Since there are several different PNG drivers for R, aroma tries to
automatically find one that works. Try the following in a fresh R
session:
library("aroma.core");
pngDev <- findPngDevice(transparent=FALSE);
pngDev("foo.png", width=840, height=640); plot(1:10); dev.off();
Is foo.png empty? What does
print(pngDev)
show?
/Henrik
On Tue, Jan 17, 2012 at 2:53 PM, Steven McKinney <smckin...@bccrc.ca> wrote:
>
> Hi all,
>
> I am having no luck running ChromosomeExplorer - I keep getting zero byte PNG
> files
> and I'm seeing a warning message but as yet have been unable to figure out
> which
> function is issuing the warning.
>
> The warning is
>
> libpng warning: Application built with libpng-1.2.26 but running with 1.5.2
>
> as in this snippet from the long output at the end of the email.
>
> 20120117 12:32:46| Adding segmentation results...done
> 20120117 12:32:46| Adding additional annotations...
> 20120117 12:32:46| Adding additional annotations...done
> 20120117 12:32:46| Plotting graph...done
> libpng warning: Application built with libpng-1.2.26 but running with 1.5.2
> 20120117 12:32:46| Pathname:
> reports/BCGIall/ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/cbs/8926256,Pri,s1,GenomeWideSNP_6,total,chr17,x0002.png
> 20120117 12:32:46| Dimensions: 590x400
> 20120117 12:32:46| Ticks by: 1.000000
> 20120117 12:32:46| Plotting graph...
> 20120117 12:32:46| Creating empty plot...
> 20120117 12:32:46| Creating empty plot...done
> 20120117 12:32:46| Adding axes and rulers...
> 20120117 12:32:46| Adding axes and rulers...done
>
>
> I have updated my PNG library to 1.5.2 and have reinstalled CRAN and
> Bioconductor
> packages from source. I tried to reinstall aroma.affymetrix packages from
> source
> with options()$pkgType = "source" but aroma.affymetrix packages do not show
> any compilation
> activity - so I'm a bit stumped as to where the libpng warning is coming from.
>
> Session info is
>
>
>
>> sessionInfo()
> R version 2.14.1 Patched (2012-01-11 r58090)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods base
>
> other attached packages:
> [1] GLAD_2.16.1 Cairo_1.5-1 RColorBrewer_1.0-5
> [4] aroma.affymetrix_2.4.0 affxparser_1.26.2 aroma.apd_0.2.0
> [7] R.huge_0.3.0 aroma.core_2.4.2 aroma.light_1.22.0
> [10] matrixStats_0.4.3 R.rsp_0.7.1 R.cache_0.5.2
> [13] R.filesets_1.1.4 digest_0.5.1 R.utils_1.9.9
> [16] R.oo_1.8.3 R.methodsS3_1.2.1
>>
>
>
>
> My aroma session looks like
>
>
> require("aroma.affymetrix")
>
> log <- verbose <- Arguments$getVerbose(-10, timestamp=TRUE)
> ## Don't display too many decimals.
> options(digits=5)
>
>
> dsList <- list()
>
> dsList[["GenomeWideSNP_6"]] <- doCRMAv2("BCGIall", chipType =
> "GenomeWideSNP_6,Full", verbose = TRUE)
> dsList[["Mapping250K_Nsp"]] <- doCRMAv2("BCGIall", chipType =
> "Mapping250K_Nsp", plm = "RmaCnPlm", verbose = TRUE)
> dsList[["Mapping250K_Sty"]] <- doCRMAv2("BCGIall", chipType =
> "Mapping250K_Sty", plm = "RmaCnPlm", verbose = TRUE)
>
> dataSet <- "BCGIall";
> tags <- "ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY"; # Tags added by CRMAv2
> chipType <- "GenomeWideSNP_6";
> ds <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags, chipType=chipType);
>
> sm <- CbsModel(ds);
> print(sm)
> fit(sm, verbose=-10);
>
> pathname <- writeRegions(sm, verbose=verbose);
>
> dataSetN <- "BCGIall";
> tagsN <- "ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY"; # Tags added by CRMAv2
> chipTypeN <- "Mapping250K_Nsp";
> dsN <- AromaUnitTotalCnBinarySet$byName(dataSetN, tags=tagsN,
> chipType=chipTypeN);
> smN <- CbsModel(dsN);
> print(smN)
> fit(smN, verbose=-10);
>
> dataSetS <- "BCGIall";
> tagsS <- "ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY"; # Tags added by CRMAv2
> chipTypeS <- "Mapping250K_Sty";
> dsS <- AromaUnitTotalCnBinarySet$byName(dataSetS, tags=tagsS,
> chipType=chipTypeS);
> smS <- CbsModel(dsS);
> print(smS)
> fit(smS, verbose=-10);
>
>
> # Link the ChromosomeExplorer to the segmentation model
> ceG <- ChromosomeExplorer(sm);
> print(ceG);
>
> # Fit the model for a few chromosomes
> process(ceG, chromosomes=c(17), verbose=verbose);
>
> and this yields hundreds of zero byte png files.
>
> Any ideas on how to get ChromosomeExplorer operational would be appreciated.
>
>
>
> Steven McKinney
>
> Statistician
> Molecular Oncology and Breast Cancer Program
> British Columbia Cancer Research Centre
>
>
>
> Some verbose output showing the png warning, and the output when attempting to
> install aroma.affymetrix materials from source follows:
>
>
>
> The following object(s) are masked from 'package:base':
>
> attach, detach, environment, gc, load, save
>
> R.utils v1.9.9 (2012-01-11) successfully loaded. See ?R.utils for help.
>
> Attaching package: 'R.utils'
>
> The following object(s) are masked from 'package:utils':
>
> timestamp
>
> The following object(s) are masked from 'package:base':
>
> cat, commandArgs, getOption, inherits, isOpen, lapply, parse,
> remove, warnings
>
> [Previously saved workspace restored]
>
>> .help.ESS <- help
>> options(STERM='iESS', editor='emacsclient')
>> require("aroma.affymetrix")
> Loading required package: aroma.affymetrix
> Loading required package: R.filesets
> Loading required package: digest
> R.filesets v1.1.4 (2011-11-19) successfully loaded. See ?R.filesets for help.
>
> Attaching package: 'R.filesets'
>
> The following object(s) are masked from 'package:base':
>
> append, readLines, sapply
>
> Loading required package: aroma.core
> Loading required package: R.cache
> R.cache v0.5.2 (2011-10-05) successfully loaded. See ?R.cache for help.
>
>
> Attaching package: 'R.cache'
>
> The following object(s) are masked from 'package:R.filesets':
>
> getChecksum
>
> Loading required package: R.rsp
> R.rsp v0.7.1 (2011-11-28) successfully loaded. See ?R.rsp for help.
> Type browseRsp() to open the RSP main menu in your browser.
