[Rd] problems (seg-faults) while trying to compile for older suse versions
Hi! While preparing 2.13.2 in the build service I get stuck for some older releases of openSUSE / SLED. While it built fine for 2.13.1 now I get segfaults in 'make docs' and do so only for 32-bit architectures. This is not urgent, because only older releases are affected, nevertheless I would like to understand the cause. Attached are what I think the relevant parts of a build-log, including tracebacks of some segfaults. Any hint greatly appreciated. Detlef __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-devel (2.14 alpha) Windows binary
On Wed, 5 Oct 2011, Peter Dalgaard wrote: I suspect that the Windows build system just hasn't caught on to the short time between 2.13.2 and the start of run-in for 2.14.0. I think the usual logic is that pre-releases of the next version replace the patch releases of the old one (by definition, there shouldn't be updates to 2.13.2 anyway). Correct, but it also does not have a 'R 2.15.0 devel' (not that there is such a thing: R-devel does not have a version number). In fact it has ncftp /pub/R/bin/windows/base > ls -l ... -rw-rw-r--1 01001 40213201 Sep 30 19:18 R-2.13.2-win.exe -rw-rw-r--1 01001 41018043 Oct 4 11:49 R-2.13.2patched-win.exe -rw-rw-r--1 01001 47707488 Oct 2 10:45 R-2.14.0dev-win.exe ... so R-2.14.0dev-win.exe would be a pretty good surrogate for R 2.14.0 alpha until that is available. -pd On Oct 5, 2011, at 00:46 , Dan Tenenbaum wrote: Hello, This question popped up on the bioc-devel list, I'm forwarding it here. I know that sources for R-2.14 alpha can be found here: http://cran.r-project.org/src/base-prerelease/ But the OP (below) is asking about Windows binaries. Dan -- Forwarded message -- From: Stefan McKinnon Høj-Edwards Date: 2011/10/4 Subject: Re: [Bioc-devel] Bioc 2.9 New Package submissions. The October deadlines are fast approaching. To: "bioc-de...@r-project.org" According to the BioC release plan, we should use R-2.14.0 devel-alpha to check our packages. But on cran, we can either choose R 2.13.2 (http://cran.r-project.org/bin/windows/base/) or R 2.15.0 devel (http://cran.r-project.org/bin/windows/base/rdevel.html). Am I missing something? And will it again be possible to get the binaries for Windows of the 2.14.0 devel-alpha? Kind regards Stefan McKinnon Høj-Edwards Dept. of Molecular Biology and Genetics Ph.D. Fellow Aarhus University Blichers Allé 20, Postboks 50 DK-8830 Tjele Tel.: +45 8715 7969 Tel.: +45 8715 6000 Email: stefan.hoj-edwa...@agrsci.dk Web: www.agrsci.dk -Oprindelig meddelelse- Date: Mon, 03 Oct 2011 16:36:15 -0700 From: Marc Carlson To: bioc-de...@r-project.org Subject: [Bioc-devel] Bioc 2.9 New Package submissions. The October deadlines are fast approaching. Message-ID: <4e8a46ef.3030...@fhcrc.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear Bioconductor developers, This announcement is for package authors who are in the process of developing packages for inclusion in the upcoming 2.9 release of Bioconductor in October. The deadline to make a submission for this release is going to be October 10th, 2011. Packages submitted after the deadline will probably not provide us with sufficient time for inclusion in this release. Earlier submissions are encouraged as it provides more time to correct issues raised during the review process and probably has an improved chance of making it into the release. If you do not have your package ready in time for this deadline, your package will still be included in our development branch of Bioconductor and will be scheduled for inclusion in the subsequent release version of Bioconductor. Other important deadlines to consider are listed on our Release schedule. If you have packages in the repository (and most of you do), it is probably a good idea to follow the following link and see the other deadlines that are approaching. http://www.bioconductor.org/developers/release-schedule/ Sincerely, The Biocore Team ___ bioc-de...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] problems (seg-faults) while trying to compile for older suse versions
On Wed, 5 Oct 2011, Detlef Steuer wrote: Hi! While preparing 2.13.2 in the build service I get stuck for some older releases of openSUSE / SLED. While it built fine for 2.13.1 now I get segfaults in 'make docs' and do so only for 32-bit architectures. This is not urgent, because only older releases are affected, nevertheless I would like to understand the cause. Attached are what I think the relevant parts of a build-log, including tracebacks of some segfaults. Nothing came through. But it seems specific to your system (and no one reported anything in the run up to 2.13.2, including the RC test period nor with 2.13.1 patched). There is no problem with e.g. i686 Fedora 14. Any hint greatly appreciated. Detlef -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] suppressing stderr output from system() calls
Dear list,
I'm trying to suppress/redirect/squash the output from commands like
install.packages, or download.file. The problem is that none of: sink(...,
type="message"), sink(..., type="output"), capture.output, suppressMessages are
quite doing the trick. Output gets written to the stderr stream, despite any
combination of the above suppression commands.
According to ?sink:
Messages sent to stderr() (including those from message, warning and
stop) can be diverted by sink(type = "message") (see below).
I'm pretty sure it's the system(), or .Internal() calls which are the culprit,
which currently write the majority (all?) of their output to the stderr stream.
Simple example:
con <- file("stderr.txt", "w")
sink(con, type="message")
system("ls")
sink(NULL, type="message")
close(con)
# instead of the output going to stderr.txt, it gets printed to the console.
# no good either
capture.output(system("ls"))
character(0)
This is an issue, since i'm writing GenePattern modules to run R code, and if
anything is written to stderr, then the job gets hit with a 'job failed'
status, when all that might have happened is an R package got installed, or a
file got downloaded via FTP.
Any ideas? Can system() and .Internal() output be redirected to stdout?
cheers,
Mark
sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
>
-
Mark Cowley, PhD
Pancreatic Cancer Program | Peter Wills Bioinformatics Centre
Garvan Institute of Medical Research, Sydney, Australia
-
[[alternative HTML version deleted]]
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] suppressing stderr output from system() calls
See ?system, in particular ignore.stdout, ignore.stderr and intern.
Cheers,
Simon
On Oct 5, 2011, at 5:36 AM, Mark Cowley wrote:
> Dear list,
> I'm trying to suppress/redirect/squash the output from commands like
> install.packages, or download.file. The problem is that none of: sink(...,
> type="message"), sink(..., type="output"), capture.output, suppressMessages
> are quite doing the trick. Output gets written to the stderr stream, despite
> any combination of the above suppression commands.
> According to ?sink:
> Messages sent to Œstderr()‚ (including those from Œmessage‚, Œwarning‚ and
> Œstop‚) can be diverted by Œsink(type = "message")‚ (see below).
>
> I'm pretty sure it's the system(), or .Internal() calls which are the
> culprit, which currently write the majority (all?) of their output to the
> stderr stream.
>
> Simple example:
> con <- file("stderr.txt", "w")
> sink(con, type="message")
> system("ls")
> sink(NULL, type="message")
> close(con)
> # instead of the output going to stderr.txt, it gets printed to the console.
>
> # no good either
> capture.output(system("ls"))
> character(0)
>
> This is an issue, since i'm writing GenePattern modules to run R code, and if
> anything is written to stderr, then the job gets hit with a 'job failed'
> status, when all that might have happened is an R package got installed, or a
> file got downloaded via FTP.
>
> Any ideas? Can system() and .Internal() output be redirected to stdout?
>
> cheers,
> Mark
>
>
> sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>>
>
>
>
> -
> Mark Cowley, PhD
>
> Pancreatic Cancer Program | Peter Wills Bioinformatics Centre
> Garvan Institute of Medical Research, Sydney, Australia
> -
>
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] suppressing stderr output from system() calls
See ?system2 to answer your subject line.
But you seem confused about external programs and R's own stdout()
connection. Have you read the R News article on connections?
On Wed, 5 Oct 2011, Mark Cowley wrote:
Dear list,
I'm trying to suppress/redirect/squash the output from commands like install.packages, or
download.file. The problem is that none of: sink(..., type="message"), sink(...,
type="output"), capture.output, suppressMessages are quite doing the trick. Output gets
written to the stderr stream, despite any combination of the above suppression commands.
According to ?sink:
Messages sent to ?stderr()? (including those from ?message?, ?warning? and ?stop?) can be
diverted by ?sink(type = "message")? (see below).
I'm pretty sure it's the system(), or .Internal() calls which are the culprit,
which currently write the majority (all?) of their output to the stderr stream.
Simple example:
con <- file("stderr.txt", "w")
sink(con, type="message")
system("ls")
sink(NULL, type="message")
close(con)
# instead of the output going to stderr.txt, it gets printed to the console.
# no good either
capture.output(system("ls"))
character(0)
This is an issue, since i'm writing GenePattern modules to run R code, and if
anything is written to stderr, then the job gets hit with a 'job failed'
status, when all that might have happened is an R package got installed, or a
file got downloaded via FTP.
Any ideas? Can system() and .Internal() output be redirected to stdout?
cheers,
Mark
sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
-
Mark Cowley, PhD
Pancreatic Cancer Program | Peter Wills Bioinformatics Centre
Garvan Institute of Medical Research, Sydney, Australia
-
[[alternative HTML version deleted]]
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] suppressing stderr output from system() calls
On 10/05/2011 02:36 AM, Mark Cowley wrote:
Dear list,
I'm trying to suppress/redirect/squash the output from commands like
install.packages, or download.file. The problem is that none of:
sink(..., type="message"), sink(..., type="output"), capture.output,
suppressMessages are quite doing the trick. Output gets written to
the stderr stream, despite any combination of the above suppression
commands.
Hi Mark --
For download.file, the argument quiet=TRUE suppresses output messages;
this option can be used in ... for install.packages, too (according to
the documentation). This is good enough to quieten the regular chatter
on a successful operation. To catch errors and suppress warnings also,
maybe a construct like
url = "http://r-project.org/doesnotexist";
tryCatch(suppressWarnings(
capture.output(download.file(url, tempfile(), quiet=TRUE))),
error=function(...) {})
Martin
According to ?sink:
Messages sent to ‘stderr()’ (including those from ‘message’, ‘warning’ and ‘stop’) can be
diverted by ‘sink(type = "message")’ (see below).
I'm pretty sure it's the system(), or .Internal() calls which are the culprit,
which currently write the majority (all?) of their output to the stderr stream.
Simple example:
con<- file("stderr.txt", "w")
sink(con, type="message")
system("ls")
sink(NULL, type="message")
close(con)
# instead of the output going to stderr.txt, it gets printed to the console.
# no good either
capture.output(system("ls"))
character(0)
This is an issue, since i'm writing GenePattern modules to run R code, and if
anything is written to stderr, then the job gets hit with a 'job failed'
status, when all that might have happened is an R package got installed, or a
file got downloaded via FTP.
