Hi Henrik
Below is the same output including sessionInfo() when it did not work, as well
as when it worked. Sorry for the inconvenience. Thanks!
Johan
##### Worked on Mac #####
> library(aroma.affymetrix)
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.2.0 (2010-03-13) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.7.3 (2010-06-04) successfully loaded. See ?R.oo for help.
R.utils v1.5.0 (2010-08-04) successfully loaded. See ?R.utils for help.
Loading required package: R.filesets
Loading required package: digest
R.filesets v0.8.3 (2010-07-06) successfully loaded. See ?R.filesets for help.
Loading required package: aroma.core
Loading required package: R.cache
R.cache v0.3.0 (2010-03-13) successfully loaded. See ?R.cache for help.
Loading required package: R.rsp
R.rsp v0.3.6 (2009-09-16) successfully loaded. See ?R.rsp for help.
Type browseRsp() to open the RSP main menu in your browser.
Loading required package: matrixStats
matrixStats v0.2.1 (2010-04-05) successfully loaded. See ?matrixStats for help.
Loading required package: aroma.light
aroma.light v1.16.1 (2010-06-23) successfully loaded. See ?aroma.light for help.
aroma.core v1.7.0 (2010-07-26) successfully loaded. See ?aroma.core for help.
Loading required package: aroma.apd
Loading required package: R.huge
R.huge v0.2.0 (2009-10-16) successfully loaded. See ?R.huge for help.
Loading required package: affxparser
aroma.apd v0.1.7 (2009-10-16) successfully loaded. See ?aroma.apd for help.
aroma.affymetrix v1.7.0 (2010-07-26) successfully loaded. See ?aroma.affymetrix
for help.
Warning message:
'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
>
> ####### Read and check that CDFs etc is ok #####
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/GenomeWideSNP_6
Filename: GenomeWideSNP_6,Full.cdf
Filesize: 470.44MB
Chip type: GenomeWideSNP_6,Full
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 1881415
Cells per unit: 3.66
Number of QC units: 4
>
> gi <- getGenomeInformation(cdf)
> print(gi)
UgpGenomeInformation:
Name: GenomeWideSNP_6
Tags: Full,na26,HB20080821
Full name: GenomeWideSNP_6,Full,na26,HB20080821
Pathname:
annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na26,HB20080821.ugp
File size: 8.97 MB (9407937 bytes)
RAM: 0.00 MB
Chip type: GenomeWideSNP_6,Full
>
> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
> print(acs)
AromaCellSequenceFile:
Name: GenomeWideSNP_6
Tags: HB20080710
Full name: GenomeWideSNP_6,HB20080710
Pathname:
annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,HB20080710.acs
File size: 170.92 MB (179217531 bytes)
RAM: 0.00 MB
Number of data rows: 6892960
File format: v1
Dimensions: 6892960x26
Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1
Footer: <createdOn>20080710 22:47:02
PDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6</chipType><srcFile><filename>GenomeWideSNP_6.probe_tab</filename><filesize>341479928</filesize><checksum>2037c033c09fd8f7c06bd042a77aef15</checksum></srcFile><srcFile2><filename>GenomeWideSNP_6.CN_probe_tab</filename><filesize>96968290</filesize><checksum>3dc2d3178f5eafdbea9c8b6eca88a89c</checksum></srcFile2>
Chip type: GenomeWideSNP_6
Platform: Affymetrix
> ###########
> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-apple-darwin9.8.0
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.affymetrix_1.7.0 aroma.apd_0.1.7 affxparser_1.20.0
R.huge_0.2.0 aroma.core_1.7.0
[6] aroma.light_1.16.1 matrixStats_0.2.1 R.rsp_0.3.6
R.cache_0.3.0 R.filesets_0.8.3
[11] digest_0.4.2 R.utils_1.5.0 R.oo_1.7.3
R.methodsS3_1.2.0
loaded via a namespace (and not attached):
[1] tools_2.11.1
Warning message:
'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
#################
##### DID NOT WORK Unix ###
library(aroma.affymetrix)
Loading required package: R.filesets
Loading required package: digest
R.filesets v1.1.0 (2011-07-24) successfully loaded. See ?R.filesets for help.
Loading required package: aroma.core
Loading required package: R.cache
R.cache v0.5.1 (2011-08-31) 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 v0.6.2 (2011-07-27) successfully loaded. See ?R.rsp for help.
Type browseRsp() to open the RSP main menu in your browser.
Loading required package: matrixStats
matrixStats v0.2.2 (2010-10-06) successfully loaded. See ?matrixStats for help.
Loading required package: aroma.light
aroma.light v1.20.0 (2011-04-12) successfully loaded. See ?aroma.light for help.
aroma.core v2.2.0 (2011-09-01) successfully loaded. See ?aroma.core for help.
Attaching package: 'aroma.core'
The following object(s) are masked from 'package:base':
.Machine, append, apply, cat, colMeans, colSums, getOption, lapply,
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.
