disable
    Design setting set to default for function plot.fsa : units, ladder, offScaleCol, offScalePch, offScaleCex, bg, fg, title, xlab, ylab, ylim, xaxt, yaxt, bty, xaxp, nticks, all.bp, disable
    Design setting set to default for function model : groupColors, threshold, disable
    Design setting set to default for function classify : plot, disable
    Processing d:/RCompile/CRANpkg/lib/4.2/MLPA/extdata/fsa/A1270.fsa
    FSA metadata : user="VR", machine="3130-18321022", runModule.name="TCTM2", runModule.version="15", runProtocole.name="TCTM2", runProtocole.version="1", runStart="2013-04-24 10:41:42", runStop="2013-04-24 11:05:10", collectionStart="2013-04-24 10:52:06", collectionStop="2013-04-24 11:05:06", injectionTime="3"
    Error in rect(xleft = sapply(design$PEAKS$ranges, "[", 1), xright = sapply(design$PEAKS$ranges, :
     invalid RGB specification
    Calls: GEP.process -> rect
    Execution halted
Flavor: r-devel-windows-x86_64

Version: 1.10.0
Check: examples
Result: ERROR
    Running examples in 'MLPA-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: GEP.process
    > ### Title: MLPA peak detection
    > ### Aliases: GEP.process GEP.interface
    >
    > ### ** Examples
    >
    > # Working in temporary directory
    > output <- sprintf("%s/test.log", tempdir())
    >
    > # See files before analysis
    > dir(system.file("extdata", package="MLPA"))
    [1] "ab1" "design.conf" "fsa" "rescue.conf"
    >
    > # Launch analysis in package directory
    > GEP.process(
    + input = system.file("extdata/fsa", package="MLPA"),
    + design = system.file("extdata/design.conf", package="MLPA"),
    + output = output
    + )
    Tue Oct 12 18:27:52 2021
    MLPA 1.10.0
    
    Design file : C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\MLPA\MLPA.Rcheck\MLPA\extdata\design.conf [c3ede9beca2291307483391447ba9be1]
    Design setting set to default for function GEP.process : overwrite, gene.cex, file.line, mar, progressBar, disable
    Design setting set to default for function read.fsa : applyLowess, processed, meta.extra, disable
    Design setting set to default for function align.fsa : channel, fullLadder, useLadder, outThreshold, noiseLevel, surePeaks, trim, maskOffScale, rMin, rescue, ylim, disable
    Design setting set to default for function peaks.fsa : logTransform, lowThreshold, channels, noiseRange, primerRange, disable
    Design setting set to default for function plot.fsa : units, ladder, offScaleCol, offScalePch, offScaleCex, bg, fg, title, xlab, ylab, ylim, xaxt, yaxt, bty, xaxp, nticks, all.bp, disable
    Design setting set to default for function model : groupColors, threshold, disable
    Design setting set to default for function classify : plot, disable
    Processing C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/MLPA/MLPA.Rcheck/MLPA/extdata/fsa/A1270.fsa
    FSA metadata : user="VR", machine="3130-18321022", runModule.name="TCTM2", runModule.version="15", runProtocole.name="TCTM2", runProtocole.version="1", runStart="2013-04-24 10:41:42", runStop="2013-04-24 11:05:10", collectionStart="2013-04-24 10:52:06", collectionStop="2013-04-24 11:05:06", injectionTime="3"
    Error in rect(xleft = sapply(design$PEAKS$ranges, "[", 1), xright = sapply(design$PEAKS$ranges, :
     invalid RGB specification
    Calls: GEP.process -> rect
    Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT