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joined R-today
12 messages · Simon Pickett, Liviu Andronic, Dimitri Liakhovitski +3 more
Hi,
Check out the FAQ on the home page about installing packages.
You need to
1. Install the package from a local mirror, you can do this from the drop
down menu ("Install packages")
2. then call the package using "library(name of the package)"
It helps to know where your R library directory is on your computer.
HTH Simon.
----- Original Message -----
From: "Bala subramanian" <bala.biophysics at gmail.com>
To: <r-help at r-project.org>
Sent: Tuesday, April 21, 2009 9:34 AM
Subject: [R] joined R-today
Friends, I am a newbie to R. Just installed and started with R. I installed netcdf library (netcdf-4.0.tar.gz) and then ncdf package of R from CRAN with the following command. R CMD INSTALL --configure-args="-with-netcdf_incdir=/usr/local/netcdf/include -with-netcdf_libdir=/usr/local/netcdf/lib" ncdf_1.6.tar.gz The installation was successful. But when i try to use ncdf inside R, i get the following error. Kindly help me how to resolve the problem.
trjfile<-system.file('test.netcdf',package='bio3d')
trj<-read.ncdf(trjfile)
Loading required package: ncdf Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/usr/lib/R/library/ncdf/libs/ncdf.so': /usr/lib/R/library/ncdf/libs/ncdf.so: cannot restore segment prot after reloc: Permission denied Error in read.ncdf(trjfile) : Please install the ncdf package from CRAN Thanks in advance, Bala [[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list 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.
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On Tue, Apr 21, 2009 at 11:57 AM, Bala subramanian
<bala.biophysics at gmail.com> wrote:
Dear Simon, I installed the ncdf package in the way you suggested but still i got the same error i got before. I haves pasted below the installation log and errors.
Does ncdf depend on netcdf [1]? If so, perhaps it is missing, or is
not up-to-date. Also, it's a good habit to install.packages('ncdf',
dep=TRUE).
Regards,
Liviu
[1] http://www.unidata.ucar.edu/software/netcdf/
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Try to install from scratch from a different mirror. Dimitri On Tue, Apr 21, 2009 at 6:21 AM, Bala subramanian
<bala.biophysics at gmail.com> wrote:
Hi, Yes ncdf needs netcdf, netcdf is already installed in my fedora10. I reinstalled ncdf with the following option
install.packages('ncdf',dep=TRUE)
library(ncdf)> library(ncdf)
Error in dyn.load(file, DLLpath = DLLpath, ...) : ?unable to load shared library '/usr/lib/R/library/ncdf/libs/ncdf.so': ?/usr/lib/R/library/ncdf/libs/ncdf.so: cannot restore segment prot after reloc: Permission denied Error in library(ncdf) : .First.lib failed for 'ncdf' Again the same error, Bala On Tue, Apr 21, 2009 at 12:12 PM, Liviu Andronic <landronimirc at gmail.com>wrote:
On Tue, Apr 21, 2009 at 11:57 AM, Bala subramanian <bala.biophysics at gmail.com> wrote:
Dear Simon, I installed the ncdf package in the way you suggested but still i got the same error i got before. I haves pasted below the installation log and errors.
Does ncdf depend on netcdf [1]? If so, perhaps it is missing, or is
not up-to-date. Also, it's a good habit to install.packages('ncdf',
dep=TRUE).
Regards,
Liviu
[1] http://www.unidata.ucar.edu/software/netcdf/
? ? ? ?[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list 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.
Dimitri Liakhovitski MarketTools, Inc. Dimitri.Liakhovitski at markettools.com
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Bala subramanian wrote:
Hi, I tried to install from four different mirrors. The result is the same. I dnt understand what the following error means. /usr/lib/R/library/ncdf/libs/ncdf.so: cannot restore segment prot after reloc: Permission denied Error in library(ncdf) : .First.lib failed for 'ncdf' I even tried to change the permission of ncdf.so but still i am not able to load the library.
Nothing to do with the download. I think SElinux is getting in your way (so your unstated system could be RedHat Enterprise Linux?). Contact your sysadm or google for the error message. (One of the hits suggests that you might need to run chcon -t texrel_shlib_t ncdf.so but, well, no warranties...)
