Re: [Rd] warning upon automatic close of connection
Gabor Grothendieck [EMAIL PROTECTED] writes: I noticed that under R 2.6.0 there is a warning about closing the connection in the code from this post: https://stat.ethz.ch/pipermail/r-help/2007-September/140601.html which is evidently related to the following from the NEWS file: o Connections will be closed if there is no R object referring to them. A warning is issued if this is done, either at garbage collection or if all the connection slots are in use. If we use read.table directly it still happens: # use Lines and Lines2 from cited post library(zoo) DF1 - read.table(textConnection(Lines), header = TRUE) DF2 - read.table(textConnection(Lines2), header = TRUE) z1 - zoo(as.matrix(DF1[-1]), as.Date(DF1[,1], %d/%m/%Y)) z2 - zoo(as.matrix(DF2[-1]), as.Date(DF2[,1], %d/%m/%Y)) both - merge(z1, z2) plot(na.approx(both)) R.version.string # Vista [1] R version 2.6.0 alpha (2007-09-06 r42791) Is this annoying warning really necessary? I assume we can get rid of it by explicitly naming and closing the connections but surely there should be a way to avoid the warning without going to those lengths. Up until the change you mention above it really was necessary to name and close all connections. Short scripts run in fresh R sessions may not have had problems with code like you have written above, but longer programs or shorter ones run in a long running R session would run out of connections. Now that connections have weak reference semantics, one can ask whether this behavior should be standard and no warning issued. I would have thought that read.table opens the connection then it would close it itself so no warning would need to be generated. In your example, read.table is _not_ opening the connection. You are passing an open connection which has no symbol bound to it: foo = c = textConnection(foo) c descriptionclass mode text foo textConnection r text opened can readcan write openedyes no But I think passing a closed connection would cause the same sort of issue. It seems that there are two notions of closing a connection: (i) close as the opposite of open, and (ii) clean up the entire connection object. I haven't looked closely at the code here, so I could be wrong, but I'm basing this guess on the following: file(foo) description classmodetext openedcan read foo file r textclosed yes can write yes ## start new R session for (i in 1:75) file(foo) gc() warnings()[1:3] gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 149603 4.0 35 9.4 35 9.4 Vcells 101924 0.8 786432 6.0 486908 3.8 There were 50 or more warnings (use warnings() to see the first 50) warnings()[1:3] $`closing unused connection 76 (foo)` NULL $`closing unused connection 75 (foo)` NULL $`closing unused connection 74 (foo)` NULL -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Font problem (PR#9906)
Full_Name: M. Muñoz Márquez Version: 2.3.1 OS: Ubuntu Submission from: (NULL) (150.214.231.66) Here is the reply to the edit command using gnome edit(data.frame()) Erro en dataentry(datalist, modes) : invalid device Además: Warning message: unable to create fontset -*-fixed-medium-r-normal--13-*-*-*-*-*-*-* Sys.getlocale() [1] LC_CTYPE=es_ES.UTF-8;LC_NUMERIC=C;LC_TIME=es_ES.UTF-8;LC_COLLATE=es_ES.UTF-8;LC_MONETARY=es_ES.UTF-8;LC_MESSAGES=es_ES.UTF-8;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=C;LC_IDENTIFICATION=C Under kde it works fine. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Font problem (PR#9906)
