Re: [Rd] Bug in R -e "command"
Hi Dirk, all:
your answer prompted me to look in another place, and yes I need to
withdraw the bug report: it was a problem on our side.
Thanks,
Oleg
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3803
oskl...@maninvestments.com
> -Original Message-
> From: Dirk Eddelbuettel [mailto:e...@debian.org]
> Sent: 07 May 2010 15:43
> To: Sklyar, Oleg (London)
> Cc: r-devel@r-project.org
> Subject: Re: [Rd] Bug in R -e "command"
>
>
> On 7 May 2010 at 15:23, Sklyar, Oleg (London) wrote:
> | Hi all:
> |
> | since about a month we encountered a problem with R -e
> command: spaces
> | in the "command" of R -e "command" are no more tolerated. This same
> | issue affects 2.11 patched (05-05-2010), 2.10.1, and
> current devel (at
> | least the one of two weeks ago).
> |
> | (I skip the mid of the printouts, replaced with ...)
> |
> | * R -e "message('aaa aaa')"
> | ARGUMENT 'aaa')' __ignored__
>
> Isn't that a shell quoting issue? I tend to keep the
> apostrophe on the
> outside and the double-quote on the inside:
>
> e...@ron:~> R --slave -e 'message("aaa aaa")'
> aaa aaa
> e...@ron:~> r -e 'message("aaa aaa")'
> aaa aaa
> e...@ron:~> Rscript -e 'message("aaa aaa")'
> aaa aaa
>
> but also note
>
> e...@ron:~> R --slave -e "message(\"aaa aaa\")"
> aaa aaa
> e...@ron:~> R --slave -e "message('aaa aaa')"
> aaa aaa
> e...@ron:~>
>
> so I can't even replicate your issue. What what it's worth,
> the cut&paste
> above came from M-x shell inside Emacs.
>
> e...@ron:~> dpkg -l r-base-core littler bash emacs23 | tail -4
> ii bash 4.1-3 The GNU Bourne Again SHell
> ii emacs2323.1+1-5 The GNU Emacs editor (with
> GTK+ user interfa
> ii littler0.1.3-1GNU R scripting and
> command-line front-end
> ii r-base-core2.11.0-1 GNU R core of statistical
> computation and gr
> e...@ron:~>
>
> |
> |
> | R version 2.11.0 Patched (2010-05-05 r51914)
> | Copyright (C) 2010 The R Foundation for Statistical Computing
> | ...
> |
> | > message('aaa
> | +
> | +
> |
> | * /releases/R/2.10/bin/R -e "message('aaa aaa')"
> | ARGUMENT 'aaa')' __ignored__
> |
> |
> | R version 2.10.1 Patched (2010-03-27 r51474)
> | Copyright (C) 2010 The R Foundation for Statistical Computing
> | ...
> |
> | > message('aaa
> | +
> | +
> |
> | WORKING OLD VERSION:
> |
> | * /share/R/20090611/bin/R -e "message('aaa aaa')"
> |
> | R version 2.9.0 (2009-04-17)
> | Copyright (C) 2009 The R Foundation for Statistical Computing
> | ...
> |
> | > message('aaa aaa')
> | aaa aaa
> | >
> | >
> |
> |
> | Dr Oleg Sklyar
> | Research Technologist
> | AHL / Man Investments Ltd
> | +44 (0)20 7144 3803
> | oskl...@maninvestments.comno more
> |
> |
> **
> | Please consider the environment before printing this email
> or its attachments.
> | The contents of this email are for the named addressees
> ...{{dropped:19}}
> |
> | __
> | R-devel@r-project.org mailing list
> | https://stat.ethz.ch/mailman/listinfo/r-devel
>
> --
> Regards, Dirk
>
**
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[Rd] Use of R in C#
I have a C# program that requires the run of a logistic regression. I have
downloaded the R 2.11 package, and have added the following references to my
code:
STATCONNECTORCLNTLib;
StatConnectorCommonLib;
STATCONNECTORSRVLib;
In my code I have:
StatConnector scs = new STATCONNECTORSRVLib.StatConnectorClass();
scs.Init("R");
The init step returns the below error which seems to indicate a connection
failure.