>
> Attaching package: 'R.rsp'
>
> The following object(s) are masked from 'package:R.filesets':
>
> getHeader
>
> The following object(s) are masked from 'package:base':
>
> flush, restart, stop, write
>
> Loading required package: matrixStats
> matrixStats v0.4.3 (2011-12-11) successfully loaded. See ?matrixStats for
> help.
> Loading required package: aroma.light
> aroma.light v1.22.0 (2011-10-31) successfully loaded. See ?aroma.light for
> help.
> aroma.core v2.4.2 (2012-01-14) successfully loaded. See ?aroma.core for help.
>
> Attaching package: 'aroma.core'
>
> The following object(s) are masked from 'package:base':
>
> .Machine, append, apply, colMeans, colSums, library, require,
> sapply
>
> Loading required package: aroma.apd
> Loading required package: R.huge
> R.huge v0.3.0 (2011-07-23) successfully loaded. See ?R.huge for help.
>
> Attaching package: 'R.huge'
>
> The following object(s) are masked from 'package:aroma.core':
>
> readHeader
>
> The following object(s) are masked from 'package:R.filesets':
>
> getExtension, getFileSize, getPathname
>
> The following object(s) are masked from 'package:base':
>
> as.vector, colnames, flush, isOpen, ncol, nrow, rowMeans, rowSums,
> rownames
>
> Loading required package: affxparser
> aroma.apd v0.2.0 (2011-07-23) successfully loaded. See ?aroma.apd for help.
> aroma.affymetrix v2.4.0 (2012-01-11) successfully loaded. See
> ?aroma.affymetrix for help.
>
> Attaching package: 'aroma.affymetrix'
>
> The following object(s) are masked from 'package:affxparser':
>
> readCdfDataFrame, writeCdf
>
> The following object(s) are masked from 'package:R.rsp':
>
> write
>
> The following object(s) are masked from 'package:grDevices':
>
> boxplot.stats
>
> The following object(s) are masked from 'package:methods':
>
> getPackageName
>
> The following object(s) are masked from 'package:base':
>
> append, apply, colMeans, colSums, library, require, sapply, write
>
>> log <- verbose <- Arguments$getVerbose(-10, timestamp=TRUE)
>> options(digits=5)
>> ceG <- ChromosomeExplorer(sm);
>> print(ceG);
> ChromosomeExplorer:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Number of arrays: 29
> Path: reports/BCGIall/ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/cbs
> RAM: 0.00MB
>> process(ceG, chromosomes=c(17), verbose=verbose);
> 20120117 12:32:12|Generating ChromosomeExplorer report...
> 20120117 12:32:12| Setting up ChromosomeExplorer report files...
> 20120117 12:32:12| Copying template files...
> 20120117 12:32:12| Source path:
> /Library/Frameworks/R.framework/Versions/2.14/Resources/library/aroma.core/reports/includes
> 20120117 12:32:12| Destination path: reports/includes
> 20120117 12:32:13| Copying template files...done
> 20120117 12:32:13| Setting up ChromosomeExplorer report files...done
> 20120117 12:32:13| Explorer output version: 3
> 20120117 12:32:13| Compiling ChromosomeExplorer.onLoad.js.rsp...
> 20120117 12:32:13| Source:
> /Library/Frameworks/R.framework/Versions/2.14/Resources/library/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
> 20120117 12:32:13| Output path:
> reports/BCGIall/ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> 20120117 12:32:13| Scanning directories for available chip types...
> 20120117 12:32:13| Detected chip types: GenomeWideSNP_6
> 20120117 12:32:13| Scanning directories for available chip types...done
> 20120117 12:32:13| Scanning image files for available zooms...
> 20120117 12:32:13| Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64
> 20120117 12:32:13| Scanning image files for available zooms...done
> 20120117 12:32:13| Scanning directory for subdirectories...
> 20120117 12:32:13| Detected (or default) sets: cbs
> 20120117 12:32:13| Scanning directory for subdirectories...done
> 20120117 12:32:13| Compiling RSP...
> member data.class dimension objectSize
> 1 chipTypes character 1 104
> 2 chrLayers character 0 40
> 3 chromosomeLabels character 25 1440
> 4 sampleLabels character 29 1664
> 5 sampleLayers character 0 40
> 6 samples character 29 2824
> 7 sets character 1 96
> 8 zooms numeric 7 72
> 20120117 12:32:29| Sample names:
> [1] "8920330" "8922989" "8923725" "8925425" "8926256" "8926698" "9001632"
> [8] "9020428" "9024612" "9024665" "9026737" "9027169" "9027278" "9120972"
> [15] "9122766" "9124090" "9124112" "9125645" "9127113" "9201148" "9221533"
> [22] "9221856" "9222154" "9224617" "9225674" "9226281" "9226775" "9250414"
> [29] "9325860"
> 20120117 12:32:29| Full sample names:
> [1] "8920330,Pri,s1,GenomeWideSNP_6,total"
> …
> [29] "9325860,Pri,s1,GenomeWideSNP_6,total"
> 20120117 12:32:29| Compiling RSP...done
> 20120117 12:32:29| Compiling ChromosomeExplorer.onLoad.js.rsp...done
> Loading required package: RColorBrewer
> Loading required package: Cairo
> libpng warning: Application built with libpng-1.2.26 but running with 1.5.2
> 20120117 12:32:30| Building tuple of reference sets...
> 20120117 12:32:30| No reference available.
> 20120117 12:32:30| Calculating average copy-number signals...
> 20120117 12:32:30| Retrieving average unit signals across 29 arrays...
> AromaUnitTotalCnBinaryFile:
> Name: .average-signals-median-mad
> Tags: 6589c2a646c64ff53f537cbfdf55bd1c
> Full name: .average-signals-median-mad,6589c2a646c64ff53f537cbfdf55bd1c
> Pathname:
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/.average-signals-median-mad,6589c2a646c64ff53f537cbfdf55bd1c.asb
> File size: 7.18 MB (7526026 bytes)
> RAM: 0.00 MB
> Number of data rows: 1881415
> File format: v1
> Dimensions: 1881415x1
> Column classes: double
> Number of bytes per column: 4
> Footer: <createdOn>20120112 19:02:28
> PST</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6,Full</chipType><srcDetails><nbrOfFiles>29</nbrOfFiles><checkSum>fa8127c3abf3321b996278459fffd8df</checkSum></srcDetails><params><meanName>median</meanName><sdName>mad</sdName></params>
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full
> 20120117 12:32:31| Retrieving average unit signals across 29 arrays...done
> 20120117 12:32:31| Calculating average copy-number signals...done
> 20120117 12:32:31| Building tuple of reference sets...done
> 20120117 12:32:31| Using reference tuple:
> AromaUnitTotalCnBinarySetTuple:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Chip types: GenomeWideSNP_6
> AromaUnitTotalCnBinarySet:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Full name: BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Number of files: 29
> Names: .average-signals-median-mad, .average-signals-median-mad,
> .average-signals-median-mad, ..., .average-signals-median-mad [29]
> Path (to the first file):
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
> Total file size: 208.14 MB
> RAM: 0.03MB
> RAM: 0.00MB
> 20120117 12:32:32| Extract DataFileMatrix...