OS: Ubuntu 7.10 Gutsy Gibbon GNOME: 2.19.92 (build: 04/09/07) Linux 2.6.22-10-generic #1 SMP x86_64 GNU/Linux It works perfectly fine here with 2 recent versions of R (errors because dialogues closed without any data): * ~: Rd R version 2.7.0 Under development (unstable) (2007-09-06 r42789) edit(data.frame()) Error in max(lengths) : invalid 'type' (list) of argument * ~: R R version 2.5.1 (2007-06-27) edit(data.frame()) Error in max(..., na.rm = na.rm) : invalid 'type' (list) of argument On Wed, 2007-09-12 at 16:52 +0200, [EMAIL PROTECTED] wrote: Full_Name: M. Muñoz Márquez Version: 2.3.1 OS: Ubuntu Submission from: (NULL) (150.214.231.66) Here is the reply to the edit command using gnome edit(data.frame()) Erro en dataentry(datalist, modes) : invalid device Además: Warning message: unable to create fontset -*-fixed-medium-r-normal--13-*-*-*-*-*-*-* Sys.getlocale() [1] LC_CTYPE=es_ES.UTF-8;LC_NUMERIC=C;LC_TIME=es_ES.UTF-8;LC_COLLATE=es_ES.UTF-8;LC_MONETARY=es_ES.UTF-8;LC_MESSAGES=es_ES.UTF-8;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=C;LC_IDENTIFICATION=C Under kde it works fine. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Dr Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, UK * +44-1223-494466 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Font problem (PR#9906)
On Wed, Sep 12, 2007 at 04:52:19PM +0200, [EMAIL PROTECTED] wrote: Full_Name: M. Muñoz Márquez Version: 2.3.1 Note that this is over a year out of date ... OS: Ubuntu ... even though the R FAQ tells you that you can get current R versions for Ubuntu from all CRAN mirror with a simple apt-get. Submission from: (NULL) (150.214.231.66) Here is the reply to the edit command using gnome edit(data.frame()) Erro en dataentry(datalist, modes) : invalid device Además: Warning message: unable to create fontset -*-fixed-medium-r-normal--13-*-*-*-*-*-*-* Sys.getlocale() [1] LC_CTYPE=es_ES.UTF-8;LC_NUMERIC=C;LC_TIME=es_ES.UTF-8;LC_COLLATE=es_ES.UTF-8;LC_MONETARY=es_ES.UTF-8;LC_MESSAGES=es_ES.UTF-8;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=C;LC_IDENTIFICATION=C Under kde it works fine. Demonstrating that it is a local admin problem that your fonts aren't right. IIRC there was an Ubuntu issue that /etc/X11/xorg.conf ended up with a misspecified font path. FWIW, I use Section Files FontPath/usr/share/fonts/X11/misc FontPath/usr/share/fonts/X11/cyrillic FontPath/usr/share/fonts/X11/100dpi/:unscaled FontPath/usr/share/fonts/X11/75dpi/:unscaled FontPath/usr/share/fonts/X11/Type1 FontPath/usr/share/fonts/X11/100dpi FontPath/usr/share/fonts/X11/75dpi # FontPath/usr/share/X11/fonts/misc FontPath/usr/share/X11/fonts/cyrillic FontPath/usr/share/X11/fonts/100dpi/:unscaled FontPath/usr/share/X11/fonts/75dpi/:unscaled FontPath/usr/share/X11/fonts/Type1 FontPath/usr/share/X11/fonts/100dpi FontPath/usr/share/X11/fonts/75dpi FontPath/usr/share/X11/fonts/misc # path to defoma fonts FontPath/var/lib/defoma/x-ttcidfont-conf.d/dirs/TrueType EndSection Hoep this helps, Dirk __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Three out of two people have difficulties with fractions. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] installing packages (PR#9907)
Full_Name: Alexander Jerneck Version: 2.4.0 (2006-10-03) OS: Gentoo (2.6.17-custom kernel) Submission from: (NULL) (130.91.92.78) I had trouble installing R packages, either from inside R or from the commandline, with R complaining about not finding /usr/bin/pwd I have pwd in /bin/ so I created a symlink from /usr/bin/pwd to /bin/pwd and now I can install packages. I do not know where the original problem is however. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] could not find function in R CMD check [solved, but is this an R bug?]
On Wed, 2007-09-12 at 11:31 +0200, Uwe Ligges wrote:
Perhaps Namespace issues? But no further ideas. You might want to make
your package available at some URL so that people can look at it and help...
Uwe Ligges
Thanks. The problem lay elsewhere. I was able to fix it by adding
library(mspath)
to the top of the .R file in data/ that defined some data using the
package's functions In other words
---
library(mspath)
### from various papers on errors in reading fibrosis scores
rousselet.jr - readingError(c(.91, .09, 0, 0, 0,
.11, .78, .11, 0, 0,
0, .17, .75, .08, 0,
0, .06, .44, .50, 0,
0, 0, 0, .07, .93),
byrow=TRUE, nrow=5, ncol=5)
-
works as data/readingErrorData.R, but without the library() call I get
the error shown in my original message (see below). readingError() is a
function defined in my package.