System.Runtime.InteropServices.COMException was unhandled
Message="Exception from HRESULT: 0x80040013"
Source="Interop.STATCONNECTORSRVLib"
ErrorCode=-2147221485
Any ideas?
Jeff Abrams
Research Engineer
Auction Analytics, Microsoft
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[Rd] update.packages fails with directory not found
Windows XP. I have just updated to R 2.11.0 and then run update.packages. In the series of updates, a few will succeed, then I get a failure like package 'mvtnorm' successfully unpacked and MD5 sums checked package 'party' successfully unpacked and MD5 sums checked package 'PBSmodelling' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]="c:\Program Files\R\Library/PBSmodelling": The system cannot find the file specified Indeed, the path is missing, though it was there when I issued the update.packages command. ??? -- Mike Prager, NC, USA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] update.packages fails with directory not found
Mike Prager wrote: Windows XP. I have just updated to R 2.11.0 and then run update.packages. In the series of updates, a few will succeed, then I get a failure like package 'mvtnorm' successfully unpacked and MD5 sums checked package 'party' successfully unpacked and MD5 sums checked package 'PBSmodelling' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]="c:\Program Files\R\Library/PBSmodelling": The system cannot find the file specified Is that a cut and paste of the error message? Normally R would double the backslashes when displaying a string, so it looks as though you've somehow got a path containing the control characters \P, \R, and \L. Did you set the lib.loc argument when you called update.packages? Duncan Murdoch Indeed, the path is missing, though it was there when I issued the update.packages command. ??? -- Mike Prager, NC, USA __ 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] Use of R in C#
This is not about R, but about the StatConnector project which has its
own mailing lists.
On Fri, 7 May 2010, Jeff Abrams wrote:
I have a C# program that requires the run of a logistic regression. I have
downloaded the R 2.11 package, and have added the following references to my
code:
STATCONNECTORCLNTLib;
StatConnectorCommonLib;
STATCONNECTORSRVLib;
In my code I have:
StatConnector scs = new STATCONNECTORSRVLib.StatConnectorClass();
scs.Init("R");
The init step returns the below error which seems to indicate a connection
failure.
System.Runtime.InteropServices.COMException was unhandled
Message="Exception from HRESULT: 0x80040013"
Source="Interop.STATCONNECTORSRVLib"
ErrorCode=-2147221485
Any ideas?
Jeff Abrams
Research Engineer
Auction Analytics, Microsoft
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--
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
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Re: [Rd] update.packages fails with directory not found
On Mon, 10 May 2010 06:33:54 -0400, Duncan Murdoch wrote: >Mike Prager wrote: >> Windows XP. I have just updated to R 2.11.0 and then run >> update.packages. In the series of updates, a few will succeed, then I >> get a failure like >> >> >> package 'mvtnorm' successfully unpacked and MD5 sums checked >> package 'party' successfully unpacked and MD5 sums checked >> package 'PBSmodelling' successfully unpacked and MD5 sums checked >> Error in normalizePath(path) : >> path[1]="c:\Program Files\R\Library/PBSmodelling": The system cannot >> find the file specified >> > >Is that a cut and paste of the error message? Normally R would double >the backslashes when displaying a string, so it looks as though you've >somehow got a path containing the control characters \P, \R, and \L. >Did you set the lib.loc argument when you called update.packages? Thank you! Yes, it's cut and paste. I did not set lib.loc in the call (made through the Rgui.exe menu system), but I have the library location defined in the environment: R_LIBS=c:/Program Files/R/Library I've been using this approach for several years, and it's worked without problem until now. MHP >> >> Indeed, the path is missing, though it was there when I issued the >> update.packages command. >> __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] update.packages fails with directory not found