Any ideas? Can system() and .Internal() output be redirected to stdout?
cheers,
Mark
sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
-
Mark Cowley, PhD
Pancreatic Cancer Program | Peter Wills Bioinformatics Centre
Garvan Institute of Medical Research, Sydney, Australia
-
[[alternative HTML version deleted]]
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-devel (2.14 alpha) Windows binary
An automated build (done on winbuilder) will take a few days: people are too busy this week. For the time being, I have put a current Windows installer for R 2.14.0 alpha at http://www.stats.ox.ac.uk/pub/RWin/R-2.14.0alpha-win.exe I am unlikely to update it often (and I too am busy this week). On Wed, 5 Oct 2011, Prof Brian Ripley wrote: On Wed, 5 Oct 2011, Peter Dalgaard wrote: I suspect that the Windows build system just hasn't caught on to the short time between 2.13.2 and the start of run-in for 2.14.0. I think the usual logic is that pre-releases of the next version replace the patch releases of the old one (by definition, there shouldn't be updates to 2.13.2 anyway). Correct, but it also does not have a 'R 2.15.0 devel' (not that there is such a thing: R-devel does not have a version number). In fact it has ncftp /pub/R/bin/windows/base > ls -l ... -rw-rw-r--1 01001 40213201 Sep 30 19:18 R-2.13.2-win.exe -rw-rw-r--1 01001 41018043 Oct 4 11:49 R-2.13.2patched-win.exe -rw-rw-r--1 01001 47707488 Oct 2 10:45 R-2.14.0dev-win.exe ... so R-2.14.0dev-win.exe would be a pretty good surrogate for R 2.14.0 alpha until that is available. -pd On Oct 5, 2011, at 00:46 , Dan Tenenbaum wrote: Hello, This question popped up on the bioc-devel list, I'm forwarding it here. I know that sources for R-2.14 alpha can be found here: http://cran.r-project.org/src/base-prerelease/ But the OP (below) is asking about Windows binaries. Dan -- Forwarded message -- From: Stefan McKinnon Høj-Edwards Date: 2011/10/4 Subject: Re: [Bioc-devel] Bioc 2.9 New Package submissions. The October deadlines are fast approaching. To: "bioc-de...@r-project.org" According to the BioC release plan, we should use R-2.14.0 devel-alpha to check our packages. But on cran, we can either choose R 2.13.2 (http://cran.r-project.org/bin/windows/base/) or R 2.15.0 devel (http://cran.r-project.org/bin/windows/base/rdevel.html). Am I missing something? And will it again be possible to get the binaries for Windows of the 2.14.0 devel-alpha? Kind regards Stefan McKinnon Høj-Edwards Dept. of Molecular Biology and Genetics Ph.D. Fellow Aarhus University Blichers Allé 20, Postboks 50 DK-8830 Tjele Tel.: +45 8715 7969 Tel.: +45 8715 6000 Email: stefan.hoj-edwa...@agrsci.dk Web: www.agrsci.dk -Oprindelig meddelelse- Date: Mon, 03 Oct 2011 16:36:15 -0700 From: Marc Carlson To: bioc-de...@r-project.org Subject: [Bioc-devel] Bioc 2.9 New Package submissions. The October deadlines are fast approaching. Message-ID: <4e8a46ef.3030...@fhcrc.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear Bioconductor developers, This announcement is for package authors who are in the process of developing packages for inclusion in the upcoming 2.9 release of Bioconductor in October. The deadline to make a submission for this release is going to be October 10th, 2011. Packages submitted after the deadline will probably not provide us with sufficient time for inclusion in this release. Earlier submissions are encouraged as it provides more time to correct issues raised during the review process and probably has an improved chance of making it into the release. If you do not have your package ready in time for this deadline, your package will still be included in our development branch of Bioconductor and will be scheduled for inclusion in the subsequent release version of Bioconductor. Other important deadlines to consider are listed on our Release schedule. If you have packages in the repository (and most of you do), it is probably a good idea to follow the following link and see the other deadlines that are approaching. http://www.bioconductor.org/developers/release-schedule/ Sincerely, The Biocore Team ___ bioc-de...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, htt
Re: [Rd] R-devel (2.14 alpha) Windows binary
On Wed, Oct 5, 2011 at 10:04 AM, Prof Brian Ripley wrote: > An automated build (done on winbuilder) will take a few days: people are too > busy this week. > > For the time being, I have put a current Windows installer for R 2.14.0 > alpha at > http://www.stats.ox.ac.uk/pub/RWin/R-2.14.0alpha-win.exe > I am unlikely to update it often (and I too am busy this week). It looks like R 2.14.0 alpha is available on CRAN: http://cran.r-project.org/bin/windows/base/rdevel.html Thanks, Dan > > On Wed, 5 Oct 2011, Prof Brian Ripley wrote: > >> On Wed, 5 Oct 2011, Peter Dalgaard wrote: >> >>> I suspect that the Windows build system just hasn't caught on to the >>> short time between 2.13.2 and the start of run-in for 2.14.0. I think the >>> usual logic is that pre-releases of the next version replace the patch >>> releases of the old one (by definition, there shouldn't be updates to 2.13.2 >>> anyway). >> >> Correct, but it also does not have a 'R 2.15.0 devel' (not that there is >> such a thing: R-devel does not have a version number). In fact it has >> >> ncftp /pub/R/bin/windows/base > ls -l >> ... >> -rw-rw-r-- 1 0 1001 40213201 Sep 30 19:18 R-2.13.2-win.exe >> -rw-rw-r-- 1 0 1001 41018043 Oct 4 11:49 >> R-2.13.2patched-win.exe >> -rw-rw-r-- 1 0 1001 47707488 Oct 2 10:45 >> R-2.14.0dev-win.exe >> ... >> >> so R-2.14.0dev-win.exe would be a pretty good surrogate for R 2.14.0 alpha >> until that is available. >> >>> >>> -pd >>> >>> On Oct 5, 2011, at 00:46 , Dan Tenenbaum wrote: >>> Hello, This question popped up on the bioc-devel list, I'm forwarding it here. I know that sources for R-2.14 alpha can be found here: http://cran.r-project.org/src/base-prerelease/ But the OP (below) is asking about Windows binaries. Dan -- Forwarded message -- From: Stefan McKinnon Høj-Edwards Date: 2011/10/4 Subject: Re: [Bioc-devel] Bioc 2.9 New Package submissions. The October deadlines are fast approaching. To: "bioc-de...