[BioC] defect in bioconductor doc examples
Dick Beyer
dbeyer@u.washington.edu
Mon, 22 Jul 2002 15:26:01 -0700 (PDT)
I am trying to work through the examples in, for example, C:\Program Files\R\rw1051\library\marrayPlots\html\maPlot.html
This is what I see:
...
Notes:
C:/PROGRA~1/R/rw1051/library/marrayInput/data/SwirlSample.txt
> data(swirl)
Error: restore file may be from a newer version of R -- no data loaded
I am running R 1.5.1
Thanks,
Dick
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Richard P. Beyer, Ph.D. University of Washington
Tel.:(206) 616 7378 Environmental Health, Box 354695
Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100
Seattle, WA 98105-6099
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On Mon, 22 Jul 2002 bioconductor-request@stat.math.ethz.ch wrote:
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> Today's Topics:
>
> 1. trouble with rhdf5 and hdf5.datasets (Laurent Gautier)
> 2. Re: trouble with rhdf5 and hdf5.datasets (Byron Ellis)
> 3. Re: trouble with rhdf5 and hdf5.datasets (Byron Ellis)
> 4. Re: trouble with rhdf5 and hdf5.datasets (Vincent Carey 525-2265)
> 5. Re: trouble with rhdf5 and hdf5.datasets (Byron Ellis)
> 6. Re: trouble with rhdf5 and hdf5.datasets (Laurent Gautier)
> 7. Re: trouble with rhdf5 and hdf5.datasets (Laurent Gautier)
> 8. Re: trouble with rhdf5 and hdf5.datasets (Byron Ellis)
>
> --__--__--
>
> Message: 1
> Date: Sun, 21 Jul 2002 14:30:34 +0200
> From: Laurent Gautier <laurent@cbs.dtu.dk>
> To: bioconductor@stat.math.ethz.ch
> Subject: [BioC] trouble with rhdf5 and hdf5.datasets
>
> Dear all,
>
> I observed unexplainable things with rhdf5. I do not
> know if they could be avoided.
>
> I am trying to access datasets in a group using the
> function 'do.call' with "$" (since the name of the
> dataset will only be known at run-time)... and I have
> a hard time with that (example below). Does anybody
> have experience with that ?
>
>
> ## example from the help file
> > mad <- hdf5.open("microarray.h5")
> > # Create a new group inside the file
> > hdf5.group(mad,"chip1")
> > hdf5.dataset(mad$chip1,"raw", dim=c(534,534))
> >
> > raw <- mad$chip1$raw
> > for(i in 1:534)
> + { raw[i,1:534] <- runif(534) }
>
> >
> > do.call("$", list("mad", "chip1"))
> NULL
>
> # uh, uh....
>
>
> > mad$chip1
> Name Type Date Comment
> [1] raw Dataset 21/07/2002 16:26
>
> # let's try again...
>
> > do.call("$", list("mad", "chip1"))
> NULL
> > mad
> Name Type Date Comment
> [1] chip1 Group
>
> # show stopper
>
> > mad[[1]]
> Segmentation fault
>
>
>
>
>
> Thanks,
>
>
>
>
> Laurent
>
>
>
>
>
>
> --
> --------------------------------------------------------------
> Laurent Gautier CBS, Building 208, DTU
> PhD. Student DK-2800 Lyngby,Denmark
> tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent
>
> --__--__--
>
> Message: 2
> Date: Sun, 21 Jul 2002 10:00:06 -0400 (EDT)
> From: Byron Ellis <bellis@hsph.harvard.edu>
> To: Laurent Gautier <laurent@cbs.dtu.dk>
> cc: bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] trouble with rhdf5 and hdf5.datasets
>
> You should be able to use the standard "[[" semantics when accessing
> groups or datasets under rhdf5. this elimnates the need for the "do.call"
>
> Byron Ellis (bellis@hsph.harvard.edu)
> "Oook" - The Librarian
>
> Please finger bellis@hsph.harvard.edu for PGP keys
>
> On Sun, 21 Jul 2002, Laurent Gautier wrote:
>
> > Dear all,
> >
> > I observed unexplainable things with rhdf5. I do not
> > know if they could be avoided.
