The reason lies in the messages:
<simpleError in loadNamespace(name): there is no package called 'RColorBrewer'>
DETAILS: The framework (axes, cytoband etc) for each figure is
generated but when the data points are to be plotted, the RColorBrewer
package is loaded and since it is missing an error is thrown.
So, install RColorBrewer, e.g. install.packages("RColorBrewer") and
retry (don't forget to remove your fault PNGs).
Works?
/Henrik
PS. The RColorBrewer failed to install when you did
hbInstall("aroma.affymetrix") in the first place; please pay attention
to error messages (warnings are ok).
PS2. I'll try to update the package so it gives a more informative
error message early on if RColorBrewer is missing.
On Wed, Jul 1, 2009 at 2:32 AM, Myriam Peyrard<[email protected]> wrote:
>
> Dear Henrik,
>
> I deleted reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/ and all its
> subdirectories. Then did: process(ce, arrays=1, chromosomes=19, verbose=-20)
> and here is the entire output:
>
> Generating ChromosomeExplorer report...
> Setting up ChromosomeExplorer report files...
> Copying template files...
> Source path: C:/Program/R/R-2.9.0/library/aroma.core/reports/includes
> Destination path: reports/includes
> Copying template files...done
> Setting up ChromosomeExplorer report files...done
> Copying ChromosomeExplorer.html...
> Source pathname:
> C:/Program/R/R-2.9.0/library/aroma.core/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer.html
> Destination pathname:
> reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/ChromosomeExplorer.html
> Copying ChromosomeExplorer.html...done
> Explorer output version: 3
> Compiling ChromosomeExplorer.onLoad.js.rsp...
> Source:
> C:/Program/R/R-2.9.0/library/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
> Output path: reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY
> Scanning directories for available chip types...
> Detected chip types: GenomeWideSNP_6
> Scanning directories for available chip types...done
> Scanning image files for available zooms...
> Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64, 128
> Scanning image files for available zooms...done
> Scanning directory for subdirectories...
> Detected (or default) sets: cbs
> Scanning directory for subdirectories...done
> Compiling RSP...
> Compiling RSP...done
> Compiling ChromosomeExplorer.onLoad.js.rsp...done
> Loading required package: Cairo
> Building tuple of reference sets...
> No reference available.
> Calculating average chip effects...
> Retrieving average cell signals across 28 arrays...
> CnChipEffectFile:
> Name: .average-intensities-median-mad
> Tags: efde1e008fb579a08aa5cda998829722
> Full name:
> .average-intensities-median-mad,efde1e008fb579a08aa5cda998829722
> Pathname:
> plmData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/.average-intensities-median-mad,efde1e008fb579a08aa5cda998829722.CEL
> File size: 26.95 MB (28258317 bytes)
> RAM: 0.01 MB
> File format: v4 (binary; XDA)
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full,monocell
> Timestamp: 2009-06-09 15:53:34
> Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
> combineAlleles: logi TRUE)
> Retrieving average cell signals across 28 arrays...done
> Calculating average chip effects...done
> Building tuple of reference sets...done
> Using reference tuple:
> ChipEffectSetTuple:
> Name: CLP
> Tags: ACC,ra,-XY,AVG,+300,A+B,FLN,-XY
> Chip types: GenomeWideSNP_6
> CnChipEffectSet:
> Name: CLP
> Tags: ACC,ra,-XY,AVG,+300,A+B,FLN,-XY
> Path: plmData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full,monocell
> Number of arrays: 28
> Names: .average-intensities-median-mad,
> .average-intensities-median-mad, ..., .average-intensities-median-mad
> Time period: 2009-06-09 15:53:34 -- 2009-06-09 15:53:34
> Total file size: 754.58MB
> RAM: 0.03MB
> Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
> combineAlleles: logi TRUE)
> RAM: 0.00MB
> Chip-effect tags:
> Reference tags: 8b8a924f5c9bdfda0388908c4f526ac6
> Array #1 ('MP01_LKG12') of 1 on chromosome 19...
> Loading results from file...
> Pathname:
> cbsData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/MP01_LKG12,chr19,8b8a924f5c9bdfda0388908c4f526ac6.xdr
> Fit object: DNAcopy
> Loading results from file...done
> Calling onFit.CopyNumberSegmentationModel() hooks...
> Plotting MP01_LKG12 for chromosome 19 [63.79MB]...
> Pathname:
> reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/MP01_LKG12,chr19,x0001.png
> Dimensions: 291x400
> Ticks by: 1.000000
> Plotting graph...
> Loading required package: GLAD
> [1] "Have fun with GLAD"
> <simpleError in loadNamespace(name): there is no package called
> 'RColorBrewer'>
> Pathname:
> reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/MP01_LKG12,chr19,x0002.png
> Dimensions: 483x400
> Ticks by: 1.000000
> Plotting graph...
> <simpleError in loadNamespace(name): there is no package called
> 'RColorBrewer'>
> Pathname:
> reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/MP01_LKG12,chr19,x0004.png
> Dimensions: 865x400
> Ticks by: 1.000000
> Plotting graph...
> <simpleError in loadNamespace(name): there is no package called
> 'RColorBrewer'>
> Pathname:
> reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/MP01_LKG12,chr19,x0008.png
> Dimensions: 1631x400
> Ticks by: 1.000000
> Plotting graph...
> <simpleError in loadNamespace(name): there is no package called
> 'RColorBrewer'>
> Pathname:
> reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/MP01_LKG12,chr19,x0016.png
> Dimensions: 3162x400
> Ticks by: 0.100000
> Plotting graph...