Bala On Tue, Apr 21, 2009 at 2:03 PM, Dimitri Liakhovitski <ld7631 at gmail.com>wrote:
Try to install from scratch from a different mirror. Dimitri On Tue, Apr 21, 2009 at 6:21 AM, Bala subramanian <bala.biophysics at gmail.com> wrote:
Hi, Yes ncdf needs netcdf, netcdf is already installed in my fedora10. I reinstalled ncdf with the following option
install.packages('ncdf',dep=TRUE)
library(ncdf)> library(ncdf)
Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/usr/lib/R/library/ncdf/libs/ncdf.so': /usr/lib/R/library/ncdf/libs/ncdf.so: cannot restore segment prot after reloc: Permission denied Error in library(ncdf) : .First.lib failed for 'ncdf' Again the same error, Bala On Tue, Apr 21, 2009 at 12:12 PM, Liviu Andronic <landronimirc at gmail.com wrote:
On Tue, Apr 21, 2009 at 11:57 AM, Bala subramanian <bala.biophysics at gmail.com> wrote:
Dear Simon, I installed the ncdf package in the way you suggested but still i got
the
same error i got before. I haves pasted below the installation log and errors.
Does ncdf depend on netcdf [1]? If so, perhaps it is missing, or is
not up-to-date. Also, it's a good habit to install.packages('ncdf',
dep=TRUE).
Regards,
Liviu
[1] http://www.unidata.ucar.edu/software/netcdf/
[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list 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. -- Dimitri Liakhovitski MarketTools, Inc. Dimitri.Liakhovitski at markettools.com
[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list 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.
O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
On Apr 21, 2009, at 9:28 AM, Peter Dalgaard wrote:
Bala subramanian wrote:
Hi, I tried to install from four different mirrors. The result is the same. I dnt understand what the following error means. /usr/lib/R/library/ncdf/libs/ncdf.so: cannot restore segment prot after reloc: Permission denied Error in library(ncdf) : .First.lib failed for 'ncdf' I even tried to change the permission of ncdf.so but still i am not able to load the library.
Nothing to do with the download. I think SElinux is getting in your way (so your unstated system could be RedHat Enterprise Linux?). Contact your sysadm or google for the error message. (One of the hits suggests that you might need to run chcon -t texrel_shlib_t ncdf.so but, well, no warranties...)
The OP did indicate that F10 was the platform: https://stat.ethz.ch/pipermail/r-help/attachments/20090421/65ee5d6e/attachment.pl so I would agree here that SELinux is almost certainly the culprit as it does control relocation. If you have the SE Troubleshoot daemon running, you should get a yellow star/badge symbol on one of your desktop dock panels. Typically, if you click on this, it will bring up a dialog window that will have some specific suggestions for resolving the problem. You can see some visual examples here: https://fedoraproject.org/wiki/Design/SETroubleshootUsabilityImprovements More info on SETroubleshoot here: https://fedorahosted.org/setroubleshoot/ HTH, Marc Schwartz
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Bala, I would not advocate disabling SELinux entirely to resolve this issue. SELinux is one of the key security features of Fedora Linux and some other Linux distributions that have adopted it. It has already been demonstrated to be robust with respect to so-called zero-day attacks. I would first look to take a more surgical approach to resolve this particular issue with this package. Using the SETroubleshoot daemon is the easiest way to accomplish this as it will provide specific instructions. As with any security approach, there are trade-offs between security and usability, but SELinux as a mandatory access control system is well worthwhile keeping in place. BTW, as a future reference, there is a r-sig-fedora list: https://stat.ethz.ch/mailman/listinfo/r-sig-fedora HTH, Marc
On Apr 21, 2009, at 9:56 AM, Bala subramanian wrote:
Dear Marc and Peter, Thank you so much. In fact disabling the SElinux solved the problem. Bala On Tue, Apr 21, 2009 at 4:43 PM, Marc Schwartz <marc_schwartz at me.com> wrote: On Apr 21, 2009, at 9:28 AM, Peter Dalgaard wrote: Bala subramanian wrote: Hi, I tried to install from four different mirrors. The result is the same. I dnt understand what the following error means. /usr/lib/R/library/ncdf/libs/ncdf.so: cannot restore segment prot after reloc: Permission denied Error in library(ncdf) : .First.lib failed for 'ncdf' I even tried to change the permission of ncdf.so but still i am not able to load the library. Nothing to do with the download. I think SElinux is getting in your way (so your unstated system could be RedHat Enterprise Linux?). Contact your sysadm or google for the error message. (One of the hits suggests that you might need to run chcon -t texrel_shlib_t ncdf.so but, well, no warranties...) The OP did indicate that F10 was the platform: https://stat.ethz.ch/pipermail/r-help/attachments/20090421/65ee5d6e/attachment.pl so I would agree here that SELinux is almost certainly the culprit as it does control relocation. If you have the SE Troubleshoot daemon running, you should get a yellow star/badge symbol on one of your desktop dock panels. Typically, if you click on this, it will bring up a dialog window that will have some specific suggestions for resolving the problem. You can see some visual examples here: https://fedoraproject.org/wiki/Design/SETroubleshootUsabilityImprovements More info on SETroubleshoot here: https://fedorahosted.org/setroubleshoot/ HTH, Marc Schwartz