> >
> > I am trying to access datasets in a group using the
> > function 'do.call' with "$" (since the name of the
> > dataset will only be known at run-time)... and I have
> > a hard time with that (example below). Does anybody
> > have experience with that ?
> >
> >
> > ## example from the help file
> > > mad <- hdf5.open("microarray.h5")
> > > # Create a new group inside the file
> > > hdf5.group(mad,"chip1")
> > > hdf5.dataset(mad$chip1,"raw", dim=c(534,534))
> > >
> > > raw <- mad$chip1$raw
> > > for(i in 1:534)
> > + { raw[i,1:534] <- runif(534) }
> >
> > >
> > > do.call("$", list("mad", "chip1"))
> > NULL
> >
> > # uh, uh....
> >
> >
> > > mad$chip1
> > Name Type Date Comment
> > [1] raw Dataset 21/07/2002 16:26
> >
> > # let's try again...
> >
> > > do.call("$", list("mad", "chip1"))
> > NULL
> > > mad
> > Name Type Date Comment
> > [1] chip1 Group
> >
> > # show stopper
> >
> > > mad[[1]]
> > Segmentation fault
> >
> >
> >
> >
> >
> > Thanks,
> >
> >
> >
> >
> > Laurent
> >
> >
> >
> >
> >
> >
> > --
> > --------------------------------------------------------------
> > Laurent Gautier CBS, Building 208, DTU
> > PhD. Student DK-2800 Lyngby,Denmark
> > tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
>
>
> --__--__--
>
> Message: 3
> Date: Sun, 21 Jul 2002 10:01:58 -0400 (EDT)
> From: Byron Ellis <bellis@hsph.harvard.edu>
> To: Laurent Gautier <laurent@cbs.dtu.dk>
> cc: bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] trouble with rhdf5 and hdf5.datasets
>
> Whoops, didn't scroll down that last bit...did you try mad[["chip1"]]?
>
> Byron Ellis (bellis@hsph.harvard.edu)
> "Oook" - The Librarian
>
> Please finger bellis@hsph.harvard.edu for PGP keys
>
> On Sun, 21 Jul 2002, Laurent Gautier wrote:
>
> > Dear all,
> >
> > I observed unexplainable things with rhdf5. I do not
> > know if they could be avoided.
> >
> > I am trying to access datasets in a group using the
> > function 'do.call' with "$" (since the name of the
> > dataset will only be known at run-time)... and I have
> > a hard time with that (example below). Does anybody
> > have experience with that ?
> >
> >
> > ## example from the help file
> > > mad <- hdf5.open("microarray.h5")
> > > # Create a new group inside the file
> > > hdf5.group(mad,"chip1")
> > > hdf5.dataset(mad$chip1,"raw", dim=c(534,534))
> > >
> > > raw <- mad$chip1$raw
> > > for(i in 1:534)
> > + { raw[i,1:534] <- runif(534) }
> >
> > >
> > > do.call("$", list("mad", "chip1"))
> > NULL
> >
> > # uh, uh....
> >
> >
> > > mad$chip1
> > Name Type Date Comment
> > [1] raw Dataset 21/07/2002 16:26
> >
> > # let's try again...
> >
> > > do.call("$", list("mad", "chip1"))
> > NULL
> > > mad
> > Name Type Date Comment
> > [1] chip1 Group
> >
> > # show stopper
> >
> > > mad[[1]]
> > Segmentation fault
> >
> >
> >
> >
> >
> > Thanks,
> >
> >
> >
> >
> > Laurent
> >
> >
> >
> >
> >
> >
> > --
> > --------------------------------------------------------------
> > Laurent Gautier CBS, Building 208, DTU
> > PhD. Student DK-2800 Lyngby,Denmark
> > tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
>
>
> --__--__--
>
> Message: 4
> Date: Sun, 21 Jul 2002 10:12:33 -0400 (EDT)
> From: Vincent Carey 525-2265 <stvjc@channing.harvard.edu>
> To: Laurent Gautier <laurent@cbs.dtu.dk>
> cc: bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] trouble with rhdf5 and hdf5.datasets
>
> > >
> > > do.call("$", list("mad", "chip1"))
> > NULL
>
> here you want to refer to mad, not its name, do not use "mad"
>
> do.call("$", list(mad, "chip1"))
>
> should work
>
> also i have noted that there is a problem in some of the
> doc -- specifically the man page for
> hdf5.open -- that refers to hdf5.create.group.