Does any of this inndicate a bug or undesirable feature in R?
First, it seems a little odd that I need to include loading the library
in data that is defined in the same library. I think I've noticed
similar behavior in other places, maybe the code snippets that accompany
the documentation pages (that is, one needs library(mypackage) in order
for the snippets to check out).
Second, should R CMD check fail so completely and opaquely in this
situation?
Ross Boylan wrote:
During R CMD check I get this:
** building package indices ...
Error in eval(expr, envir, enclos) : could not find function
readingError
Execution halted
ERROR: installing package indices failed
The check aborts there. readingError is a function I just added; for
reference
setClass(readingError, contains=matrix)
readingError - function(...) new(readingError, matrix(...))
which is in readingError.R in the project's R subdirectory.
Some code in the data directory invokes readingError, and the .Rd file
includes \alias{readingError}, \alias{readingError-class},
\name{readingError-class} and an example invoking readingError.
I'm using R 2.5.1 as packaged for Debian GNU/Linux.
Does anyone have an idea what's going wrong here, or how to fix or debug
it?
The code seems to work OK when I use it from ESS.
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[Rd] trivial typo in ?strip.default
under factor.levels: specicifying __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] installing packages (PR#9907)
On Wed, 12 Sep 2007, [EMAIL PROTECTED] wrote: Full_Name: Alexander Jerneck Version: 2.4.0 (2006-10-03) OS: Gentoo (2.6.17-custom kernel) Submission from: (NULL) (130.91.92.78) I had trouble installing R packages, either from inside R or from the commandline, with R complaining about not finding /usr/bin/pwd I have pwd in /bin/ so I created a symlink from /usr/bin/pwd to /bin/pwd and now I can install packages. I do not know where the original problem is however. This is NOT A BUG. Likely, you do not have /bin on your path. Check Sys.getenv(PATH) install.packages() works fine on all my Gentoo boxes with R installed as per the instructions in $R_HOME/doc/manual/R-admin.html __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] installing packages (PR#9907)
I don't think this is a bug in R.
I believe a (not too) recent change in Gentoo removed /usr/bin/pwd so
that the only one left is /bin/pwd. R seems to remember from install
time where to find these utilities, and probably found /usr/bin/pwd when
you installed the not recent version of R. You found one workaround, and
another would be a fresh install of R.
Paul
[EMAIL PROTECTED] wrote:
Full_Name: Alexander Jerneck
Version: 2.4.0 (2006-10-03)
OS: Gentoo (2.6.17-custom kernel)
Submission from: (NULL) (130.91.92.78)
I had trouble installing R packages, either from inside R or from the
commandline, with R complaining about not finding /usr/bin/pwd
I have pwd in /bin/ so I created a symlink from /usr/bin/pwd to /bin/pwd and
now
I can install packages. I do not know where the original problem is however.
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La version française suit le texte anglais.
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Re: [Rd] installing packages (PR#9907)
[EMAIL PROTECTED] wrote: Full_Name: Alexander Jerneck Version: 2.4.0 (2006-10-03) OS: Gentoo (2.6.17-custom kernel) Submission from: (NULL) (130.91.92.78) I had trouble installing R packages, either from inside R or from the commandline, with R complaining about not finding /usr/bin/pwd I have pwd in /bin/ so I created a symlink from /usr/bin/pwd to /bin/pwd and now I can install packages. I do not know where the original problem is however. Please don't report it as a bug then! Or at least do more of your homework first. As far as I can see, this is handled by the configure script which goes looking for pwd and records the result in $GETWD (in Makeconf and the INSTALL and REMOVE scripts). If you compile on one system and run on another, strange things can and will happen if they do not have things in the same places. There are a few other places where pwd is called directly (texi2dvi and libtool) but I don't think that can give the error message you describe. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
