See below.
On 18/04/15 12:04, Jim Lemon wrote:
Hi Iryna,
The two paths seem to be a "user" path (one beneath your home
directory) and a "system" path (one in another branch of the directory
tree). You usually have to have superuser privileges to write files in
the second. In most *NIX systems you use "su" to become "root" (the
superuser), and if you can do this, then perform the update.
Jim:
(1) The OP seems to be using a Mac OSX system (which has Unix underlying
a great deal of gloppedy obfuscating point-and-click crap).
(2) My reading of the help for install.packages() leads me to believe
that by default the requested package should be installed into the
*first* entry of .libPaths(), whence no superuser privileges should be
required. It is mysterious to me why the system seems to be intent on
using the *second* entry of .libPaths() so that superuser privileges
*are* required.
(3) Since this is Mac OSX stuff, the OP might get better mileage by
posting on R-Sig-Mac.
cheers,
Rolf
Jim
On Fri, Apr 17, 2015 at 7:25 PM, Iryna Nikolayeva
<iryna.v.nikolay...@gmail.com> wrote:
Dear R project members,
I have an issue while automatically updating packages.
For the packages installed in my second library, while automatically updating I get
the following "Permission denied” messages(details below).
I suppose I know where this problem comes from:
I had installed a few different versions of R.
And now I have 2 library paths:
.libPaths()
[1] "/Users/iryna/Library/R/3.1/library"
[2] "/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library”
And for some reason R just doesn’t have rights to update packages in my second
library.
Do you know why is that? How should I fix this issue?
Here is the error message:
* installing *source* package ‘mgcv’ ...
** package ‘mgcv’ successfully unpacked and MD5 sums checked
mv: rename
/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv
to
/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/00LOCK-mgcv/mgcv:
Permission denied
Warning in file.copy(f, instdir, TRUE) :
problem copying ./NAMESPACE to
/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv/NAMESPACE:
Permission denied
Warning in file(file, ifelse(append, "a", "w")) :
cannot open file
'/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv/DESCRIPTION':
Permission denied
Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
ERROR: installing package DESCRIPTION failed for package ‘mgcv’
* removing
‘/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv’
Here are some additional information on my settings:
version
_
platform x86_64-apple-darwin13.4.0
arch x86_64
os darwin13.4.0
system x86_64, darwin13.4.0
status
major 3
minor 1.2
year 2014
month 10
day 31
svn rev 66913
language R
version.string R version 3.1.2 (2014-10-31)
nickname Pumpkin Helmet
Thanks in advance for your help,
—
Iryna Nikolayeva
--
Rolf Turner
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
Home phone: +64-9-480-4619
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