> the latter has been supplanted, it seems, by hdf5.group.
>
> i did reproduce your segfault, that needs to be looked at.
> unfortunately the weather here is very nice....
>
>
> --__--__--
>
> Message: 5
> Date: Sun, 21 Jul 2002 10:17:28 -0400 (EDT)
> From: Byron Ellis <bellis@hsph.harvard.edu>
> To: Vincent Carey 525-2265 <stvjc@channing.harvard.edu>
> cc: Laurent Gautier <laurent@cbs.dtu.dk>, bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] trouble with rhdf5 and hdf5.datasets
>
> The problem, I believe, is that HDF5 makes no guarrantee about the
> ordering of the groups/datasets at any particular time (i.e. mad[[1]]
> today is not neccessarily mad[[1]] tomorrow). At the very least, though, I
> should go through and fix it so it fails gracefully :-)
>
> Byron Ellis (bellis@hsph.harvard.edu)
> "Oook" - The Librarian
>
> Please finger bellis@hsph.harvard.edu for PGP keys
>
> On Sun, 21 Jul 2002, Vincent Carey 525-2265 wrote:
>
> > > >
> > > > do.call("$", list("mad", "chip1"))
> > > NULL
> >
> > here you want to refer to mad, not its name, do not use "mad"
> >
> > do.call("$", list(mad, "chip1"))
> >
> > should work
> >
> > also i have noted that there is a problem in some of the
> > doc -- specifically the man page for
> > hdf5.open -- that refers to hdf5.create.group.
> > the latter has been supplanted, it seems, by hdf5.group.
> >
> > i did reproduce your segfault, that needs to be looked at.
> > unfortunately the weather here is very nice....
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
>
>
> --__--__--
>
> Message: 6
> Date: Sun, 21 Jul 2002 15:33:59 +0200
> From: Laurent Gautier <laurent@cbs.dtu.dk>
> To: Byron Ellis <bellis@hsph.harvard.edu>
> Cc: Vincent Carey 525-2265 <stvjc@channing.harvard.edu>,
> Laurent Gautier <laurent@cbs.dtu.dk>, bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] trouble with rhdf5 and hdf5.datasets
>
> On Sun, Jul 21, 2002 at 10:17:28AM -0400, Byron Ellis wrote:
> > The problem, I believe, is that HDF5 makes no guarrantee about the
> > ordering of the groups/datasets at any particular time (i.e. mad[[1]]
> > today is not neccessarily mad[[1]] tomorrow). At the very least, though, I
> > should go through and fix it so it fails gracefully :-)
>
>
> while you are into the segfault side of things, you may also want to
> try the following:
>
> > hdf5.open(file("whatever"))
> Segmentation fault
>
> (I know, the user is not suppposed to do that, unless he/she read the
> help file in diagonal ;) (hey, did I ?)... but doing that
> generates a
> "
> > library(rhdf5)
> Error in firstlib(which.lib.loc, package) :
> not an HDF5 file
> Error in library(rhdf5) : .First.lib failed
> "
> at the next try)
>
>
>
> L.
>
>
>
> >
> > Byron Ellis (bellis@hsph.harvard.edu)
> > "Oook" - The Librarian
> >
> > Please finger bellis@hsph.harvard.edu for PGP keys
> >
> > On Sun, 21 Jul 2002, Vincent Carey 525-2265 wrote:
> >
> > > > >
> > > > > do.call("$", list("mad", "chip1"))
> > > > NULL
> > >
> > > here you want to refer to mad, not its name, do not use "mad"
> > >
> > > do.call("$", list(mad, "chip1"))
> > >
> > > should work
> > >
> > > also i have noted that there is a problem in some of the
> > > doc -- specifically the man page for
> > > hdf5.open -- that refers to hdf5.create.group.