> 20120117 12:32:32| Array: 1
> 20120117 12:32:32| Test data sets:
> AromaUnitTotalCnBinarySetTuple:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Chip types: GenomeWideSNP_6
> AromaUnitTotalCnBinarySet:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Full name: BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Number of files: 29
> Names: 8920330, 8922989, 8923725, ..., 9325860 [29]
> Path (to the first file):
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
> Total file size: 208.15 MB
> RAM: 0.03MB
> RAM: 0.00MB
> 20120117 12:32:33| Reference data sets:
> AromaUnitTotalCnBinarySetTuple:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Chip types: GenomeWideSNP_6
> AromaUnitTotalCnBinarySet:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Full name: BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Number of files: 29
> Names: .average-signals-median-mad, .average-signals-median-mad,
> .average-signals-median-mad, ..., .average-signals-median-mad [29]
> Path (to the first file):
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
> Total file size: 208.14 MB
> RAM: 0.03MB
> RAM: 0.00MB
> 20120117 12:32:33| Test data files:
> $`GenomeWideSNP_6,Full`
> AromaUnitTotalCnBinaryFile:
> Name: 8920330
> Tags: Pri,s1,GenomeWideSNP_6,total
> Full name: 8920330,Pri,s1,GenomeWideSNP_6,total
> Pathname:
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/8920330,Pri,s1,GenomeWideSNP_6,total.asb
> File size: 7.18 MB (7526125 bytes)
> RAM: 0.00 MB
> Number of data rows: 1881415
> File format: v1
> Dimensions: 1881415x1
> Column classes: double
> Number of bytes per column: 4
> Footer: <createdOn>20120111 18:17:32
> PST</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6,Full</chipType><srcFile><srcDataSet>BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY</srcDataSet><srcChipType>GenomeWideSNP_6,Full,monocell</srcChipType><srcFullName>8920330,Pri,s1,GenomeWideSNP_6,chipEffects</srcFullName><srcChecksum>1f639a8761882ad9caf2e972979c1060</srcChecksum></srcFile>
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full
>
> attr(,"class")
> [1] "AromaUnitTotalCnBinaryFileList" "GenericDataFileList"
> [3] "list"
> 20120117 12:32:34| Extract DataFileMatrix...done
> 20120117 12:32:34| Genomic-signal tags: Pri,s1,GenomeWideSNP_6,total
> 20120117 12:32:34| Reference tags: 180d5db58c214f6dfd3317e1226be405
> 20120117 12:32:34| Array #1 ('8920330') of 29 on chromosome 17...
> 20120117 12:32:34| Loading results from file...
> 20120117 12:32:34| Pathname:
> cbsData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/8920330,Pri,s1,GenomeWideSNP_6,total,chr17,180d5db58c214f6dfd3317e1226be405.xdr
> 20120117 12:32:34| Fit object: DNAcopy
> 20120117 12:32:34| Loading results from file...done
> 20120117 12:32:34| Calling onFit.CopyNumberSegmentationModel() hooks...
> 20120117 12:32:34| Plotting 8920330 for chromosome 17 [81.69MB]...
> used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 1617525 86.4 2564037 137.0 2403845 128.4
> Vcells 9267933 70.8 21923899 167.3 21373040 163.1
> 20120117 12:32:34| Plotting 8920330 for chromosome 17 [81.69MB]...done
> 20120117 12:32:34| Calling onFit.CopyNumberSegmentationModel() hooks...done
> 20120117 12:32:34| Array #1 ('8920330') of 29 on chromosome 17...done
> 20120117 12:32:34| Extract DataFileMatrix...
> 20120117 12:32:34| Array: 2
> 20120117 12:32:34| Test data sets:
> AromaUnitTotalCnBinarySetTuple:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Chip types: GenomeWideSNP_6
> AromaUnitTotalCnBinarySet:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Full name: BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Number of files: 29
> Names: 8920330, 8922989, 8923725, ..., 9325860 [29]
> Path (to the first file):
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
> Total file size: 208.15 MB
> RAM: 0.03MB
> RAM: 0.00MB
> 20120117 12:32:35| Reference data sets:
> AromaUnitTotalCnBinarySetTuple:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Chip types: GenomeWideSNP_6
> AromaUnitTotalCnBinarySet:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Full name: BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Number of files: 29
> Names: .average-signals-median-mad, .average-signals-median-mad,
> .average-signals-median-mad, ..., .average-signals-median-mad [29]
> Path (to the first file):
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
> Total file size: 208.14 MB
> RAM: 0.03MB
> RAM: 0.00MB
> 20120117 12:32:35| Test data files:
> $`GenomeWideSNP_6,Full`
> AromaUnitTotalCnBinaryFile:
> Name: 8922989
> Tags: Pri,s1,GenomeWideSNP_6,total
> Full name: 8922989,Pri,s1,GenomeWideSNP_6,total
> Pathname:
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/8922989,Pri,s1,GenomeWideSNP_6,total.asb
> File size: 7.18 MB (7526125 bytes)
> RAM: 0.00 MB
> Number of data rows: 1881415
> File format: v1
> Dimensions: 1881415x1
> Column classes: double
> Number of bytes per column: 4
> Footer: <createdOn>20120111 18:17:37
> PST</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6,Full</chipType><srcFile><srcDataSet>BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY</srcDataSet><srcChipType>GenomeWideSNP_6,Full,monocell</srcChipType><srcFullName>8922989,Pri,s1,GenomeWideSNP_6,chipEffects</srcFullName><srcChecksum>9fce566927e0df6cf710236c9494937d</srcChecksum></srcFile>
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full
>
> attr(,"class")
> [1] "AromaUnitTotalCnBinaryFileList" "GenericDataFileList"
> [3] "list"
> 20120117 12:32:36| Extract DataFileMatrix...done
> 20120117 12:32:36| Genomic-signal tags: Pri,s1,GenomeWideSNP_6,total
> 20120117 12:32:36| Reference tags: 180d5db58c214f6dfd3317e1226be405
> 20120117 12:32:36| Array #2 ('8922989') of 29 on chromosome 17...
> 20120117 12:32:36| Loading results from file...
> 20120117 12:32:36| Pathname:
> cbsData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/8922989,Pri,s1,GenomeWideSNP_6,total,chr17,180d5db58c214f6dfd3317e1226be405.xdr
> 20120117 12:32:36| Fit object: DNAcopy
> 20120117 12:32:36| Loading results from file...done
> 20120117 12:32:36| Calling onFit.CopyNumberSegmentationModel() hooks...
> 20120117 12:32:36| Plotting 8922989 for chromosome 17 [81.69MB]...