> <simpleError in loadNamespace(name): there is no package called
> 'RColorBrewer'>
> Pathname:
> reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/MP01_LKG12,chr19,x0032.png
> Dimensions: 6224x400
> Ticks by: 0.100000
> Plotting graph...
> <simpleError in loadNamespace(name): there is no package called
> 'RColorBrewer'>
> Pathname:
> reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/MP01_LKG12,chr19,x0064.png
> Dimensions: 12348x400
> Ticks by: 0.100000
> Plotting graph...
> <simpleError in loadNamespace(name): there is no package called
> 'RColorBrewer'>
> Pathname:
> reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/MP01_LKG12,chr19,x0128.png
> Dimensions: 24596x400
> Ticks by: 0.010000
> Plotting graph...
> <simpleError in loadNamespace(name): there is no package called
> 'RColorBrewer'>
> used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 501451 13.4 818163 21.9 818163 21.9
> Vcells 964929 7.4 7116089 54.3 8718065 66.6
> Plotting graph...done
> Plotting graph...done
> Plotting graph...done
> Plotting graph...done
> Plotting graph...done
> Plotting graph...done
> Plotting graph...done
> Plotting graph...done
> Plotting MP01_LKG12 for chromosome 19 [63.79MB]...done
> Calling onFit.CopyNumberSegmentationModel() hooks...done
> Array #1 ('MP01_LKG12') of 1 on chromosome 19...done
> Explorer output version: 3
> Compiling ChromosomeExplorer.onLoad.js.rsp...
> Source:
> C:/Program/R/R-2.9.0/library/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
> Output path: reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY
> Scanning directories for available chip types...
> Detected chip types: GenomeWideSNP_6
> Scanning directories for available chip types...done
> Scanning image files for available zooms...
> Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64, 128
> Scanning image files for available zooms...done
> Scanning directory for subdirectories...
> Detected (or default) sets: cbs
> Scanning directory for subdirectories...done
> Compiling RSP...
> Compiling RSP...done
> Compiling ChromosomeExplorer.onLoad.js.rsp...done
> Writing CN regions...
> Array #1 ('MP01_LKG12') of 1...
> Extracting regions from all fits...
> Obtaining CN model fits (or fit if missing)...
> Building tuple of reference sets...
> No reference available.
> Calculating average chip effects...
> Retrieving average cell signals across 28 arrays...
> CnChipEffectFile:
> Name: .average-intensities-median-mad
> Tags: efde1e008fb579a08aa5cda998829722
> Full name:
> .average-intensities-median-mad,efde1e008fb579a08aa5cda998829722
> Pathname:
> plmData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/.average-intensities-median-mad,efde1e008fb579a08aa5cda998829722.CEL
> File size: 26.95 MB (28258317 bytes)
> RAM: 0.01 MB
> File format: v4 (binary; XDA)
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full,monocell
> Timestamp: 2009-06-09 15:53:34
> Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
> combineAlleles: logi TRUE)
> Retrieving average cell signals across 28 arrays...done
> Calculating average chip effects...done
> Building tuple of reference sets...done
> Using reference tuple:
> ChipEffectSetTuple:
> Name: CLP
> Tags: ACC,ra,-XY,AVG,+300,A+B,FLN,-XY
> Chip types: GenomeWideSNP_6
> CnChipEffectSet:
> Name: CLP
> Tags: ACC,ra,-XY,AVG,+300,A+B,FLN,-XY
> Path: plmData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full,monocell
> Number of arrays: 28
> Names: .average-intensities-median-mad,
> .average-intensities-median-mad, ..., .average-intensities-median-mad
> Time period: 2009-06-09 15:53:34 -- 2009-06-09 15:53:34
> Total file size: 754.58MB
> RAM: 0.03MB
> Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
> combineAlleles: logi TRUE)
> RAM: 0.00MB
> Chip-effect tags:
> Reference tags: 8b8a924f5c9bdfda0388908c4f526ac6
> Array #1 ('MP01_LKG12') of 1 on chromosome 19...
> Loading results from file...
> Pathname:
> cbsData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/MP01_LKG12,chr19,8b8a924f5c9bdfda0388908c4f526ac6.xdr
> Fit object: DNAcopy
> Loading results from file...done
> Calling onFit.CopyNumberSegmentationModel() hooks...
> Calling onFit.CopyNumberSegmentationModel() hooks...done
> Array #1 ('MP01_LKG12') of 1 on chromosome 19...done
> Obtaining CN model fits (or fit if missing)...done
> Extracting regions for chromosome #19...
> Extracting regions for chromosome #19...done
> Extracted regions:
> 'data.frame': 9 obs. of 5 variables:
> $ chromosome: int 19 19 19 19 19 19 19 19 19
> $ start : num 41911 19748108 40163133 49033800 49744084 ...
> $ stop : num 19746740 40162854 49033180 49743930 56705958 ...
> $ mean : num 0.1123 0.0474 0.0909 -0.01 0.1035 ...
> $ count : int 8887 8182 4739 554 3291 1697 1002 1811 136
> Extracting regions from all fits...done
> Pathname:
> cbsData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY,regions.xls
> Array #1 ('MP01_LKG12') of 1...done
> Writing CN regions...done
> Generating ChromosomeExplorer report...done
> [1] TRUE
> Warning messages:
> 1: In library(package, lib.loc = lib.loc, character.only = TRUE,
> logical.return = TRUE, :
> there is no package called 'Cairo'
> 2: In method(static, ...) :
> Ghostscript not found. Searched directories: C:/gs, C:\Program/gs,
> /gs, C:\Program\Delade filer/gs
>>
> And the PNG in
> reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/
> are all as before!!!
>
> Myriam
>
> >
>
--~--~---------~--~----~------------~-------~--~----~
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traceback(), and 3) to post a complete code example.
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