> > > the latter has been supplanted, it seems, by hdf5.group.
> > >
> > > i did reproduce your segfault, that needs to be looked at.
> > > unfortunately the weather here is very nice....
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor@stat.math.ethz.ch
> > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > >
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
> --
> --------------------------------------------------------------
> Laurent Gautier CBS, Building 208, DTU
> PhD. Student DK-2800 Lyngby,Denmark
> tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent
>
> --__--__--
>
> Message: 7
> Date: Sun, 21 Jul 2002 16:00:06 +0200
> From: Laurent Gautier <laurent@cbs.dtu.dk>
> To: Vincent Carey 525-2265 <stvjc@channing.harvard.edu>
> Cc: Laurent Gautier <laurent@cbs.dtu.dk>, bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] trouble with rhdf5 and hdf5.datasets
>
> On Sun, Jul 21, 2002 at 10:12:33AM -0400, Vincent Carey 525-2265 wrote:
> > > >
> > > > do.call("$", list("mad", "chip1"))
> > > NULL
> >
> > here you want to refer to mad, not its name, do not use "mad"
> >
> > do.call("$", list(mad, "chip1"))
> >
> > should work
>
>
> ... hohooo... it looks like it should be outside too
> (since I start to have dumb questions...) (unfortunately
> the weather is not particularly nice here)
>
>
> Thanks,
>
>
>
> L.
>
>
>
>
> >
> > also i have noted that there is a problem in some of the
> > doc -- specifically the man page for
> > hdf5.open -- that refers to hdf5.create.group.
> > the latter has been supplanted, it seems, by hdf5.group.
> >
> > i did reproduce your segfault, that needs to be looked at.
> > unfortunately the weather here is very nice....
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
> --
> --------------------------------------------------------------
> Laurent Gautier CBS, Building 208, DTU
> PhD. Student DK-2800 Lyngby,Denmark
> tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent
>
> --__--__--
>
> Message: 8
> Date: Sun, 21 Jul 2002 20:18:31 -0400 (EDT)
> From: Byron Ellis <bellis@hsph.harvard.edu>
> To: Laurent Gautier <laurent@cbs.dtu.dk>
> cc: Vincent Carey 525-2265 <stvjc@channing.harvard.edu>,
> bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] trouble with rhdf5 and hdf5.datasets
>
> It was nice enough here that I spend the entire day on my motorcycle
> rather than working on this ;-)
>
> Byron Ellis (bellis@hsph.harvard.edu)
> "Oook" - The Librarian
>
> Please finger bellis@hsph.harvard.edu for PGP keys
>
> On Sun, 21 Jul 2002, Laurent Gautier wrote:
>
> > On Sun, Jul 21, 2002 at 10:12:33AM -0400, Vincent Carey 525-2265 wrote:
> > > > >
> > > > > do.call("$", list("mad", "chip1"))
> > > > NULL
> > >
> > > here you want to refer to mad, not its name, do not use "mad"
> > >
> > > do.call("$", list(mad, "chip1"))
> > >
> > > should work
> >
> >
> > ... hohooo... it looks like it should be outside too
> > (since I start to have dumb questions...) (unfortunately
> > the weather is not particularly nice here)
> >
> >
> > Thanks,
> >
> >
> >
> > L.
> >
> >
> >
> >
> > >
> > > also i have noted that there is a problem in some of the
> > > doc -- specifically the man page for
> > > hdf5.open -- that refers to hdf5.create.group.
> > > the latter has been supplanted, it seems, by hdf5.group.
> > >
> > > i did reproduce your segfault, that needs to be looked at.
> > > unfortunately the weather here is very nice....
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor@stat.math.ethz.ch
> > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
> > --
> > --------------------------------------------------------------
> > Laurent Gautier CBS, Building 208, DTU
> > PhD. Student DK-2800 Lyngby,Denmark
> > tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
>
>
>
> --__--__--
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
>
> End of Bioconductor Digest
>