The answers are dispersed below........
> > I just wanted to update you on the issue of creating Windows shortcuts
> > to point to the correct directory.
>
> > So the CDF files I want to use is on a mapped network drive - it is
> > mapped to my "P Drive":
>
> > P:\ANNOTATION\aromaAffymetrix\annotationData\chipTypes\HuGene-1_0-st-
> > v1\HuGene-1_0-st-v1,r3.cdf
>
> > I created the following shortcut in my working experiment directory,
> > "P:\EXPERIMENTS\NCHRI\TEST\CEL\annotationData.lnk", with the following
> > in the Target box:
>
> > P:\ANNOTATION\aromaAffymetrix\annotationData
>
> Did you create that by "drag'n'drop' by a right clicking or did you
> edit the "Target box" manually? Always do the drag'n'drop, because
> the property box of a Windows Shortcut does not show all internal
> fields or the shortcut and editing it is not safe.
Yes, I used drag and drop. I just checked the Target box to confirm.
> > When I type in the command
>
> > cdf <- AffymetrixCdfFile$fromChipType("MoGene-1_0-st-v1",tags="r3")
>
> > it throws an error because it is unable to find the file. Displaying
> > the path reveals:
>
> >> Arguments$getReadablePath("annotationData")
> > [1] "//RES2K3FS01/RESAffymetrix/ANNOTATION/aromaAffymetrix/
> > annotationData"
>
> What happens if you do:
>
> path <- Arguments$getReadablePath("annotationData");
> print(list.files(path=path));
$ path
[1] "//RES2K3FS01/RESAffymetrix/ANNOTATION/aromaAffymetrix/
annotationData"
$ print(list.files(path=path))
[1] "chipTypes"
> path2 <- filePath(path, "MoGene-1_0-st-v1");
> print(path2);
> print(file.info(path2));
> print(list.files(path=path2));
$ print(path2);
[1] "//RES2K3FS01/RESAffymetrix/ANNOTATION/aromaAffymetrix/
annotationData/MoGene-1_0-st-v1"
$ print(file.info(path2));
size
//RES2K3FS01/RESAffymetrix/ANNOTATION/aromaAffymetrix/annotationData/
MoGene-1_0-st-v1 NA
isdir
//RES2K3FS01/RESAffymetrix/ANNOTATION/aromaAffymetrix/annotationData/
MoGene-1_0-st-v1 NA
mode
//RES2K3FS01/RESAffymetrix/ANNOTATION/aromaAffymetrix/annotationData/
MoGene-1_0-st-v1 <NA>
mtime
//RES2K3FS01/RESAffymetrix/ANNOTATION/aromaAffymetrix/annotationData/
MoGene-1_0-st-v1 <NA>
ctime
//RES2K3FS01/RESAffymetrix/ANNOTATION/aromaAffymetrix/annotationData/
MoGene-1_0-st-v1 <NA>
atime
//RES2K3FS01/RESAffymetrix/ANNOTATION/aromaAffymetrix/annotationData/
MoGene-1_0-st-v1 <NA>
exe
//RES2K3FS01/RESAffymetrix/ANNOTATION/aromaAffymetrix/annotationData/
MoGene-1_0-st-v1 <NA>
$ print(list.files(path=path2));
character(0)
Warning message:
In list.files(path = path2) :
list.files: '//RES2K3FS01/RESAffymetrix/ANNOTATION/aromaAffymetrix/
annotationData/MoGene-1_0-st-v1' is not a readable directory
>
>
>
> > So it looks as though the issue is that "P:\" is being replaced by R
> > with the actual name of the Network drive. If I copy the
> > annotationData directory to my C:\ and create the shortcut to point
> > there it works just fine, but the arguments command returns "C:\":
>
> >> Arguments$getReadablePath("annotationData")
> > [1] "C:/annotationData"
>
> So, if I understand you correctly, you are saying that "shortcuting"
> to another location on the local C: drive works, but when you try to
> do the same for a drive unit (P:) mounted to a network drive, then you
> do not get the drive unit path, but the network path. Correct?
Yes, that's correct
> The Windows Shortcut file format is unfortunately not public and my
> implementation relies on a reverse engineered description of it. I
> know there are multiple "paths" in the file and that I might have
> update the code such that locally mounted paths are returned before
> network drive paths.
>
> Could you please forward me the problematic windows shortcut file
> (*.lnk) by doing the following:
>
> library("R.utils");
> gzip("annotationData.lnk", remove=FALSE);
>
> That will create an annotationData.lnk.gz file, which you can email to
> either the list or to me directly.
I'll e-mail to you directly.
>
>
> > If there is a way around it that's great, but if not I can live with
> > just creating a copy of the annotation data on on my local machine.
> > Thought I should post my experience in case others go through the
> > same.
>
> We should be able to solve this one way or the other.
>
> /Henrik
>
>
>
> > Thanks,
>
> > Peter
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