[BioC] defect in bioconductor doc examples
Sandrine Dudoit
sandrine@stat.berkeley.edu
Tue, 23 Jul 2002 12:20:59 -0700 (PDT)
Hi Dick,
Thanks for reporting this problem. We are working on fixing it.
Best,
Sandrine
-------------------------------------------------------------------------------
Sandrine Dudoit, Ph.D. E-mail: sandrine@stat.berkeley.edu
Assistant Professor Tel: (510) 643-1108
Division of Biostatistics Fax: (510) 643-5163
School of Public Health http://www.stat.berkeley.edu/~sandrine
University of California, Berkeley
140 Earl Warren Hall, #7360
Berkeley, CA 94720-7360
-------------------------------------------------------------------------------
On Mon, 22 Jul 2002, Dick Beyer wrote:
> 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
> *******************************************************************************
> 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
> *******************************************************************************
>
>
>
>
>
>
>
>
> On Mon, 22 Jul 2002 bioconductor-request@stat.math.ethz.ch wrote:
>
> > Send Bioconductor mailing list submissions to
> > bioconductor@stat.math.ethz.ch
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > or, via email, send a message with subject or body 'help' to
> > bioconductor-request@stat.math.ethz.ch
> >
> > You can reach the person managing the list at
> > bioconductor-admin@stat.math.ethz.ch
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Bioconductor digest..."
> >
> >
> > 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
> >
>
>
>
>
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>