@r-project.org" According to the BioC release plan, we should use R-2.14.0 devel-alpha to check our packages. But on cran, we can either choose R 2.13.2 (http://cran.r-project.org/bin/windows/base/) or R 2.15.0 devel (http://cran.r-project.org/bin/windows/base/rdevel.html). Am I missing something? And will it again be possible to get the binaries for Windows of the 2.14.0 devel-alpha? Kind regards Stefan McKinnon Høj-Edwards Dept. of Molecular Biology and Genetics Ph.D. Fellow Aarhus University Blichers Allé 20, Postboks 50 DK-8830 Tjele Tel.: +45 8715 7969 Tel.: +45 8715 6000 Email: stefan.hoj-edwa...@agrsci.dk Web: www.agrsci.dk -Oprindelig meddelelse- Date: Mon, 03 Oct 2011 16:36:15 -0700 From: Marc Carlson To: bioc-de...@r-project.org Subject: [Bioc-devel] Bioc 2.9 New Package submissions. The October deadlines are fast approaching. Message-ID: <4e8a46ef.3030...@fhcrc.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear Bioconductor developers, This announcement is for package authors who are in the process of developing packages for inclusion in the upcoming 2.9 release of Bioconductor in October. The deadline to make a submission for this release is going to be October 10th, 2011. Packages submitted after the deadline will probably not provide us with sufficient time for inclusion in this release. Earlier submissions are encouraged as it provides more time to correct issues raised during the review process and probably has an improved chance of making it into the release. If you do not have your package ready in time for this deadline, your package will still be included in our development branch of Bioconductor and will be scheduled for inclusion in the subsequent release version of Bioconductor. Other important deadlines to consider are listed on our Release schedule. If you have packages in the repository (and most of you do), it is probably a good idea to follow the following link and see the other deadlines that are approaching. http://www.bioconductor.org/developers/release-schedule/ Sincerely, The Biocore Team ___ bioc-de...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel >>> >>> -- >>> Peter Dalgaard, Professor,
Re: [Rd] R-devel (2.14 alpha) Windows binary
On 05/10/2011 1:06 PM, Dan Tenenbaum wrote: On Wed, Oct 5, 2011 at 10:04 AM, Prof Brian Ripley wrote: > An automated build (done on winbuilder) will take a few days: people are too > busy this week. > > For the time being, I have put a current Windows installer for R 2.14.0 > alpha at > http://www.stats.ox.ac.uk/pub/RWin/R-2.14.0alpha-win.exe > I am unlikely to update it often (and I too am busy this week). It looks like R 2.14.0 alpha is available on CRAN: http://cran.r-project.org/bin/windows/base/rdevel.html That's temporary: R-devel should point to R-devel, not to the alpha. Soon there will be three links: one for R-patched (based on 2.13.2, probably without any changes unless some emergency crops up), one for R-testing (the alpha, beta, RC series), and one for R-devel (2.15.0-to-be). "Soon" might mean tomorrow, or it might take longer. Duncan Murdoch Thanks, Dan > > On Wed, 5 Oct 2011, Prof Brian Ripley wrote: > >> On Wed, 5 Oct 2011, Peter Dalgaard wrote: >> >>> I suspect that the Windows build system just hasn't caught on to the >>> short time between 2.13.2 and the start of run-in for 2.14.0. I think the >>> usual logic is that pre-releases of the next version replace the patch >>> releases of the old one (by definition, there shouldn't be updates to 2.13.2 >>> anyway). >> >> Correct, but it also does not have a 'R 2.15.0 devel' (not that there is >> such a thing: R-devel does not have a version number). In fact it has >> >> ncftp /pub/R/bin/windows/base> ls -l >> ... >> -rw-rw-r--1 01001 40213201 Sep 30 19:18 R-2.13.2-win.exe >> -rw-rw-r--1 01001 41018043 Oct 4 11:49 >> R-2.13.2patched-win.exe >> -rw-rw-r--1 01001 47707488 Oct 2 10:45 >> R-2.14.0dev-win.exe >> ... >> >> so R-2.14.0dev-win.exe would be a pretty good surrogate for R 2.14.0 alpha >> until that is available. >> >>> >>> -pd >>> >>> On Oct 5, 2011, at 00:46 , Dan Tenenbaum wrote: >>> Hello, This question popped up on the bioc-devel list, I'm forwarding it here. I know that sources for R-2.14 alpha can be found here: http://cran.r-project.org/src/base-prerelease/ But the OP (below) is asking about Windows binaries. Dan -- Forwarded message -- From: Stefan McKinnon Høj-Edwards Date: 2011/10/4 Subject: Re: [Bioc-devel] Bioc 2.9 New Package submissions. The October deadlines are fast approaching. To: "bioc-de...@r-project.org" According to the BioC release plan, we should use R-2.14.0 devel-alpha to check our packages. But on cran, we can either choose R 2.13.2 (http://cran.r-project.org/bin/windows/base/) or R 2.15.0 devel (http://cran.r-project.org/bin/windows/base/rdevel.html). Am I missing something? And will it again be possible to get the binaries for Windows of the 2.14.0 devel-alpha? Kind regards Stefan McKinnon Høj-Edwards Dept. of Molecular Biology and Genetics Ph.D. Fellow Aarhus University Blichers Allé 20, Postboks 50 DK-8830 Tjele Tel.: +45 8715 7969 Tel.: +45 8715 6000 Email: stefan.hoj-edwa...@agrsci.dk Web: www.agrsci.dk -Oprindelig meddelelse- Date: Mon, 03 Oct 2011 16:36:15 -0700 From: Marc Carlson To: bioc-de...@r-project.org Subject: [Bioc-devel] Bioc 2.9 New Package submissions. The October deadlines are fast approaching. Message-ID:<4e8a46ef.3030...@fhcrc.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear Bioconductor developers, This announcement is for package authors who are in the process of developing packages for inclusion in the upcoming 2.9 release of Bioconductor in October. The deadline to make a submission for this release is going to be October 10th, 2011. Packages submitted after the deadline will probably not provide us with sufficient time for inclusion in this release. Earlier submissions are encouraged as it provides more time to correct issues raised during the review process and probably has an improved chance of making it into the release. If you do not have your package ready in time for this deadline, your package will still be included in our development branch of Bioconductor and will be scheduled for inclusion in the subsequent release version of Bioconductor. Other important deadlines to consider are listed on our Release schedule. If you have packages in the repository (and most of you do), it is probably a good idea to follow the following link and see the other deadlines that are