On 10/05/2010 8:28 AM, Mike Prager wrote: On Mon, 10 May 2010 06:33:54 -0400, Duncan Murdoch wrote: >Mike Prager wrote: >> Windows XP. I have just updated to R 2.11.0 and then run >> update.packages. In the series of updates, a few will succeed, then I >> get a failure like >> >> >> package 'mvtnorm' successfully unpacked and MD5 sums checked >> package 'party' successfully unpacked and MD5 sums checked >> package 'PBSmodelling' successfully unpacked and MD5 sums checked >> Error in normalizePath(path) : >> path[1]="c:\Program Files\R\Library/PBSmodelling": The system cannot >> find the file specified >> > >Is that a cut and paste of the error message? Normally R would double >the backslashes when displaying a string, so it looks as though you've >somehow got a path containing the control characters \P, \R, and \L. >Did you set the lib.loc argument when you called update.packages? Thank you! Yes, it's cut and paste. I did not set lib.loc in the call (made through the Rgui.exe menu system), but I have the library location defined in the environment: R_LIBS=c:/Program Files/R/Library I've been using this approach for several years, and it's worked without problem until now. I can't seem to reproduce this. If it happens reproducibly on your system, could you please do the following: print the result of installed.packages()["PBSmodelling",], .libPaths() and sessionInfo()? A possible workaround is to get the names of all of your packages in the Library folder and install them, rather than using the update.packages() function. This may fail if some of them aren't on CRAN or the other repositories. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] update.packages fails with directory not found
On Mon, 10 May 2010, Duncan Murdoch wrote: On 10/05/2010 8:28 AM, Mike Prager wrote: On Mon, 10 May 2010 06:33:54 -0400, Duncan Murdoch wrote: >Mike Prager wrote: >> Windows XP. I have just updated to R 2.11.0 and then run >> update.packages. In the series of updates, a few will succeed, then I >> get a failure like >> >> >> package 'mvtnorm' successfully unpacked and MD5 sums checked >> package 'party' successfully unpacked and MD5 sums checked >> package 'PBSmodelling' successfully unpacked and MD5 sums checked >> Error in normalizePath(path) : >> path[1]="c:\Program Files\R\Library/PBSmodelling": The system cannot >> find the file specified >> > >Is that a cut and paste of the error message? Normally R would double >the backslashes when displaying a string, so it looks as though you've >somehow got a path containing the control characters \P, \R, and \L. >Did you set the lib.loc argument when you called update.packages? Thank you! Yes, it's cut and paste. The message coming from C (do_normalizepath) not R. I did not set lib.loc in the call (made through the Rgui.exe menu system), but I have the library location defined in the environment: R_LIBS=c:/Program Files/R/Library I've been using this approach for several years, and it's worked without problem until now. I can't seem to reproduce this. If it happens reproducibly on your system, could you please do the following: print the result of installed.packages()["PBSmodelling",], .libPaths() and sessionInfo()? A possible workaround is to get the names of all of your packages in the Library folder and install them, rather than using the update.packages() function. This may fail if some of them aren't on CRAN or the other repositories. I think he has a permissions issue on that directory. I'd remove it manually after a reboot, then re-install. (Reboot because it may be open in some crashed process.) I've seen this in Vista/7 several times, but of course permissions are more of a hindrance there. -- 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] update.packages fails with directory not found
