Thanks for the useful details. I'll add it to the todo list to
provide more advanced automatic troubleshooting and more clear error
message (probably R.cache or R.utils is involved here).
/Henrik
On Thu, May 5, 2011 at 12:47 PM, richland <yiping.f...@gmail.com> wrote:
> Hi, Henrik,
>
> Thanks a lot for the quick reply. Problem solved. I ran
> aroma.affymetrix before. I had a .Rcache/aroma.affymetrix in my home
> directory.
>
> Later system admin changed my uid. So when I ran aroma.affymetrix
> again, I wan not able to write to that directory. That's where the
> error "data set could not be setup for this path, because:
> cannot open the connection" comes from.
>
> cheers,
>
> Richland
>
>
>
>
>
> On May 5, 1:30 pm, Henrik Bengtsson <henrik.bengts...@aroma-
> project.org> wrote:
>> Hi,
>>
>> unfortunately there is no option to turn off locating *.saf files part
>> of the package installation (I'll see if I can add one for the next
>> release). However, it's strange if that would be the cause for you
>> problem, but on the other hand strange things happens all the time.
>>
>> For troubleshooting, see what the following does:
>>
>> sas <- SampleAnnotationSet$loadAll(verbose=-5);
>> print(sas);
>>
>> for (kk in seq(sas)) {
>> saf <- getFile(sas, kk);
>> print(saf);
>> df <- readDataFrame(saf, verbose=-5);
>> str(df);
>>
>> } # for (kk ...)
>>
>> Do you get an error? If so, for what file? Please provide a
>> traceback() report upon errors. Does the other SAF files work, i.e.
>> if you try manually with different 'kk':s will they load?
>>
>> Cheers,
>>
>> Henrik
>>
>> On Thu, May 5, 2011 at 9:00 AM, richland <yiping.f...@gmail.com> wrote:
>> > Hi,list,
>>
>> > Here is my basic set up under my current working directory:~/project/
>>
>> > rawData/M7/GenomeWideSNP_6/
>> > 23..CEL SJO023-snp6.CEL 25-snp6.CEL,26-snp6.CEL ...
>>
>> > ==
>> > annotationData/chipTypes/GenomeWideSNP_6/
>>
>> > GenomeWideSNP_6,Full.cdf
>> > GenomeWideSNP_6,Full,na30,hg18,HB20100215.ufl
>> > GenomeWideSNP_6,Full,na30,hg18,HB20100215.ugp
>> > GenomeWideSNP_6,HB20080710.acs
>>
>> > I don't need sample information so there is no samples/ directory
>> > under annotationData
>>
>> > I'm using R/2.12.0, aroma.affymetrix v2.1.0 (2011-04-08)
>>
>> > #
>> > ibrary(aroma.affymetrix)
>> > verbose <- Arguments$getVerbose(-8)
>> > timestampOn(verbose)
>>
>> > chipType <- "GenomeWideSNP_6"
>>
>> > cdf<- AffymetrixCdfFile$byChipType(chipType,tags="Full")
>>
>> > print(cdf) # ok
>>
>> > dataSetName<-"M7";
>> > cs <- AffymetrixCelSet$byName(dataSetName,
>> > cdf=cdf, verbose=-10)
>> > failed:
>>
>> > it found all 6 cell files, but keeps looking form saf file in /
>> > nfs_exports/apps/64-bit/gnu-apps/R/libraries/2.12.0/aroma.affymetrix/
>> > annotationData/samples/HapMap270.saf"
>>
>> > ########################
>> > Trying path #1 of 1...
>> > Path: rawData/M7/GenomeWideSNP_6
>> > Defining AffymetrixCelSet from files...
>> > Defining an AffymetrixCelSet object from files...
>> > Path: rawData/M7/GenomeWideSNP_6
>> > Pattern: [.](c|C)(e|E)(l|L)$
>> > File class: AffymetrixCelFile
>> > Scanning directory for files...
>> > Found 6 files/directories.
>> > Found 6 files.