> used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 1618300 86.5 2564037 137.0 2564037 137.0
> Vcells 9269670 70.8 21923899 167.3 21499914 164.1
> 20120117 12:32:36| Plotting 8922989 for chromosome 17 [81.69MB]...done
> 20120117 12:32:36| Calling onFit.CopyNumberSegmentationModel() hooks...done
> 20120117 12:32:36| Array #2 ('8922989') of 29 on chromosome 17...done
> 20120117 12:32:36| Extract DataFileMatrix...
> 20120117 12:32:36| Array: 3
> 20120117 12:32:36| Test data sets:
> AromaUnitTotalCnBinarySetTuple:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Chip types: GenomeWideSNP_6
> AromaUnitTotalCnBinarySet:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Full name: BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Number of files: 29
> Names: 8920330, 8922989, 8923725, ..., 9325860 [29]
> Path (to the first file):
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
> Total file size: 208.15 MB
> RAM: 0.03MB
> RAM: 0.00MB
> 20120117 12:32:37| Reference data sets:
> AromaUnitTotalCnBinarySetTuple:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Chip types: GenomeWideSNP_6
> AromaUnitTotalCnBinarySet:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Full name: BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Number of files: 29
> Names: .average-signals-median-mad, .average-signals-median-mad,
> .average-signals-median-mad, ..., .average-signals-median-mad [29]
> Path (to the first file):
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
> Total file size: 208.14 MB
> RAM: 0.03MB
> RAM: 0.00MB
> 20120117 12:32:37| Test data files:
> $`GenomeWideSNP_6,Full`
> AromaUnitTotalCnBinaryFile:
> Name: 8923725
> Tags: Pri,s1,GenomeWideSNP_6,total
> Full name: 8923725,Pri,s1,GenomeWideSNP_6,total
> Pathname:
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/8923725,Pri,s1,GenomeWideSNP_6,total.asb
> File size: 7.18 MB (7526125 bytes)
> RAM: 0.00 MB
> Number of data rows: 1881415
> File format: v1
> Dimensions: 1881415x1
> Column classes: double
> Number of bytes per column: 4
> Footer: <createdOn>20120111 18:17:41
> PST</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6,Full</chipType><srcFile><srcDataSet>BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY</srcDataSet><srcChipType>GenomeWideSNP_6,Full,monocell</srcChipType><srcFullName>8923725,Pri,s1,GenomeWideSNP_6,chipEffects</srcFullName><srcChecksum>ae314becdbb896cde169fd307bbc82d7</srcChecksum></srcFile>
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full
>
> attr(,"class")
> [1] "AromaUnitTotalCnBinaryFileList" "GenericDataFileList"
> [3] "list"
> 20120117 12:32:38| Extract DataFileMatrix...done
> 20120117 12:32:38| Genomic-signal tags: Pri,s1,GenomeWideSNP_6,total
> 20120117 12:32:38| Reference tags: 180d5db58c214f6dfd3317e1226be405
> 20120117 12:32:38| Array #3 ('8923725') of 29 on chromosome 17...
> 20120117 12:32:38| Loading results from file...
> 20120117 12:32:38| Pathname:
> cbsData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/8923725,Pri,s1,GenomeWideSNP_6,total,chr17,180d5db58c214f6dfd3317e1226be405.xdr
> 20120117 12:32:38| Fit object: DNAcopy
> 20120117 12:32:38| Loading results from file...done
> 20120117 12:32:38| Calling onFit.CopyNumberSegmentationModel() hooks...
> 20120117 12:32:38| Plotting 8923725 for chromosome 17 [81.69MB]...
> used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 1618305 86.5 2564037 137.0 2564037 137.0
> Vcells 9269567 70.8 21923899 167.3 21500950 164.1
> 20120117 12:32:38| Plotting 8923725 for chromosome 17 [81.69MB]...done
> 20120117 12:32:38| Calling onFit.CopyNumberSegmentationModel() hooks...done
> 20120117 12:32:38| Array #3 ('8923725') of 29 on chromosome 17...done
> 20120117 12:32:38| Extract DataFileMatrix...
> 20120117 12:32:38| Array: 4
> 20120117 12:32:38| Test data sets:
> AromaUnitTotalCnBinarySetTuple:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Chip types: GenomeWideSNP_6
> AromaUnitTotalCnBinarySet:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Full name: BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Number of files: 29
> Names: 8920330, 8922989, 8923725, ..., 9325860 [29]
> Path (to the first file):
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
> Total file size: 208.15 MB
> RAM: 0.03MB
> RAM: 0.00MB
> 20120117 12:32:39| Reference data sets:
> AromaUnitTotalCnBinarySetTuple:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Chip types: GenomeWideSNP_6
> AromaUnitTotalCnBinarySet:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Full name: BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Number of files: 29
> Names: .average-signals-median-mad, .average-signals-median-mad,
> .average-signals-median-mad, ..., .average-signals-median-mad [29]
> Path (to the first file):
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
> Total file size: 208.14 MB
> RAM: 0.03MB
> RAM: 0.00MB
> 20120117 12:32:40| Test data files:
> $`GenomeWideSNP_6,Full`
> AromaUnitTotalCnBinaryFile:
> Name: 8925425
> Tags: Pri,s1,GenomeWideSNP_6,total
> Full name: 8925425,Pri,s1,GenomeWideSNP_6,total
> Pathname:
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/8925425,Pri,s1,GenomeWideSNP_6,total.asb
> File size: 7.18 MB (7526125 bytes)
> RAM: 0.00 MB
> Number of data rows: 1881415
> File format: v1
> Dimensions: 1881415x1
> Column classes: double
> Number of bytes per column: 4
> Footer: <createdOn>20120111 18:17:46
> PST</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6,Full</chipType><srcFile><srcDataSet>BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY</srcDataSet><srcChipType>GenomeWideSNP_6,Full,monocell</srcChipType><srcFullName>8925425,Pri,s1,GenomeWideSNP_6,chipEffects</srcFullName><srcChecksum>4f45fbdd197c7ae4ece405fe63cbf645</srcChecksum></srcFile>
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full
>
> attr(,"class")
> [1] "AromaUnitTotalCnBinaryFileList" "GenericDataFileList"
> [3] "list"
> 20120117 12:32:40| Extract DataFileMatrix...done
> 20120117 12:32:40| Genomic-signal tags: Pri,s1,GenomeWideSNP_6,total
> 20120117 12:32:40| Reference tags: 180d5db58c214f6dfd3317e1226be405
> 20120117 12:32:40| Array #4 ('8925425') of 29 on chromosome 17...
> 20120117 12:32:40| Loading results from file...
> 20120117 12:32:40| Pathname:
> cbsData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/8925425,Pri,s1,GenomeWideSNP_6,total,chr17,180d5db58c214f6dfd3317e1226be405.xdr
> 20120117 12:32:40| Fit object: DNAcopy
> 20120117 12:32:40| Loading results from file...done
> 20120117 12:32:40| Calling onFit.CopyNumberSegmentationModel() hooks...
> 20120117 12:32:40| Plotting 8925425 for chromosome 17 [81.69MB]...
> 20120117 12:32:40| Pathname:
> reports/BCGIall/ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/cbs/8925425,Pri,s1,GenomeWideSNP_6,total,chr17,x0064.png
> 20120117 12:32:40| Dimensions: 15785x400
> 20120117 12:32:40| Ticks by: 0.100000
> 20120117 12:32:40| Plotting graph...
> 20120117 12:32:40| Creating empty plot...
> 20120117 12:32:40| Creating empty plot...done
> 20120117 12:32:40| Adding axes and rulers...
> 20120117 12:32:40| Adding axes and rulers...done
> 20120117 12:32:40| Adding cytoband...
> 20120117 12:32:40| Adding cytoband...done
> 20120117 12:32:40| Adding CN grid lines...
> 20120117 12:32:40| Adding CN grid lines...done
> 20120117 12:32:40| Adding data points...
> 20120117 12:32:42| Adding data points...done
> 20120117 12:32:42| Adding segmentation results...
> 20120117 12:32:42| Adding segmentation results...done
> 20120117 12:32:42| Adding additional annotations...
> 20120117 12:32:42| Adding additional annotations...done
> 20120117 12:32:42| Plotting graph...done
> libpng warning: Application built with libpng-1.2.26 but running with 1.5.2
> used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 1622755 86.7 2564037 137.0 2564037 137.0
> Vcells 9696796 74.0 21923899 167.3 21500950 164.1
> 20120117 12:32:42| Plotting 8925425 for chromosome 17 [81.69MB]...done
> 20120117 12:32:42| Calling onFit.CopyNumberSegmentationModel() hooks...done
> 20120117 12:32:42| Array #4 ('8925425') of 29 on chromosome 17...done
> 20120117 12:32:42| Extract DataFileMatrix...
> 20120117 12:32:42| Array: 5
> 20120117 12:32:42| Test data sets:
> AromaUnitTotalCnBinarySetTuple:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Chip types: GenomeWideSNP_6
> AromaUnitTotalCnBinarySet:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Full name: BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Number of files: 29
> Names: 8920330, 8922989, 8923725, ..., 9325860 [29]
> Path (to the first file):
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
> Total file size: 208.15 MB
> RAM: 0.03MB
> RAM: 0.00MB
> 20120117 12:32:43| Reference data sets:
> AromaUnitTotalCnBinarySetTuple:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Chip types: GenomeWideSNP_6
> AromaUnitTotalCnBinarySet:
> Name: BCGIall
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Full name: BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Number of files: 29
> Names: .average-signals-median-mad, .average-signals-median-mad,
> .average-signals-median-mad, ..., .average-signals-median-mad [29]
> Path (to the first file):
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
> Total file size: 208.14 MB
> RAM: 0.03MB
> RAM: 0.00MB
> 20120117 12:32:44| Test data files:
> $`GenomeWideSNP_6,Full`
> AromaUnitTotalCnBinaryFile:
> Name: 8926256
> Tags: Pri,s1,GenomeWideSNP_6,total
> Full name: 8926256,Pri,s1,GenomeWideSNP_6,total
> Pathname:
> totalAndFracBData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/8926256,Pri,s1,GenomeWideSNP_6,total.asb
> File size: 7.18 MB (7526125 bytes)
> RAM: 0.00 MB
> Number of data rows: 1881415
> File format: v1
> Dimensions: 1881415x1
> Column classes: double
> Number of bytes per column: 4
> Footer: <createdOn>20120111 18:17:50
> PST</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6,Full</chipType><srcFile><srcDataSet>BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY</srcDataSet><srcChipType>GenomeWideSNP_6,Full,monocell</srcChipType><srcFullName>8926256,Pri,s1,GenomeWideSNP_6,chipEffects</srcFullName><srcChecksum>7661a803b93a7437b4ad5d2a3eae380c</srcChecksum></srcFile>
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full
>
> attr(,"class")
> [1] "AromaUnitTotalCnBinaryFileList" "GenericDataFileList"
> [3] "list"
> 20120117 12:32:44| Extract DataFileMatrix...done
> 20120117 12:32:44| Genomic-signal tags: Pri,s1,GenomeWideSNP_6,total
> 20120117 12:32:44| Reference tags: 180d5db58c214f6dfd3317e1226be405
> 20120117 12:32:44| Array #5 ('8926256') of 29 on chromosome 17...
> 20120117 12:32:45| Loading results from file...
> 20120117 12:32:45| Pathname:
> cbsData/BCGIall,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/8926256,Pri,s1,GenomeWideSNP_6,total,chr17,180d5db58c214f6dfd3317e1226be405.xdr
> 20120117 12:32:45| Fit object: DNAcopy
> 20120117 12:32:45| Loading results from file...done
> 20120117 12:32:45| Calling onFit.CopyNumberSegmentationModel() hooks...
> 20120117 12:32:45| Plotting 8926256 for chromosome 17 [81.69MB]...
> 20120117 12:32:45| Pathname:
> reports/BCGIall/ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/cbs/8926256,Pri,s1,GenomeWideSNP_6,total,chr17,x0001.png
> 20120117 12:32:45| Dimensions: 345x400
> 20120117 12:32:45| Ticks by: 1.000000
> 20120117 12:32:45| Plotting graph...
> 20120117 12:32:45| Creating empty plot...
> 20120117 12:32:45| Creating empty plot...done
> 20120117 12:32:45| Adding axes and rulers...
> 20120117 12:32:45| Adding axes and rulers...done
> 20120117 12:32:45| Adding cytoband...
> 20120117 12:32:45| Adding cytoband...done
> 20120117 12:32:45| Adding CN grid lines...
> 20120117 12:32:45| Adding CN grid lines...done
> 20120117 12:32:45| Adding data points...
> 20120117 12:32:46| Adding data points...done
> 20120117 12:32:46| Adding segmentation results...
> 20120117 12:32:46| Adding segmentation results...done
> 20120117 12:32:46| Adding additional annotations...
> 20120117 12:32:46| Adding additional annotations...done
> 20120117 12:32:46| Plotting graph...done
> libpng warning: Application built with libpng-1.2.26 but running with 1.5.2
> 20120117 12:32:46| Pathname:
> reports/BCGIall/ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/cbs/8926256,Pri,s1,GenomeWideSNP_6,total,chr17,x0002.png
> 20120117 12:32:46| Dimensions: 590x400
> 20120117 12:32:46| Ticks by: 1.000000
> 20120117 12:32:46| Plotting graph...
> 20120117 12:32:46| Creating empty plot...
> 20120117 12:32:46| Creating empty plot...done
> 20120117 12:32:46| Adding axes and rulers...
> 20120117 12:32:46| Adding axes and rulers...done
> 20120117 12:32:46| Adding cytoband...