Someone once suggested this error happened was due to the Windows 'Indexing Service' (sp?) delaying the commital of a request to rename a directory (so a subsequent request to use the renamed directory failed). Was the indexing service running when this happened? Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com > -Original Message- > From: r-devel-boun...@r-project.org > [mailto:r-devel-boun...@r-project.org] On Behalf Of Mike Prager > Sent: Monday, May 10, 2010 5:28 AM > To: r-de...@stat.math.ethz.ch > Subject: Re: [Rd] update.packages fails with directory not found > > On Mon, 10 May 2010 06:33:54 -0400, Duncan Murdoch > wrote: > > >Mike Prager wrote: > >> Windows XP. I have just updated to R 2.11.0 and then run > >> update.packages. In the series of updates, a few will > succeed, then I > >> get a failure like > >> > >> > >> package 'mvtnorm' successfully unpacked and MD5 sums checked > >> package 'party' successfully unpacked and MD5 sums checked > >> package 'PBSmodelling' successfully unpacked and MD5 sums checked > >> Error in normalizePath(path) : > >> path[1]="c:\Program Files\R\Library/PBSmodelling": The > system cannot > >> find the file specified > >> > > > >Is that a cut and paste of the error message? Normally R > would double > >the backslashes when displaying a string, so it looks as > though you've > >somehow got a path containing the control characters \P, \R, > and \L. > >Did you set the lib.loc argument when you called update.packages? > > Thank you! Yes, it's cut and paste. I did not set lib.loc in the > call (made through the Rgui.exe menu system), but I have the library > location defined in the environment: > > R_LIBS=c:/Program Files/R/Library > > I've been using this approach for several years, and it's worked > without problem until now. > > MHP > > >> > >> Indeed, the path is missing, though it was there when I issued the > >> update.packages command. > >> > > __ > 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] update.packages fails with directory not found
[New material at end] Duncan Murdoch wrote on 5/10/2010 9:33 AM: On 10/05/2010 8:28 AM, Mike Prager wrote: On Mon, 10 May 2010 06:33:54 -0400, Duncan Murdoch wrote: >Mike Prager wrote: >> Windows XP. I have just updated to R 2.11.0 and then run >> update.packages. In the series of updates, a few will succeed, then I >> get a failure like >> >> >> package 'mvtnorm' successfully unpacked and MD5 sums checked >> package 'party' successfully unpacked and MD5 sums checked >> package 'PBSmodelling' successfully unpacked and MD5 sums checked >> Error in normalizePath(path) : >> path[1]="c:\Program Files\R\Library/PBSmodelling": The system cannot >> find the file specified >> > >Is that a cut and paste of the error message? Normally R would double >the backslashes when displaying a string, so it looks as though you've >somehow got a path containing the control characters \P, \R, and \L. >Did you set the lib.loc argument when you called update.packages? Thank you! Yes, it's cut and paste. I did not set lib.loc in the call (made through the Rgui.exe menu system), but I have the library location defined in the environment: R_LIBS=c:/Program Files/R/Library I've been using this approach for several years, and it's worked without problem until now. I can't seem to reproduce this. If it happens reproducibly on your system, could you please do the following: print the result of installed.packages()["PBSmodelling",], .libPaths() and sessionInfo()? A possible workaround is to get the names of all of your packages in the Library folder and install them, rather than using the update.packages() function. This may fail if some of them aren't on CRAN or the other repositories. Duncan, thanks again. At the end of this message is a session transcript with the things you asked. Rather than edit out something that might prove important, I am sending the entire transcript. Yes, installing rather than updating is a workaround. One thing in the session log requires explanation. The two directories under .libPaths point to the same place. This is because drive D: is an alias, generated with the "subst" Windows command, for "c:/Program Files/". I had been specifying environment variable R_LIBS=d:/R/Library but to eliminate that as a potential cause of the problem, I changed it to R_LIBS=c:/Program Files/R/Library with no change in symptoms. I note that (as another user with the same issue pointed out to me in an email) there are new directories filexx (where the xx are hex digits) in the library location. These seem to be from the failed updates. For example, file1eb26e9 has one subdirectory, PBSmodeling. Something different now from when updates all succeeded in the past is that I have a large upload (to Amazon S3) running in the background. I can't guess whether this is part of the issue. A time-out on the directory rename would be a wild guess. MHP --- session transcript follows - R version 2.11.0 (2010-04-22) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. Loading required package: survival Loading required package: stats Loading required package: utils Loading required package: graphics Loading required package: splines Attaching package: 'Hmisc' The following object(s) are masked from 'package:survival': untangle.specials The following object(s) are masked from 'package:base': format.pval, round.POSIXt, trunc.POSIXt, units [Previously saved workspace restored] > update.packages(ask='graphics') trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.11/rJava_0.8-4.zip' Content type 'application/zip' length 571732 bytes (558 Kb) opened URL downloaded 558 Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.11/SparseM_0.85.zip' Content type 'application/zip' length 927538 bytes (905 Kb) opened URL downloaded 905 Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.11/strucchange_1.4-0.zip' Content type 'application/zip' length 968725 bytes (946 Kb) opened URL downloaded 946 Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.11/svMisc_0.9-57.zip' Content type 'application/zip' length 134502 bytes (131 Kb) opened URL downloaded 131 Kb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.11/vcd_1.2-8.zip' Content type 'application/zip' length 1179976 bytes (1.1 Mb) opened URL downloaded 1.1 Mb trying URL 'http://cran.wustl.edu/bin/windows/contrib/2.
[Rd] Build R static
Hi, I am having trouble building R static on Solaris 5.10. I have a
requirement to run R within a specific user account on Solaris 5.10 and I do
not have access to compilers and or shared libraries on the target machine. I
thought I could build R static ( I've build it locally on Solaris with shared
libraries) and just ftp the build to the target Solaris box. Can any help with
what ./configure & Make flags need to be set for this, assuming it is possible?
Here is what my currently built ./bin/exec/R executable is using.
$ ldd R
libRblas.so => (file not found)
libg2c.so.0 => /usr/local/lib/libg2c.so.0
libm.so.2 => /usr/lib/libm.so.2
libreadline.so.6 => /usr/local/lib/libreadline.so.6
libcurses.so.1 =>/usr/lib/libcurses.so.1
libnsl.so.1 => /usr/lib/libnsl.so.1
libsocket.so.1 =>/usr/lib/libsocket.so.1
libdl.so.1 =>/usr/lib/libdl.so.1
libiconv.so.2 => /usr/local/lib/libiconv.so.2
libicuuc.so.3 => /usr/lib/libicuuc.so.3
libicui18n.so.3 => /usr/lib/libicui18n.so.3
libc.so.1 => /usr/lib/libc.so.1
libgcc_s.so.1 => /usr/local/lib/libgcc_s.so.1
libmp.so.2 =>/usr/lib/libmp.so.2
libmd5.so.1 => /usr/lib/libmd5.so.1
libscf.so.1 => /usr/lib/libscf.so.1
libicudata.so.3 => /usr/lib/libicudata.so.3
libpthread.so.1 => /usr/lib/libpthread.so.1
libCrun.so.1 => /usr/lib/libCrun.so.1
libdoor.so.1 => /usr/lib/libdoor.so.1
libuutil.so.1 => /usr/lib/libuutil.so.1
/platform/SUNW,Sun-Fire-280R/lib/libc_psr.so.1
/platform/SUNW,Sun-Fire-280R/lib/libmd5_psr.so.1
Thanks for your help,
Alex
//
// Alex Bryant
// Software Developer
// Integrated Clinical Systems, Inc.
// 908-996-7208
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Re: [Rd] update.packages fails with directory not found
Bill, Not in my case. The Indexing Service is disabled on my PC. MHP William Dunlap wrote on 5/10/2010 10:42 AM: Someone once suggested this error happened was due to the Windows 'Indexing Service' (sp?) delaying the commital of a request to rename a directory (so a subsequent request to use the renamed directory failed). Was the indexing service running when this happened? package 'PBSmodelling' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]="c:\Program Files\R\Library/PBSmodelling": The system cannot find the file specified __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