[Rd] Question about Rweb
Greetings, I am working on creating an interactive website that will generate R-code for users based in the information they input on the site. Currently, the R-code can be generated and downloaded to be run locally on a computer with R. However, I have noticed a number of applications out there that instead submit the code directly to an R-web server. Some examples seem to be: http://www.biostatisticien.eu/cgi-bin/Rweb/buildModules.cgi http://quantpsy.org/interact/mlr2.htm http://pbil.univ-lyon1.fr/Rweb/ I would like to do something similar and set up R-web on a university server to execute my code. My trouble comes in terms of finding out more information regarding how to do this. Most of my searches of Rweb tend to point me to: http://www.math.montana.edu/Rweb/ But the associated links are all defunct. The R-Cran help pages related to R web also point to this now defunct website. I am at a loss regarding what to do. So, the question is, can someone out there tell me if it is possible to install Rweb on one of my own university servers and where can one go to learn how to do this? Thanks in advance for any advice. Scott T [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question about Rweb
On Oct 5, 2011, at 2:16 PM, Tonidandel, Scott wrote: > Greetings, > > I am working on creating an interactive website that will generate R-code for > users based in the information they input on the site. Currently, the R-code > can be generated and downloaded to be run locally on a computer with R. > However, I have noticed a number of applications out there that instead > submit the code directly to an R-web server. Some examples seem to be: > > http://www.biostatisticien.eu/cgi-bin/Rweb/buildModules.cgi > > http://quantpsy.org/interact/mlr2.htm > > http://pbil.univ-lyon1.fr/Rweb/ > > I would like to do something similar and set up R-web on a university server > to execute my code. My trouble comes in terms of finding out more information > regarding how to do this. Most of my searches of Rweb tend to point me to: > > http://www.math.montana.edu/Rweb/ > > But the associated links are all defunct. The R-Cran help pages related to R > web also point to this now defunct website. I am at a loss regarding what to > do. > > So, the question is, can someone out there tell me if it is possible to > install Rweb on one of my own university servers and where can one go to > learn how to do this? Thanks in advance for any advice. > I may be biased, but I would recommend using FastRWeb, it's much more efficient and has a lot of advantages (allows pre-loading of data and code, supports parallel connections etc.). See http://rforge.net/FastRWeb and https://www.urbanek.info/research/pub/urbanek-iasc08.pdf We use it heavily internally for a lot of things we do, so it's definitely a very active project (in fact I know about several people using it externally as well). In case you get convinced that this is a good option, please feel free to contact me if you have any questions and need any help. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question about Rweb
Hi Simon,
Any chance of getting step by instructions on setting it up to work with a
web server like Apache's httpd server (I have Apache's web server running,
actually a couple instances on different ports, and I do all my CGI
programming using Perl)?
I am not so much looking to provide a web interface for working with R, but
rather want to write CGI programs that use R for specific analyses and
graphics. I was considering writing my R scripts as usual (using the
capabilities of QRMlib and RQuantLib, in particular), and have them invoked
by a cgi script written in perl. But your description suggests it can be
made faster. Each package I looked at for doing this was interesting, but I
always got stuck at the point of figuring out how to get Apache's httpd
server to run my R scripts. Your description suggests that a request
requiring R can be just passed onto Rserve, but how does one set that up;
i.e. to pass the request arguments through to the R script, and to tell
Rserve which R script to use?
Any insights on setting this up would be appreciated.
On http://rforge.net/FastRWeb/files/, I read that FastRWeb is to be
installed using "install.packages('FastRWeb',,'http://www.rforge.net/')",
but that gives me the following message:
> install.packages('FastRWeb',,'http://www.rforge.net/')
Installing package(s) into 'C:\Users\Ted\Documents/R/win-library/2.12'
(as 'lib' is unspecified)
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package 'FastRWeb' is not available
>
This was on:
R version 2.12.0 (2010-10-15)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-mingw32/x64 (64-bit)
Thanks
Ted
> -Original Message-
> From: r-devel-boun...@r-project.org [mailto:r-devel-bounces@r-
> project.org] On Behalf Of Simon Urbanek
> Sent: October-05-11 3:06 PM
> To: Tonidandel, Scott
> Cc: r-devel@r-project.org
> Subject: Re: [Rd] Question about Rweb
>
>
> On Oct 5, 2011, at 2:16 PM, Tonidandel, Scott wrote:
>
> > Greetings,
> >
> > I am working on creating an interactive website that will generate
R-code
> [snip]
> I may be biased, but I would recommend using FastRWeb, it's much more
> efficient and has a lot of advantages (allows pre-loading of data and
code,
> supports parallel connections etc.).
>
> See
> http://rforge.net/FastRWeb
> and
> https://www.urbanek.info/research/pub/urbanek-iasc08.pdf
>
> We use it heavily internally for a lot of things we do, so it's definitely
a very
> active project (in fact I know about several people using it externally as
well).
> In case you get convinced that this is a good option, please feel free to
> contact me if you have any questions and need any help.
>
> Cheers,
> Simon
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
__
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https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question about Rweb
Hi,
On 11-10-05 01:00 PM, Ted Byers wrote:
Hi Simon,
Any chance of getting step by instructions on setting it up to work with a
web server like Apache's httpd server (I have Apache's web server running,
actually a couple instances on different ports, and I do all my CGI
programming using Perl)?
I am not so much looking to provide a web interface for working with R, but
rather want to write CGI programs that use R for specific analyses and
graphics. I was considering writing my R scripts as usual (using the
capabilities of QRMlib and RQuantLib, in particular), and have them invoked
by a cgi script written in perl. But your description suggests it can be
made faster. Each package I looked at for doing this was interesting, but I
always got stuck at the point of figuring out how to get Apache's httpd
server to run my R scripts. Your description suggests that a request
requiring R can be just passed onto Rserve, but how does one set that up;
i.e. to pass the request arguments through to the R script, and to tell
Rserve which R script to use?
Any insights on setting this up would be appreciated.
On http://rforge.net/FastRWeb/files/, I read that FastRWeb is to be
installed using "install.packages('FastRWeb',,'http://www.rforge.net/')",
The same page also shows that only the source package and the Mac binary
are available.
but that gives me the following message:
install.packages('FastRWeb',,'http://www.rforge.net/')
Installing package(s) into 'C:\Users\Ted\Documents/R/win-library/2.12'
(as 'lib' is unspecified)
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package 'FastRWeb' is not available
This was on:
R version 2.12.0 (2010-10-15)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-mingw32/x64 (64-bit)
No Windows binary.
Cheers,
H.
Thanks
Ted
-Original Message-
From: r-devel-boun...@r-project.org [mailto:r-devel-bounces@r-
project.org] On Behalf Of Simon Urbanek
Sent: October-05-11 3:06 PM
To: Tonidandel, Scott
Cc: r-devel@r-project.org
Subject: Re: [Rd] Question about Rweb
On Oct 5, 2011, at 2:16 PM, Tonidandel, Scott wrote:
Greetings,
I am working on creating an interactive website that will generate
R-code
[snip]
I may be biased, but I would recommend using FastRWeb, it's much more
efficient and has a lot of advantages (allows pre-loading of data and
code,
supports parallel connections etc.).
See
http://rforge.net/FastRWeb
and
https://www.urbanek.info/research/pub/urbanek-iasc08.pdf
We use it heavily internally for a lot of things we do, so it's definitely
a very
active project (in fact I know about several people using it externally as
well).
In case you get convinced that this is a good option, please feel free to
contact me if you have any questions and need any help.
Cheers,
Simon
__
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https://stat.ethz.ch/mailman/listinfo/r-devel
__
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
__
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Re: [Rd] Question about Rweb
Ted,
On Oct 5, 2011, at 4:00 PM, Ted Byers wrote:
> Hi Simon,
>
> Any chance of getting step by instructions on setting it up to work with a
> web server like Apache's httpd server (I have Apache's web server running,
> actually a couple instances on different ports, and I do all my CGI
> programming using Perl)?
>
The setup is really easy (it supports either CGI or PHP), but you're on the
wrong platform :P see below.
> I am not so much looking to provide a web interface for working with R, but
> rather want to write CGI programs that use R for specific analyses and
> graphics. I was considering writing my R scripts as usual (using the
> capabilities of QRMlib and RQuantLib, in particular), and have them invoked
> by a cgi script written in perl. But your description suggests it can be
> made faster. Each package I looked at for doing this was interesting, but I
> always got stuck at the point of figuring out how to get Apache's httpd
> server to run my R scripts. Your description suggests that a request
> requiring R can be just passed onto Rserve, but how does one set that up;
> i.e. to pass the request arguments through to the R script, and to tell
> Rserve which R script to use?
>
> Any insights on setting this up would be appreciated.
>
> On http://rforge.net/FastRWeb/files/, I read that FastRWeb is to be
> installed using "install.packages('FastRWeb',,'http://www.rforge.net/')",
> but that gives me the following message:
>
>> install.packages('FastRWeb',,'http://www.rforge.net/')
> Installing package(s) into 'C:\Users\Ted\Documents/R/win-library/2.12'
> (as 'lib' is unspecified)
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
> package 'FastRWeb' is not available
>>
>
> This was on:
>
> R version 2.12.0 (2010-10-15)
> Copyright (C) 2010 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
Well, technically, you can run it on Windows, but I would not recommend it.
Windows is a really bad server platform, especially with R (no fork, no
parallel connections, no unix sockets ...).
The standard configuration in FastRWeb assumes a unix server (the more common
case) and it really consists of install.packages() and then copying Rcgi from
the cgi-bin directory of the installed FastRWeb package to your web server's
cgi-bin and starting Rserve (via /var/FastRWeb/code/start). Alternatively, you
can use the PHP client from Rserve instead of CGI.
If you really want to use Windows, I have fixed the Windows build so it should
work, but you'll have to configure it by hand -- but as I said, I strongly
discourage the use of Windows for any R-related server activities - there are
too many security implications and it's far less efficient.
Cheers,
Simon
> Thanks
>
> Ted
>
>
>> -Original Message-
>> From: r-devel-boun...@r-project.org [mailto:r-devel-bounces@r-
>> project.org] On Behalf Of Simon Urbanek
>> Sent: October-05-11 3:06 PM
>> To: Tonidandel, Scott
>> Cc: r-devel@r-project.org
>> Subject: Re: [Rd] Question about Rweb
>>
>>
>> On Oct 5, 2011, at 2:16 PM, Tonidandel, Scott wrote:
>>
>>> Greetings,
>>>
>>> I am working on creating an interactive website that will generate
> R-code
>> [snip]
>> I may be biased, but I would recommend using FastRWeb, it's much more
>> efficient and has a lot of advantages (allows pre-loading of data and
> code,
>> supports parallel connections etc.).
