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Question: defect in bioconductor doc examples
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15.9 years ago by
Dick Beyer1.4k
Dick Beyer1.4k 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 > ADD COMMENTlink modified 15.9 years ago by Sandrine Dudoit170 • written 15.9 years ago by Dick Beyer1.4k 0 15.9 years ago by Sandrine Dudoit170 wrote: 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 > > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >