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and subject line Bug#350657: r-base: download.packages() assumes
/usr/local/lib/R is writeable
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From: Greg Kochanski <[EMAIL PROTECTED]>
To: Debian Bug Tracking System <[EMAIL PROTECTED]>
Subject: r-base: download.packages() assumes /usr/local/lib/R is writeable
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Package: r-base
Version: 2.2.1-2
Severity: normal
This bug can be considered to be
(1) incorrect handling of a user error, or
(2) incorrect documentation, or
(3) missing Debian documentation.
(Depending on one's mood, I suppose.)
Running download.packages("vcd") leads to
(a) a warning that it is going to attempt to write to /usr/local/lib/R,
which is not a directory to which Debian users normally
have write permission. Then, errors from lack of permission.
(b) Note that according to the R documentation, lib is a required
argument without a default, so an error should be reported even be
before a download is attempted.
(c) The resulting error message could be more helpful;
it could suggest a change to the lib argument or
perhaps other things.
So, if the intent is to have a default argument for lib,
it should be specified in help(install.packages);
if not, it should return an error.
If the intent is to install into /usr/local/lib/R on Linux
boxes, then the Debian package ought to
note somewhere (probably in /usr/share/doc/r-base/README.Debian)
that users need to be in group staff to be able to install
R packages to the default directories.
> install.packages("vcd")
Warning in install.packages("vcd") : argument 'lib' is missing: using
/usr/local/lib/R/site-library
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.uk.r-project.org/src/contrib/vcd_0.9-7.tar.gz'
Content type 'application/x-gzip' length 771160 bytes
opened URL
==================================================
downloaded 753Kb
mkdir: cannot create directory `/usr/local/lib/R/site-library/00LOCK':
Permission denied
ERROR: failed to lock directory '/usr/local/lib/R/site-library' for modifying
The downloaded packages are in
/tmp/RtmpCVx2nl/downloaded_packages
Warning messages:
1: installation of package 'vcd' had non-zero exit status in:
install.packages("vcd")
2: cannot create HTML package index in: tools:::unix.packages.html(.Library)
>
-- System Information:
Debian Release: testing/unstable
APT prefers testing
APT policy: (500, 'testing')
Architecture: i386 (i686)
Shell: /bin/sh linked to /bin/bash
Kernel: Linux 2.6.12-1-686
Locale: LANG=en_GB, LC_CTYPE=en_GB (charmap=ISO-8859-1)
Versions of packages r-base depends on:
ii r-base-core 2.2.1-2 GNU R core of statistical computin
ii r-recommended 2.2.1-2 GNU R collection of recommended pa
Versions of packages r-base recommends:
pn r-base-html <none> (no description available)
pn r-base-latex <none> (no description available)
-- no debconf information
---------------------------------------
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Date: Mon, 30 Jan 2006 20:47:33 -0600
To: Greg Kochanski <[EMAIL PROTECTED]>,
[EMAIL PROTECTED]
Subject: Re: Bug#350657: r-base: download.packages() assumes /usr/local/lib/R
is writeable
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From: Dirk Eddelbuettel <[EMAIL PROTECTED]>
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RCVD_IN_SORBS autolearn=no version=2.60-bugs.debian.org_2005_01_02
Greg,
Trying to install into /usr/local/lib/R when you are NOT root and have NOT
proviously as root given write permission to anybody else is an obvious user
error on your part.
R is cross-platform, and it makes no sense to split the semantics of the
function install.packages() across operating system.
If you design issues for R, please continue to raise those on r-help or
r-devel.
This is not a bug, and in particular not in any way that Debian deviates from
R upstream (other than the warning you get if you don't specify lib.loc).
On 31 January 2006 at 01:56, Greg Kochanski wrote:
| Package: r-base
| Version: 2.2.1-2
| Severity: normal
|
|
| This bug can be considered to be
| (1) incorrect handling of a user error, or
| (2) incorrect documentation, or
| (3) missing Debian documentation.
| (Depending on one's mood, I suppose.)
As you were asking about patches on the R list, feel free to provide one for
-- Unix only
-- creation of a temp file in R_LIBS (or the first result returned by
.libPaths() )
-- graceful abort is 2) fails.
Dirk
|
| Running download.packages("vcd") leads to
| (a) a warning that it is going to attempt to write to /usr/local/lib/R,
| which is not a directory to which Debian users normally
| have write permission. Then, errors from lack of permission.
| (b) Note that according to the R documentation, lib is a required
| argument without a default, so an error should be reported even be
| before a download is attempted.
| (c) The resulting error message could be more helpful;
| it could suggest a change to the lib argument or
| perhaps other things.
|
| So, if the intent is to have a default argument for lib,
| it should be specified in help(install.packages);
| if not, it should return an error.
|
| If the intent is to install into /usr/local/lib/R on Linux
| boxes, then the Debian package ought to
| note somewhere (probably in /usr/share/doc/r-base/README.Debian)
| that users need to be in group staff to be able to install
| R packages to the default directories.
|
|
| > install.packages("vcd")
| Warning in install.packages("vcd") : argument 'lib' is missing: using
| /usr/local/lib/R/site-library
| --- Please select a CRAN mirror for use in this session ---
| Loading Tcl/Tk interface ... done
| trying URL 'http://cran.uk.r-project.org/src/contrib/vcd_0.9-7.tar.gz'
| Content type 'application/x-gzip' length 771160 bytes
| opened URL
| ==================================================
| downloaded 753Kb
|
| mkdir: cannot create directory `/usr/local/lib/R/site-library/00LOCK':
Permission denied
| ERROR: failed to lock directory '/usr/local/lib/R/site-library' for modifying
|
| The downloaded packages are in
| /tmp/RtmpCVx2nl/downloaded_packages
| Warning messages:
| 1: installation of package 'vcd' had non-zero exit status in:
install.packages("vcd")
| 2: cannot create HTML package index in: tools:::unix.packages.html(.Library)
| >
|
|
|
|
| -- System Information:
| Debian Release: testing/unstable
| APT prefers testing
| APT policy: (500, 'testing')
| Architecture: i386 (i686)
| Shell: /bin/sh linked to /bin/bash
| Kernel: Linux 2.6.12-1-686
| Locale: LANG=en_GB, LC_CTYPE=en_GB (charmap=ISO-8859-1)
|
| Versions of packages r-base depends on:
| ii r-base-core 2.2.1-2 GNU R core of statistical
computin
| ii r-recommended 2.2.1-2 GNU R collection of recommended
pa
|
| Versions of packages r-base recommends:
| pn r-base-html <none> (no description available)
| pn r-base-latex <none> (no description available)
|
| -- no debconf information
|
--
Hell, there are no rules here - we're trying to accomplish something.
-- Thomas A. Edison
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