> 20120117 12:32:47| Adding cytoband...done
> 20120117 12:32:47| Adding CN grid lines...
> 20120117 12:32:47| Adding CN grid lines...done
> 20120117 12:32:47| Adding data points...
> 20120117 12:32:48| Adding data points...done
> 20120117 12:32:48| Adding segmentation results...
> 20120117 12:32:48| Adding segmentation results...done
> 20120117 12:32:48| Adding additional annotations...
> 20120117 12:32:48| Adding additional annotations...done
> 20120117 12:32:48| Plotting graph...done
> libpng warning: Application built with libpng-1.2.26 but running with 1.5.2
> 20120117 12:32:48| Pathname:
> reports/BCGIall/ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/cbs/8926256,Pri,s1,GenomeWideSNP_6,total,chr17,x0004.png
> 20120117 12:32:48| Dimensions: 1080x400
> 20120117 12:32:48| Ticks by: 1.000000
> 20120117 12:32:48| Plotting graph...
> 20120117 12:32:48| Creating empty plot...
> 20120117 12:32:48| Creating empty plot...done
> 20120117 12:32:48| Adding axes and rulers...
> 20120117 12:32:48| Adding axes and rulers...done
> 20120117 12:32:48| Adding cytoband...
> 20120117 12:32:48| Adding cytoband...done
> 20120117 12:32:48| Adding CN grid lines...
> 20120117 12:32:48| Adding CN grid lines...done
> 20120117 12:32:48| Adding data points...
> 20120117 12:32:50| Adding data points...done
> 20120117 12:32:50| Adding segmentation results...
> 20120117 12:32:50| Adding segmentation results...done
> 20120117 12:32:50| Adding additional annotations...
> 20120117 12:32:50| Adding additional annotations...done
> 20120117 12:32:50| Plotting graph...done
> libpng warning: Application built with libpng-1.2.26 but running with 1.5.2
> 20120117 12:32:50| Pathname:
> reports/BCGIall/ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/cbs/8926256,Pri,s1,GenomeWideSNP_6,total,chr17,x0008.png
> 20120117 12:32:50| Dimensions: 2061x400
> 20120117 12:32:50| Ticks by: 1.000000
> 20120117 12:32:50| Plotting graph...
> 20120117 12:32:50| Creating empty plot...
> 20120117 12:32:50| Creating empty plot...done
> 20120117 12:32:50| Adding axes and rulers...
> 20120117 12:32:50| Adding axes and rulers...done
> 20120117 12:32:50| Adding cytoband...
> 20120117 12:32:50| Adding cytoband...done
> 20120117 12:32:50| Adding CN grid lines...
> 20120117 12:32:50| Adding CN grid lines...done
> 20120117 12:32:50| Adding data points...
> 20120117 12:32:52| Adding data points...done
> 20120117 12:32:52| Adding segmentation results...
> 20120117 12:32:52| Adding segmentation results...done
> 20120117 12:32:52| Adding additional annotations...
> 20120117 12:32:52| Adding additional annotations...done
> 20120117 12:32:52| Plotting graph...done
> libpng warning: Application built with libpng-1.2.26 but running with 1.5.2
> 20120117 12:32:52| Pathname:
> reports/BCGIall/ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/cbs/8926256,Pri,s1,GenomeWideSNP_6,total,chr17,x0016.png
> 20120117 12:32:52| Dimensions: 4021x400
> 20120117 12:32:52| Ticks by: 0.100000
> 20120117 12:32:52| Plotting graph...
> 20120117 12:32:52| Creating empty plot...
> 20120117 12:32:52| Creating empty plot...done
> 20120117 12:32:52| Adding axes and rulers...
> 20120117 12:32:52| Adding axes and rulers...done
> 20120117 12:32:52| Adding cytoband...
> 20120117 12:32:52| Adding cytoband...done
> 20120117 12:32:52| Adding CN grid lines...
> 20120117 12:32:52| Adding CN grid lines...done
> 20120117 12:32:52| Adding data points...
> 20120117 12:32:53| Adding data points...done
> 20120117 12:32:53| Adding segmentation results...
> 20120117 12:32:53| Adding segmentation results...done
> 20120117 12:32:53| Adding additional annotations...
> 20120117 12:32:53| Adding additional annotations...done
> 20120117 12:32:53| Plotting graph...done
> libpng warning: Application built with libpng-1.2.26 but running with 1.5.2
> 20120117 12:32:53| Pathname:
> reports/BCGIall/ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/cbs/8926256,Pri,s1,GenomeWideSNP_6,total,chr17,x0032.png
> 20120117 12:32:53| Dimensions: 7942x400
> 20120117 12:32:53| Ticks by: 0.100000
> 20120117 12:32:53| Plotting graph...
> 20120117 12:32:53| Creating empty plot...
> 20120117 12:32:53| Creating empty plot...done
> 20120117 12:32:53| Adding axes and rulers...
> 20120117 12:32:53| Adding axes and rulers...done
> 20120117 12:32:53| Adding cytoband...
> 20120117 12:32:54| Adding cytoband...done
> 20120117 12:32:54| Adding CN grid lines...
> 20120117 12:32:54| Adding CN grid lines...done
> 20120117 12:32:54| Adding data points...
> C-c C-c C-c C-c
> libpng warning: Application built with libpng-1.2.26 but running with 1.5.2
> used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 1649272 88.1 2564037 137.0 2564037 137.0
> Vcells 10268654 78.4 21923899 167.3 21643624 165.2
> 20120117 12:32:55| Adding data points...done
> 20120117 12:32:55| Plotting graph...done
> 20120117 12:32:55| Plotting 8926256 for chromosome 17 [81.69MB]...done
> 20120117 12:32:55| Calling onFit.CopyNumberSegmentationModel() hooks...done
> 20120117 12:32:55| Array #5 ('8926256') of 29 on chromosome 17...done
> 20120117 12:32:55|Generating ChromosomeExplorer report...done
>> sessionInfo()
> R version 2.14.1 Patched (2012-01-11 r58090)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods base
>
> other attached packages:
> [1] GLAD_2.16.1 Cairo_1.5-1 RColorBrewer_1.0-5
> [4] aroma.affymetrix_2.4.0 affxparser_1.26.2 aroma.apd_0.2.0
> [7] R.huge_0.3.0 aroma.core_2.4.2 aroma.light_1.22.0
> [10] matrixStats_0.4.3 R.rsp_0.7.1 R.cache_0.5.2
> [13] R.filesets_1.1.4 digest_0.5.1 R.utils_1.9.9
> [16] R.oo_1.8.3 R.methodsS3_1.2.1
>>
>
>
>
>
>> hbInstall("aroma.affymetrix")
> Installing/updating: CRAN:digest (>= 0.5.1)
> Repositories: CRAN
> Package: digest (>= 0.5.1)
> Tags:
> Warning: unable to access index for repository
> http://www.bioconductor.org/src/contrib
> Updating packages: digest from repository 'DEFAULT'
> 01/01. digest: not available.