>>
>> See
>> http://rforge.net/FastRWeb
>> and
>> https://www.urbanek.info/research/pub/urbanek-iasc08.pdf
>>
>> We use it heavily internally for a lot of things we do, so it's definitely
> a very
>> active project (in fact I know about several people using it externally as
> well).
>> In case you get convinced that this is a good option, please feel free to
>> contact me if you have any questions and need any help.
>>
>> Cheers,
>> Simon
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question about Rweb
Hi Simon,
> -Original Message-
> From: Simon Urbanek [mailto:simon.urba...@r-project.org]
> Sent: October-05-11 5:07 PM
> To: Ted Byers
> Cc: 'Tonidandel, Scott'; r-devel@r-project.org
> Subject: Re: [Rd] Question about Rweb
>
> Ted,
>
> On Oct 5, 2011, at 4:00 PM, Ted Byers wrote:
>
> > Hi Simon,
> >
> > Any chance of getting step by instructions on setting it up to work
> > with a web server like Apache's httpd server (I have Apache's web
> > server running, actually a couple instances on different ports, and I
> > do all my CGI programming using Perl)?
> >
>
> The setup is really easy (it supports either CGI or PHP), but you're on
the
> wrong platform :P see below.
>
Actually, I haven't had much choice with regard to platform. I presently
work in a Windows only shop.
> [snip]
> > On http://rforge.net/FastRWeb/files/, I read that FastRWeb is to be
> > installed using
> > "install.packages('FastRWeb',,'http://www.rforge.net/')",
> > but that gives me the following message:
> >
> >> install.packages('FastRWeb',,'http://www.rforge.net/')
> > Installing package(s) into 'C:\Users\Ted\Documents/R/win-library/2.12'
> > (as 'lib' is unspecified)
> > Warning message:
> > In getDependencies(pkgs, dependencies, available, lib) :
> > package 'FastRWeb' is not available
> >>
> >
> > This was on:
> >
> > R version 2.12.0 (2010-10-15)
> > Copyright (C) 2010 The R Foundation for Statistical Computing ISBN
> > 3-900051-07-0
> > Platform: x86_64-pc-mingw32/x64 (64-bit)
> >
>
> Well, technically, you can run it on Windows, but I would not recommend
it.
> Windows is a really bad server platform, especially with R (no fork, no
parallel
> connections, no unix sockets ...).
>
Yes, I know it's limitations, but at present I have no option but to deal
with it.
> The standard configuration in FastRWeb assumes a unix server (the more
> common case) and it really consists of install.packages() and then copying
> Rcgi from the cgi-bin directory of the installed FastRWeb package to your
> web server's cgi-bin and starting Rserve (via /var/FastRWeb/code/start).
> Alternatively, you can use the PHP client from Rserve instead of CGI.
>
> If you really want to use Windows, I have fixed the Windows build so it
> should work, but you'll have to configure it by hand -- but as I said, I
strongly
> discourage the use of Windows for any R-related server activities - there
are
> too many security implications and it's far less efficient.
>
;-)
I have the machine that will be doing the real work behind several layers of
security.
How do I modify the command
""install.packages('FastRWeb',,'http://www.rforge.net/')"," so that it uses
RTools to build it for Windows?
Thanks
Ted
PS: I may have a machine soon to set up with Linux (the OS on that machine
crashed, got corrupted, so I'll have to wipe its disk and install de novo.
Is there a preferred distribution of Linux you can recommend (one for which
I can download DVD disk images so I can burn install DVDs on one of my
Windows boxes, or are they all pretty much the same?
__
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Re: [Rd] suppressing stderr output from system() calls
Thanks Martin, Simon and Brian,
They're all good suggestions for code that I write, however how can I suppress
stderr from pre-existing code. For instance, install.packages has 3 system
calls.
Perhaps a better worded question would be: how can I redirect the output of
this command:
install.packages("MASS", lib="/tmp", type="source")
As I mentioned before, sink doesn't do the trick
con <- file("stderr.txt", "w")
sink(con, type="message")
install.packages("MASS", lib="/tmp", type="source")
sink(NULL, type="message")
close(con)
Martin will be familiar with the Bioconductor package oligo, which likes to
download pd info package on the fly and install them - the embedded call to
download.file is noisy, as is the resulting installation of said package.
Short of rewriting install.package & all code which has embedded
install.packages calls, are there any other ways?
@Brian, thanks for the pointer to the news article on connections - I did learn
something there
cheers,
Mark
On 06/10/2011, at 3:59 AM, Martin Morgan wrote:
> On 10/05/2011 02:36 AM, Mark Cowley wrote:
>> Dear list,
>
>> I'm trying to suppress/redirect/squash the output from commands like
>> install.packages, or download.file. The problem is that none of:
>> sink(..., type="message"), sink(..., type="output"), capture.output,
>> suppressMessages are quite doing the trick. Output gets written to
>> the stderr stream, despite any combination of the above suppression
>> commands.
>
> Hi Mark --
>
> For download.file, the argument quiet=TRUE suppresses output messages; this
> option can be used in ... for install.packages, too (according to the
> documentation). This is good enough to quieten the regular chatter on a
> successful operation. To catch errors and suppress warnings also, maybe a
> construct like
>
> url = "http://r-project.org/doesnotexist";
> tryCatch(suppressWarnings(
>capture.output(download.file(url, tempfile(), quiet=TRUE))),
>error=function(...) {})
>
> Martin
>
>> According to ?sink:
>> Messages sent to ‘stderr()’ (including those from ‘message’, ‘warning’ and
>> ‘stop’) can be diverted by ‘sink(type = "message")’ (see below).