>> > Scanning directory for files...done
>> > Defining 6 files...
>> > 1, 2, 3, 4, 5, 6,
>> > Defining 6 files...done
>> > Allocating a new AffymetrixCelSet instance...
>> > Arguments:
>> > Number of files: 6
>> > list()
>> > Allocating a new AffymetrixCelSet instance...done
>> > Updating newly allocated AffymetrixCelSet...
>> > Updating AffymetrixCelSet...
>> > Scanning for and applying sample annotation files...
>> > Loading all SampleAnnotationSet:s...
>> > Identify all directories containing SAF files...
>> > All SAF files located:
>> > [1] "/nfs_exports/apps/64-bit/gnu-apps/R/libraries/2.12.0/
>> > aroma.affymetrix/annotationData/samples/HapMap270.saf"
>>
>> > Path (to the first file): /nfs_exports/apps/64-bit/gnu-apps/R/
>> > libraries/2.12.0/aroma.affymetrix/annotationData/samples
>> > Total file size: 0.03 MB
>> > RAM: 0.00MB
>> > Scanning for and applying sample annotation files...done
>> > Updating AffymetrixCelSet...done
>> > Defining AffymetrixCelSet from files...done
>> > Data set could not be setup for this path, because:
>> > cannot open the connection
>> > Trying path #1 of 1...done
>> > Error in list(`AffymetrixCelSet$byName(dataSetName, cdf = cdf, verbose
>> > = -10)` = <environment>, :
>>
>> > [2011-05-05 10:46:03] Exception: Failed to setup a data set for any of
>> > 1 data directories located.
>> > at throw(Exception(...))
>> > at throw.default(sprintf("Failed to setup a data set for any of %d
>> > data direct
>> > at throw(sprintf("Failed to setup a data set for any of %d data
>> > directories lo
>> > at method(static, ...)
>> > at AffymetrixCelSet$byName(dataSetName, cdf = cdf, verbose = -10)
>> > Calls: <Anonymous> ... method -> throw -> throw.default -> throw ->
>> > throw.Exception
>> > Setting up AffymetrixCelSet by name...done
>> > Execution halted
>>
>> > ===============
>> > I also tried to make a samples/ directory under annotationData/ ans
>> > made a file called M7.saf. it also failed.
>>
>> > [1] "rawData/M7/GenomeWideSNP_6"
>> > Trying path #1 of 1...
>> > Path: rawData/M7/GenomeWideSNP_6
>> > Defining AffymetrixCelSet from files...
>> > Defining an AffymetrixCelSet object from files...
>> > Path: rawData/M7/GenomeWideSNP_6
>> > Pattern: [.](c|C)(e|E)(l|L)$
>> > File class: AffymetrixCelFile
>> > Scanning directory for files...
>> > Found 6 files/directories.
>> > Found 6 files.
>> > Scanning directory for files...done
>> > Defining 6 files...
>> > 1, 2, 3, 4, 5, 6,
>> > Defining 6 files...done
>> > Allocating a new AffymetrixCelSet instance...
>> > Arguments:
>> > Number of files: 6
>> > list()
>> > Allocating a new AffymetrixCelSet instance...done
>> > Updating newly allocated AffymetrixCelSet...
>> > Updating AffymetrixCelSet...
>> > Scanning for and applying sample annotation files...
>> > Loading all SampleAnnotationSet:s...
>> > Identify all directories containing SAF files...
>> > All SAF files located:
>> > [1] "annotationData/samples/
>> > M7.saf"
>> > [2] "/nfs_exports/apps/64-bit/gnu-apps/R/libraries/2.12.0/
>> > aroma.affymetrix/annotationData/samples/HapMap270.saf"
>>
>> > It found the the M7.saf but also try to locate the other *saf files.
>>
>> > How to avoid this situation? Thanks!
>>
>> > --
>> > 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 websitehttp://www.aroma-project.org/.
>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> > To unsubscribe and other options, go tohttp://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/
>
--
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/.
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