> Installing/updating: CRAN:R.methodsS3 (>= 1.2.1)
> Repositories: CRAN
> Package: R.methodsS3 (>= 1.2.1)
> Tags:
> Warning: unable to access index for repository
> http://www.bioconductor.org/src/contrib
> Updating packages: R.methodsS3 from repository 'DEFAULT'
> 01/01. R.methodsS3: not available.
> Installing/updating: CRAN:R.oo (>= 1.8.3)
> Repositories: CRAN
> Package: R.oo (>= 1.8.3)
> Tags:
> Warning: unable to access index for repository
> http://www.bioconductor.org/src/contrib
> Updating packages: R.oo from repository 'DEFAULT'
> 01/01. R.oo: not available.
> Installing/updating: CRAN:R.utils (>= 1.9.9)
> Repositories: CRAN
> Package: R.utils (>= 1.9.9)
> Tags:
> Warning: unable to access index for repository
> http://www.bioconductor.org/src/contrib
> Updating packages: R.utils from repository 'DEFAULT'
> 01/01. R.utils: not available.
> Installing/updating: BRAJU:R.utils (>= 1.9.9)
> Repositories: BRAJU
> Package: R.utils (>= 1.9.9)
> Tags:
> Updating packages: R.utils from repository 'http://www.braju.com/R/repos'
> 01/01. R.utils: v1.9.9, i.e. up to date.
> Installing/updating: CRAN:R.cache (>= 0.5.2)
> Repositories: CRAN
> Package: R.cache (>= 0.5.2)
> Tags:
> Warning: unable to access index for repository
> http://www.bioconductor.org/src/contrib
> Updating packages: R.cache from repository 'DEFAULT'
> 01/01. R.cache: not available.
> Installing/updating: CRAN:R.rsp (>= 0.7.1)
> Repositories: CRAN
> Package: R.rsp (>= 0.7.1)
> Tags:
> Warning: unable to access index for repository
> http://www.bioconductor.org/src/contrib
> Updating packages: R.rsp from repository 'DEFAULT'
> 01/01. R.rsp: not available.
> Installing/updating: BRAJU:R.rsp (>= 0.7.1)
> Repositories: BRAJU
> Package: R.rsp (>= 0.7.1)
> Tags:
> Updating packages: R.rsp from repository 'http://www.braju.com/R/repos'
> 01/01. R.rsp: v0.7.1, i.e. up to date.
> Installing/updating: CRAN:R.huge (>= 0.3.0)
> Repositories: CRAN
> Package: R.huge (>= 0.3.0)
> Tags:
> Warning: unable to access index for repository
> http://www.bioconductor.org/src/contrib
> Updating packages: R.huge from repository 'DEFAULT'
> 01/01. R.huge: not available.
> Installing/updating: BIOC:affxparser (>= 1.22.0)
> Repositories: BIOC
> Package: affxparser (>= 1.22.0)
> Tags:
> Package up to date: affxparser (>= 1.22.0)
> Installing/updating: CRAN:aroma.apd (>= 0.2.0)
> Repositories: CRAN
> Package: aroma.apd (>= 0.2.0)
> Tags:
> Warning: unable to access index for repository
> http://www.bioconductor.org/src/contrib
> Updating packages: aroma.apd from repository 'DEFAULT'
> 01/01. aroma.apd: not available.
> Installing/updating: CRAN:R.filesets (>= 1.1.4)
> Repositories: CRAN
> Package: R.filesets (>= 1.1.4)
> Tags:
> Warning: unable to access index for repository
> http://www.bioconductor.org/src/contrib
> Updating packages: R.filesets from repository 'DEFAULT'
> 01/01. R.filesets: not available.
> Installing/updating: BRAJU:R.filesets (>= 1.1.4)
> Repositories: BRAJU
> Package: R.filesets (>= 1.1.4)
> Tags:
> Updating packages: R.filesets from repository 'http://www.braju.com/R/repos'
> 01/01. R.filesets: v1.1.4, i.e. up to date.
> Installing/updating: CRAN:matrixStats (>= 0.4.3)
> Repositories: CRAN
> Package: matrixStats (>= 0.4.3)
> Tags:
> Warning: unable to access index for repository
> http://www.bioconductor.org/src/contrib
> Updating packages: matrixStats from repository 'DEFAULT'
> 01/01. matrixStats: not available.
> Installing/updating: CRAN:RColorBrewer (>= 1.0-5)
> Repositories: CRAN
> Package: RColorBrewer (>= 1.0-5)
> Tags:
> Warning: unable to access index for repository
> http://www.bioconductor.org/src/contrib
> Updating packages: RColorBrewer from repository 'DEFAULT'
> 01/01. RColorBrewer: not available.
> Installing/updating: CRAN:aroma.light (>= 1.22.0)
> Repositories: CRAN
> Package: aroma.light (>= 1.22.0)
> Tags:
> Warning: unable to access index for repository
> http://www.bioconductor.org/src/contrib
> Updating packages: aroma.light from repository 'DEFAULT'
> 01/01. aroma.light: not available.
> Installing/updating: CRAN:aroma.core (>= 2.4.1)
> Repositories: CRAN
> Package: aroma.core (>= 2.4.1)
> Tags:
> Warning: unable to access index for repository
> http://www.bioconductor.org/src/contrib
> Updating packages: aroma.core from repository 'DEFAULT'
> 01/01. aroma.core: not available.
> Installing/updating: BRAJU:aroma.core (>= 2.4.1)
> Repositories: BRAJU
> Package: aroma.core (>= 2.4.1)
> Tags:
> Updating packages: aroma.core from repository 'http://www.braju.com/R/repos'
> 01/01. aroma.core: v2.4.1, but v2.4.2 is available, i.e. out of date.
> Updating:
> trying URL 'http://www.braju.com/R/repos/aroma.core_2.4.2.tar.gz'
> Content type 'application/x-tar' length 334905 bytes (327 Kb)
> opened URL
> ==================================================
> downloaded 327 Kb
>
> * installing *source* package ‘aroma.core’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Warning in setGenericS3.default(name, envir = envir, validators = validators)
> :
> Renamed the preexisting function colSums to colSums.default, which was
> defined in environment base.
> Warning in setGenericS3.default(name, envir = envir, validators = validators)
> :
> Renamed the preexisting function colMeans to colMeans.default, which was
> defined in environment base.
> Warning in setGenericS3.default(name, envir = envir, validators = validators)
> :
> Renamed the preexisting function apply to apply.default, which was defined
> in environment base.
> ** help
> *** installing help indices
> ** building package indices ...