>>
>> I'm pretty sure it's the system(), or .Internal() calls which are the
>> culprit, which currently write the majority (all?) of their output to the
>> stderr stream.
>>
>> Simple example:
>> con<- file("stderr.txt", "w")
>> sink(con, type="message")
>> system("ls")
>> sink(NULL, type="message")
>> close(con)
>> # instead of the output going to stderr.txt, it gets printed to the console.
>>
>> # no good either
>> capture.output(system("ls"))
>> character(0)
>>
>> This is an issue, since i'm writing GenePattern modules to run R code, and
>> if anything is written to stderr, then the job gets hit with a 'job failed'
>> status, when all that might have happened is an R package got installed, or
>> a file got downloaded via FTP.
>>
>> Any ideas? Can system() and .Internal() output be redirected to stdout?
>>
>> cheers,
>> Mark
>>
>>
>> sessionInfo()
>> R version 2.13.1 (2011-07-08)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>
>> locale:
>> [1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>>
>>
>>
>>
>> -
>> Mark Cowley, PhD
>>
>> Pancreatic Cancer Program | Peter Wills Bioinformatics Centre
>> Garvan Institute of Medical Research, Sydney, Australia
>> -
>>
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
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Re: [Rd] Question about Rweb
Ted,
On Oct 5, 2011, at 6:06 PM, Ted Byers wrote:
> Hi Simon,
>
>> -Original Message-
>> From: Simon Urbanek [mailto:simon.urba...@r-project.org]
>> Sent: October-05-11 5:07 PM
>> To: Ted Byers
>> Cc: 'Tonidandel, Scott'; r-devel@r-project.org
>> Subject: Re: [Rd] Question about Rweb
>>
>> Ted,
>>
>> On Oct 5, 2011, at 4:00 PM, Ted Byers wrote:
>>
>>> Hi Simon,
>>>
>>> Any chance of getting step by instructions on setting it up to work
>>> with a web server like Apache's httpd server (I have Apache's web
>>> server running, actually a couple instances on different ports, and I
>>> do all my CGI programming using Perl)?
>>>
>>
>> The setup is really easy (it supports either CGI or PHP), but you're on
> the
>> wrong platform :P see below.
>>
> Actually, I haven't had much choice with regard to platform. I presently
> work in a Windows only shop.
>
>> [snip]
>>> On http://rforge.net/FastRWeb/files/, I read that FastRWeb is to be
>>> installed using
>>> "install.packages('FastRWeb',,'http://www.rforge.net/')",
>>> but that gives me the following message:
>>>
install.packages('FastRWeb',,'http://www.rforge.net/')
>>> Installing package(s) into 'C:\Users\Ted\Documents/R/win-library/2.12'
>>> (as 'lib' is unspecified)
>>> Warning message:
>>> In getDependencies(pkgs, dependencies, available, lib) :
>>> package 'FastRWeb' is not available
>>>
>>> This was on:
>>>
>>> R version 2.12.0 (2010-10-15)
>>> Copyright (C) 2010 The R Foundation for Statistical Computing ISBN
>>> 3-900051-07-0
>>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>>
>>
>> Well, technically, you can run it on Windows, but I would not recommend
> it.
>> Windows is a really bad server platform, especially with R (no fork, no
> parallel
>> connections, no unix sockets ...).
>>
> Yes, I know it's limitations, but at present I have no option but to deal
> with it.
>
>> The standard configuration in FastRWeb assumes a unix server (the more
>> common case) and it really consists of install.packages() and then copying
>> Rcgi from the cgi-bin directory of the installed FastRWeb package to your
>> web server's cgi-bin and starting Rserve (via /var/FastRWeb/code/start).
>> Alternatively, you can use the PHP client from Rserve instead of CGI.
>>
>> If you really want to use Windows, I have fixed the Windows build so it
>> should work, but you'll have to configure it by hand -- but as I said, I
> strongly
>> discourage the use of Windows for any R-related server activities - there
> are
>> too many security implications and it's far less efficient.
>>
> ;-)
>
> I have the machine that will be doing the real work behind several layers of
> security.
>
> How do I modify the command
> ""install.packages('FastRWeb',,'http://www.rforge.net/')"," so that it uses
> RTools to build it for Windows?
>
Just re-run it, I have fixed the Windows build so I think the binary should be
there. I had to run after I sent the e-mail so I didn't get to check one point,
though: the Rcgi.exe binary may be either 32-bit or 64-bit which in the latter
case may be a problem on 32-bit machine, but I see you have 64-bit Windows so
you should be fine in either case.
However, you'll need to setup the FastRWeb tree. I did not change the defaults
so it still expects things to live in /var/FastRWeb by default, so if you have
Rtools, you may succeed in running the install.sh script (in the installed
FastRWeb package -- see system.file("install.sh",package="FastRWeb")) that was
designed from unix even on Windows. The only difference is that you will want
to remove the "socket ..." line from rserve.conf since Windows doesn't support
it. If you don't have Rtools, you can simply start Rserve by hand - and then
read Rserve docs about the options you have for pre-loading of packages and
code. I didn't actually test the Windows setup with a web server so feedback is
welcome.
> PS: I may have a machine soon to set up with Linux (the OS on that machine
> crashed, got corrupted, so I'll have to wipe its disk and install de novo.
> Is there a preferred distribution of Linux you can recommend (one for which
> I can download DVD disk images so I can burn install DVDs on one of my
> Windows boxes, or are they all pretty much the same?
>
Ubuntu is currently the most popular and works out of the box on most machines.
Personally, I prefer Debian on servers, but there is not a big difference.
Cheers,
Simon
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