[R-sig-Debian] Non-zero exit status for survival package
Dirk Eddelbuettel
edd at debian.org
Sun May 9 21:55:49 CEST 2010
On 9 May 2010 at 15:46, Patrick Richardson wrote:
| Fair enough Dirk,
|
| The sarcasm isn't warranted, however the console output is below. I
| apologize for the paucity of information in my previous post, however
| the error message I get from R (shown below in it "entirety") is also
| sparse in its information.
|
|
| 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.
|
|
| > install.packages("survival")
| Warning in install.packages("survival") :
| argument 'lib' is missing: using '/usr/local/lib/R/site-library'
| trying URL
| 'http://R-Forge.R-project.org/src/contrib/survival_2.35-9.tar.gz'
| Content type 'application/x-gzip' length 672383 bytes (656 Kb)
| opened URL
| ==================================================
| downloaded 656 Kb
|
| The downloaded packages are in
| ‘/tmp/RtmpxVKTiu/downloaded_packages’
| Warning message:
| In install.packages("survival") :
| installation of package 'survival' had non-zero exit status
| >
Now here is an exercise: find me the word 'error' in what you quoted.
I see Warning, and that ain't an error. You were told by R that you did not
specify a destination directory, so it picked one for you. That's all.
Now, before going any further, did you actually try to _load_ survival?
library(survival)
would do that. Also note that your neighborhood R maintainers provide a
pre-compiled r-cran-survival package for you. Which you could install via
any of the graphical or command-line oriented package managers. That doesn't
hold try for all 2300+ CRAN packages, but we try to cover the important
ones. Which includes those shipping with R itself like 'survival'.
Dirk
|
|
| On Sun, 2010-05-09 at 14:30 -0500, Dirk Eddelbuettel wrote:
| > On 9 May 2010 at 17:54, xplaner800 at comcast.net wrote:
| > | I'm using 64-bit Karmic. I've tried to install many packages (including, survival, impute, samr) and others, all with the same resulting message of terminating with non-zero exit status.
| >
| > Our mid-reading machine is currently undergoing maintenance so unless
| > you actually show us __the error message you are getting__ there is not much
| > we can do to help.
| >
| > For what it is worth, many of us use Ubuntu or Debian daily on i386 and amd64
| > or other systems and we regularly install packages. You'll get there too,
| > but you to do a little better so that we can help you.
| >
| > There is are FAQs on-line about 'how to ask good questions', see
| > e.g. http://catb.org/~esr/faqs/smart-questions.html for one such guide.
| >
| > Dirk
| >
| >
| > | Patrick
| > | ----- Original Message -----
| > | From: "Michael Rutter" <mar36 at psu.edu>
| > | To: r-sig-debian at r-project.org
| > | Sent: Sunday, May 9, 2010 10:51:02 AM GMT -05:00 US/Canada Eastern
| > | Subject: Re: [R-sig-Debian] Non-zero exit status for survival package
| > |
| > | Patrick,
| > |
| > | Can you give an example of a package that you have tried to install? Or
| > | you using 32 or 64-bit Karmic?
| > |
| > | Thanks,
| > | Michael
| > |
| > | On 05/09/2010 10:35 AM, Patrick Richardson wrote:
| > | > I'm running R 2.11 on Karmic. I'm having difficulty installing quite a
| > | > few packages with the returned error message of "installation of package
| > | > "[whatever the packages happens to be]" had non-zero exit status. I know
| > | > this message sometimes is caused by incorrect or missing java packages
| > | > and the like. I generally don't have issues with the installation of R
| > | > or R packages but I don't know where to start on this. I have looked to
| > | > ensure that I have fortran and C++ compilers installed. I want to (if I
| > | > can) avoid indiscriminately installing packages "until it starts
| > | > working". I'm not sure how to go about troubleshooting this. Could
| > | > anyone lend a hand, please?
| > | >
| > | > Thanks,
| > | > Patrick
| > | >
| > | >> sessionInfo()
| > | > R version 2.11.0 (2010-04-22)
| > | > x86_64-pc-linux-gnu
| > | >
| > | > locale:
| > | > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
| > | > LC_TIME=en_US.UTF-8
| > | > [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=C
| > | > LC_MESSAGES=en_US.UTF-8
| > | > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
| > | > LC_ADDRESS=C
| > | > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
| > | > LC_IDENTIFICATION=C
| > | >
| > | > attached base packages:
| > | > [1] stats graphics grDevices utils datasets methods
| > | > base
| > | >
| > | > loaded via a namespace (and not attached):
| > | > [1] tools_2.11.0
| > | >
| > | >> capabilities()
| > | > jpeg png tiff tcltk X11 aqua http/ftp sockets
| > | > libxml fifo cledit
| > | > TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE
| > | > TRUE TRUE TRUE
| > | > iconv NLS profmem cairo
| > | > TRUE TRUE TRUE TRUE
| > | >
| > | > _______________________________________________
| > | > R-SIG-Debian mailing list
| > | > R-SIG-Debian at r-project.org
| > | > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| > |
| > | --
| > | Dr. Michael A. Rutter
| > | School of Science
| > | Penn State Erie, The Behrend College
| > | Station Road
| > | Erie, PA 16563
| > | http://math.bd.psu.edu/faculty/rutter
| > |
| > | _______________________________________________
| > | R-SIG-Debian mailing list
| > | R-SIG-Debian at r-project.org
| > | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| > |
| > | [[alternative HTML version deleted]]
| > |
| > |
| > | ----------------------------------------------------------------------
| > | _______________________________________________
| > | R-SIG-Debian mailing list
| > | R-SIG-Debian at r-project.org
| > | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| >
|
|
--
Regards, Dirk
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