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/