> ** testing if installed package can be loaded
> * DONE (aroma.core)
>
> The downloaded packages are in
>
> ‘/private/var/folders/-I/-IwfookDG3Wu7O0-CiOMZE+++TI/-Tmp-/RtmpF2hvTz/downloaded_packages’
> Installing/updating: CRAN:aroma.affymetrix (>= 2.4.0)
> Repositories: CRAN
> Package: aroma.affymetrix (>= 2.4.0)
> Tags:
> Warning: unable to access index for repository
> http://www.bioconductor.org/src/contrib
> Updating packages: aroma.affymetrix from repository 'DEFAULT'
> 01/01. aroma.affymetrix: not available.
> Installing/updating: BRAJU:aroma.affymetrix (>= 2.4.0)
> Repositories: BRAJU
> Package: aroma.affymetrix (>= 2.4.0)
> Tags:
> Updating packages: aroma.affymetrix from repository
> 'http://www.braju.com/R/repos'
> 01/01. aroma.affymetrix: v2.4.0, i.e. up to date.
> Installing/updating: BIOC:DNAcopy (>= 1.24.0)
> Repositories: BIOC
> Package: DNAcopy (>= 1.24.0)
> Tags:
> Package up to date: DNAcopy (>= 1.24.0)
> Installing/updating: BIOC:Biobase (>= 2.9.0)
> Repositories: BIOC
> Package: Biobase (>= 2.9.0)
> Tags:
> Package up to date: Biobase (>= 2.9.0)
> Installing/updating: BIOC:preprocessCore (>= 1.8.0)
> Repositories: BIOC
> Package: preprocessCore (>= 1.8.0)
> Tags:
> Package up to date: preprocessCore (>= 1.8.0)
> Installing/updating: BIOC:gcrma (>= 2.10.0)
> Repositories: BIOC
> Package: gcrma (>= 2.10.0)
> Tags:
> Package up to date: gcrma (>= 2.10.0)
> Installing/updating: BIOC:affyio (>= 1.6.0)
> Repositories: BIOC
> Package: affyio (>= 1.6.0)
> Tags:
> Package up to date: affyio (>= 1.6.0)
> Installing/updating: BIOC:affy (>= 1.24.0)
> Repositories: BIOC
> Package: affy (>= 1.24.0)
> Tags:
> Package up to date: affy (>= 1.24.0)
> Installing/updating: CRAN:aws
> Repositories: CRAN
> Package: aws
> Tags:
> Warning: unable to access index for repository
> http://www.bioconductor.org/src/contrib
> Updating packages: aws from repository 'DEFAULT'
> 01/01. aws: not available.
> Installing/updating: CRAN:gsmoothr (>= 0.1.5)
> Repositories: CRAN
> Package: gsmoothr (>= 0.1.5)
> Tags:
> Warning: unable to access index for repository
> http://www.bioconductor.org/src/contrib
> Updating packages: gsmoothr from repository 'DEFAULT'
> 01/01. gsmoothr: not available.
> Installing/updating: BRAJU:sfit (>= 0.1.9),mac=hasBinary
> Repositories: BRAJU
> Package: sfit (>= 0.1.9)
> Tags: mac=hasBinary
> Updating packages: sfit from repository 'http://www.braju.com/R/repos'
> 01/01. sfit: v0.2.0, i.e. up to date.
> ------------------------------------------------------------
> - Trying to install patches
> ------------------------------------------------------------
> R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3 for
> help.
> R.oo v1.8.3 (2011-11-01) successfully loaded. See ?R.oo for help.
>
> Attaching package: ‘R.oo’
>
> The following object(s) are masked from ‘package:R.methodsS3’:
>
> throw.default
>
> The following object(s) are masked from ‘package:methods’:
>
> getClass, getClasses, getMethods
>
> The following object(s) are masked from ‘package:base’:
>
> attach, detach, environment, gc, load, save
>
> R.utils v1.9.9 (2012-01-11) successfully loaded. See ?R.utils for help.
>
> Attaching package: ‘R.utils’
>
> The following object(s) are masked _by_ ‘.GlobalEnv’:
>
> installPackages
>
> The following object(s) are masked from ‘package:utils’:
>
> timestamp
>
> The following object(s) are masked from ‘package:base’:
>
> cat, commandArgs, getOption, inherits, isOpen, lapply, parse, remove,
> warnings
>
> R.cache v0.5.2 (2011-10-05) successfully loaded. See ?R.cache for help.
>
> Loading required package: digest
> R.filesets v1.1.4 (2011-11-19) successfully loaded. See ?R.filesets for help.
>
> Attaching package: ‘R.filesets’
>
> The following object(s) are masked from ‘package:R.cache’:
>
> getChecksum
>
> The following object(s) are masked from ‘package:base’:
>
> append, readLines, sapply
>
> R.rsp v0.7.1 (2011-11-28) successfully loaded. See ?R.rsp for help.
> Type browseRsp() to open the RSP main menu in your browser.
>
> Attaching package: ‘R.rsp’
>
> The following object(s) are masked from ‘package:R.filesets’:
>
> getHeader
>
> The following object(s) are masked from ‘package:base’:
>
> flush, restart, stop, write
>
> matrixStats v0.4.3 (2011-12-11) successfully loaded. See ?matrixStats for
> help.
> aroma.light v1.22.0 (2011-10-31) successfully loaded. See ?aroma.light for
> help.
> aroma.core v2.4.2 (2012-01-14) successfully loaded. See ?aroma.core for help.
>
> Attaching package: ‘aroma.core’
>
> The following object(s) are masked from ‘package:base’:
>
> .Machine, append, apply, colMeans, colSums, library, require, sapply
>
> No patches available for aroma.core v2.4.2.
> Loading required package: R.huge
> R.huge v0.3.0 (2011-07-23) successfully loaded. See ?R.huge for help.
>
> Attaching package: ‘R.huge’
>
> The following object(s) are masked from ‘package:aroma.core’:
>
> readHeader
>
> The following object(s) are masked from ‘package:R.filesets’:
>
> getExtension, getFileSize, getPathname
>
> The following object(s) are masked from ‘package:base’:
>
> as.vector, colnames, flush, isOpen, ncol, nrow, rowMeans, rownames, rowSums
>
> Loading required package: affxparser
> aroma.apd v0.2.0 (2011-07-23) successfully loaded. See ?aroma.apd for help.
> aroma.affymetrix v2.4.0 (2012-01-11) successfully loaded. See
> ?aroma.affymetrix for help.
>
> Attaching package: ‘aroma.affymetrix’
>
> The following object(s) are masked from ‘package:affxparser’:
>
> readCdfDataFrame, writeCdf
>
> The following object(s) are masked from ‘package:R.rsp’:
>
> write
>
> The following object(s) are masked from ‘package:grDevices’:
>
> boxplot.stats
>
> The following object(s) are masked from ‘package:methods’:
>
> getPackageName
>
> The following object(s) are masked from ‘package:base’:
>
> append, apply, colMeans, colSums, library, require, sapply, write
>
> No patches available for aroma.affymetrix v2.4.0.
> ############################################################
> # #
> # Packages installed/updated. Please restart R. #
> # #
> ############################################################
>>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