Loading required package: affxparser
aroma.apd v0.2.0 (2011-07-23) successfully loaded. See ?aroma.apd for help.
aroma.affymetrix v2.2.0 (2011-09-01) successfully loaded. See ?aroma.affymetrix
for help.
> library("ACNE");
Loading required package: MASS
ACNE v0.4.2 (2010-09-28) successfully loaded. See ?ACNE for help.
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] ACNE_0.4.2 MASS_7.3-9 aroma.affymetrix_2.2.0
[4] affxparser_1.22.1 aroma.apd_0.2.0 R.huge_0.3.0
[7] aroma.core_2.2.0 aroma.light_1.20.0 matrixStats_0.2.2
[10] R.rsp_0.6.2 R.cache_0.5.1 R.filesets_1.1.0
[13] digest_0.5.1 R.utils_1.8.2 R.oo_1.8.2
[16] R.methodsS3_1.2.1
>
>
> ####### Read and check that CDFs etc is ok #####
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/GenomeWideSNP_6
Filename: GenomeWideSNP_6,Full.cdf
Filesize: 470.44MB
Chip type: GenomeWideSNP_6,Full
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 1881415
Cells per unit: 3.66
Number of QC units: 4
> gi <- getGenomeInformation(cdf)
> print(gi)
UgpGenomeInformation:
Name: GenomeWideSNP_6
Tags: Full,na26,HB20080821
Full name: GenomeWideSNP_6,Full,na26,HB20080821
Pathname:
annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na26,HB20080821.ugp
File size: 8.97 MB (9407937 bytes)
RAM: 0.00 MB
Chip type: GenomeWideSNP_6,Full
> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
> print(acs)
AromaCellSequenceFile:
Name: GenomeWideSNP_6
Tags: HB20080710
Full name: GenomeWideSNP_6,HB20080710
Pathname:
annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,HB20080710.acs
File size: 170.92 MB (179217531 bytes)
RAM: 0.00 MB
Number of data rows: 6892960
File format: v1
Dimensions: 6892960x26
Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1
Footer: <createdOn>20080710 22:47:02
PDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6</chipType><srcFile><filename>GenomeWideSNP_6.probe_tab</filename><filesize>341479928</filesize><checksum>2037c033c09fd8f7c06bd042a77aef15</checksum></srcFile><srcFile2><filename>GenomeWideSNP_6.CN_probe_tab</filename><filesize>96968290</filesize><checksum>3dc2d3178f5eafdbea9c8b6eca88a89c</checksum></srcFile2>
Chip type: GenomeWideSNP_6
Platform: Affymetrix
> #######
>
>
> data.set.name<-"GSE19804"
> print(paste("doing",data.set.name))
[1] "doing GSE19804"
>
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/GenomeWideSNP_6
Filename: GenomeWideSNP_6,Full.cdf
Filesize: 470.44MB
Chip type: GenomeWideSNP_6,Full
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 1881415
Cells per unit: 3.66
Number of QC units: 4
> cs <- AffymetrixCelSet$byName(data.set.name, cdf=cdf);
> cs <- extract(cs, !isDuplicated(cs))
*** caught segfault ***
address 0x7f449b4b3850, cause 'invalid permissions'
Traceback:
1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser")
2: readCelHeader(pathname)
3: getHeader.AffymetrixCelFile(this)
4: getHeader(this)
5: getTimestamp.AffymetrixCelFile(X[[19L]], ...)
6: FUN(X[[19L]], ...)
7: base::lapply(this$files, ...)
8: lapply.GenericDataFileSet(this, getTimestamp)
9: lapply(this, getTimestamp)
10: getTimestamps.AffymetrixCelSet(this)
11: getTimestamps(this)
12: isDuplicated.AffymetrixCelSet(cs)
13: isDuplicated(cs)
14: extract.GenericDataFileSet(cs, !isDuplicated(cs))
15: extract(cs, !isDuplicated(cs))
________________________________________
Från: [email protected] [[email protected]]
för Henrik Bengtsson [[email protected]]
Skickat: den 6 oktober 2011 23:43
Till: [email protected]
Ämne: Re: [aroma.affymetrix] Problems loading Affymetrix 6.0 CEL files using
AffymetrixCelSet$byName
Hi.
On Thu, Oct 6, 2011 at 2:36 PM, Johan Staaf <[email protected]> wrote:
> Hi Henrik
> I have come across a problem loading Affymetrix 6.0 CEL files using the
> AffymetrixCelSet$byName function as described below on a unix 64-bit
> machine.
>
> Interestingly, the same code has worked before on the same machine with 6.0
> CEL files, and I can load the actual CEL files successfully on a MacBook Pro
> laptop using the same code.
>
> the rights for the folders the CEL files are in are:
> drwxrwxr-x. 3 johans johans 4096 Oct 6 07:05 GSE19804
> drwxrwxr-x. 3 johans johans 4096 Oct 6 21:03 GenomeWideSNP_6
> -rwxr-xr-x. 1 johans johans 69104164 Oct 6 20:47 Lung32T.CEL
>
>
> ?
>
> Thanks!
>
> Best regards
> Johan
>
> Session info:
Almost, but need to see versions etc of everything (especially R
itself and affxparser), so sessionInfo() please.
/Henrik
>
> library(aroma.affymetrix)
> Loading required package: R.filesets
> Loading required package: digest
> R.filesets v1.1.0 (2011-07-24) successfully loaded. See ?R.filesets for
> help.
> Loading required package: aroma.core
> Loading required package: R.cache
> R.cache v0.5.1 (2011-08-31) 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 v0.6.2 (2011-07-27) successfully loaded. See ?R.rsp for help.
> Type browseRsp() to open the RSP main menu in your browser.
> Loading required package: matrixStats
> matrixStats v0.2.2 (2010-10-06) successfully loaded. See ?matrixStats for
> help.
> Loading required package: aroma.light
> aroma.light v1.20.0 (2011-04-12) successfully loaded. See ?aroma.light for
> help.
>
> aroma.core v2.2.0 (2011-09-01) successfully loaded. See ?aroma.core for
> help.
>
> Attaching package: 'aroma.core'
>
> The following object(s) are masked from 'package:base':
>
> .Machine, append, apply, cat, colMeans, colSums, getOption, lapply,
> 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.
> Loading required package: affxparser
> aroma.apd v0.2.0 (2011-07-23) successfully loaded. See ?aroma.apd for help.
> aroma.affymetrix v2.2.0 (2011-09-01) successfully loaded. See
> ?aroma.affymetrix for help.
>> library("ACNE");
> Loading required package: MASS
> ACNE v0.4.2 (2010-09-28) successfully loaded. See ?ACNE for help.
>>
>> ####### Read and check that CDFs etc is ok #####
>> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
>> print(cdf)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/GenomeWideSNP_6
> Filename: GenomeWideSNP_6,Full.cdf
> Filesize: 470.44MB
> Chip type: GenomeWideSNP_6,Full
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2572x2680
> Number of cells: 6892960
> Number of units: 1881415
> Cells per unit: 3.66
> Number of QC units: 4
>> gi <- getGenomeInformation(cdf)
>> print(gi)
> UgpGenomeInformation:
> Name: GenomeWideSNP_6
> Tags: Full,na26,HB20080821
> Full name: GenomeWideSNP_6,Full,na26,HB20080821
> Pathname:
> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na26,HB20080821.ugp
> File size: 8.97 MB (9407937 bytes)
> RAM: 0.00 MB
> Chip type: GenomeWideSNP_6,Full
>> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
>> print(acs)
> AromaCellSequenceFile:
> Name: GenomeWideSNP_6
> Tags: HB20080710
> Full name: GenomeWideSNP_6,HB20080710
> Pathname:
> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,HB20080710.acs
> File size: 170.92 MB (179217531 bytes)
> RAM: 0.00 MB
> Number of data rows: 6892960
> File format: v1
> Dimensions: 6892960x26
> Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
> raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
> Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
> Footer: <createdOn>20080710 22:47:02
> PDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6</chipType><srcFile><filename>GenomeWideSNP_6.probe_tab</filename><filesize>341479928</filesize><checksum>2037c033c09fd8f7c06bd042a77aef15</checksum></srcFile><srcFile2><filename>GenomeWideSNP_6.CN_probe_tab</filename><filesize>96968290</filesize><checksum>3dc2d3178f5eafdbea9c8b6eca88a89c</checksum></srcFile2>
> Chip type: GenomeWideSNP_6
> Platform: Affymetrix
>> #######
>>
>>
>> data.set.name<-"GSE19804"
>> print(paste("doing",data.set.name))
> [1] "doing GSE19804"
>>
>> cdf
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/GenomeWideSNP_6
> Filename: GenomeWideSNP_6,Full.cdf
> Filesize: 470.44MB
> Chip type: GenomeWideSNP_6,Full
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2572x2680
> Number of cells: 6892960
> Number of units: 1881415
> Cells per unit: 3.66
> Number of QC units: 4
>> cs <- AffymetrixCelSet$byName(data.set.name, cdf=cdf);
>> cs <- extract(cs, !isDuplicated(cs))
>
>
> *** caught segfault ***
> address 0x7f449b4b3850, cause 'invalid permissions'
>
> Traceback:
> 1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser")
> 2: readCelHeader(pathname)
> 3: getHeader.AffymetrixCelFile(this)
> 4: getHeader(this)
> 5: getTimestamp.AffymetrixCelFile(X[[19L]], ...)
> 6: FUN(X[[19L]], ...)
> 7: base::lapply(this$files, ...)
> 8: lapply.GenericDataFileSet(this, getTimestamp)
> 9: lapply(this, getTimestamp)
> 10: getTimestamps.AffymetrixCelSet(this)
> 11: getTimestamps(this)
> 12: isDuplicated.AffymetrixCelSet(cs)
> 13: isDuplicated(cs)
> 14: extract.GenericDataFileSet(cs, !isDuplicated(cs))
> 15: extract(cs, !isDuplicated(cs))
>
> --
> 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 [email protected]
> 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 [email protected]
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 [email protected]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
