Dear Helpers, I am new in Linux and R, trying to update packages I need in my work, but repeatedly I failed for reasons I do not understand. First, I use:> update.packages()Then, I choose nearest mirror and accept update of 'Design' package:> Design : > Version 2.0-9 installed in /usr/lib/R/site-library > Version 2.0-12 available at http://cran.r-mirror.de > Update (y/N/c)? yFinally, after successful download, installation starts and fails:> trying URL 'http://cran.r-mirror.de/src/contrib/Design_2.0-12.tar.gz' > Content type 'application/x-gzip' length 329401 bytes > opened URL > =================================================> downloaded 321Kb > > * Installing *source* package 'Design' ... > ** libs > g77 -fPIC -g -O2 -c lrmfit.f -o lrmfit.o > g77 -fPIC -g -O2 -c mlmats.f -o mlmats.o > g77 -fPIC -g -O2 -c robcovf.f -o robcovf.o > gcc -shared -o Design.so lrmfit.o mlmats.o robcovf.o -lg2c -lm-lgcc_s -L/usr/lib/R/lib -lR> /usr/bin/ld: crti.o: No such file: No such file or directory > collect2: ld returned 1 exit status > make: *** [Design.so] Error 1 > ERROR: compilation failed for package 'Design' > ** Removing '/usr/lib/R/site-library/Design' > ** Restoring previous '/usr/lib/R/site-library/Design' > > The downloaded packages are in > /tmp/RtmphbLWxZ/downloaded_packages > Warning message: > installation of package 'Design' had non-zero exit status in:install.packages(update[, "Package"], instlib, contriburl = contriburl, I am using following R under Ubuntu - Linux: platform = "i386-pc-linux-gnu" arch = "i386" os = "linux-gnu" system = "i386, linux-gnu" major = "2" minor = "2.1" year = "2005" month = "12" day = "20" "svn rev" = "36812" language = "R" I would be really thankful if anyone could give me explanation of what I am doing wrong and how can I make update. Sincerely, Petar Milin Assistant Professor Department of Psychology University of Novi Sad Serbia and Montenegro
You may need to install glibc-devel or glibc-dev, depending on how Ubuntu works and depending on how you installed it. (For Fedora, these are called "devel".) You may be missing a great many "devel" rpms, such as readline-devel, blas-devel, and so on, which you will need for other packages. I'm not sure how you are supposed to know this, if it is true, although you must of course start by looking at the error message itself, which tells you that the problem is not finding crti.o. Appendix C1 of the installation and administration guide does mention the need for "dev(el)," but does not mention glibc in particular. When these things happen to me, I search for the missing file, in this case crti.o, on Google or on some repository of rpms, such as http://rpm.pbone.net. In this case, there is a lot of discussion on Google about the very error message you got, although it is probabaly all misleading. You can also see whether you actually have the file somewhere by saying slocate crti.o If you find it, you can discover which rpm it is part of by using its full path, e.g., rpm -qf /usr/lib/crti.o Jon On 12/31/05 12:27, Petar Milin wrote:> > Dear Helpers, > I am new in Linux and R, trying to update packages I need in my work, > but repeatedly I failed for reasons I do not understand. > First, I use: > > update.packages() > Then, I choose nearest mirror and accept update of 'Design' package: > > Design : > > Version 2.0-9 installed in /usr/lib/R/site-library > > Version 2.0-12 available at http://cran.r-mirror.de > > Update (y/N/c)? y > Finally, after successful download, installation starts and fails: > > trying URL 'http://cran.r-mirror.de/src/contrib/Design_2.0-12.tar.gz' > > Content type 'application/x-gzip' length 329401 bytes > > opened URL > > =================================================> > downloaded 321Kb > > > > * Installing *source* package 'Design' ... > > ** libs > > g77 -fPIC -g -O2 -c lrmfit.f -o lrmfit.o > > g77 -fPIC -g -O2 -c mlmats.f -o mlmats.o > > g77 -fPIC -g -O2 -c robcovf.f -o robcovf.o > > gcc -shared -o Design.so lrmfit.o mlmats.o robcovf.o -lg2c -lm > -lgcc_s -L/usr/lib/R/lib -lR > > /usr/bin/ld: crti.o: No such file: No such file or directory > > collect2: ld returned 1 exit status > > make: *** [Design.so] Error 1 > > ERROR: compilation failed for package 'Design' > > ** Removing '/usr/lib/R/site-library/Design' > > ** Restoring previous '/usr/lib/R/site-library/Design' > > > > The downloaded packages are in > > /tmp/RtmphbLWxZ/downloaded_packages > > Warning message: > > installation of package 'Design' had non-zero exit status in: > install.packages(update[, "Package"], instlib, contriburl = contriburl, > > I am using following R under Ubuntu - Linux: > platform = "i386-pc-linux-gnu" > arch = "i386" > os = "linux-gnu" > system = "i386, linux-gnu" > major = "2" > minor = "2.1" > year = "2005" > month = "12" > day = "20" > "svn rev" = "36812" > language = "R" > > I would be really thankful if anyone could give me explanation of what I > am doing wrong and how can I make update. > > Sincerely, > Petar Milin > Assistant Professor > Department of Psychology > University of Novi Sad > Serbia and Montenegro > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html-- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron
On 31 December 2005 at 12:27, Petar Milin wrote:
| I am new in Linux and R, trying to update packages I need in my work,
| but repeatedly I failed for reasons I do not understand.
| First, I use:
| > update.packages()
| Then, I choose nearest mirror and accept update of 'Design' package:
| > Design :
| > Version 2.0-9 installed in /usr/lib/R/site-library
| > Version 2.0-12 available at http://cran.r-mirror.de
[...]
| > gcc -shared -o Design.so lrmfit.o mlmats.o robcovf.o -lg2c -lm
| -lgcc_s -L/usr/lib/R/lib -lR
| > /usr/bin/ld: crti.o: No such file: No such file or directory
[...]
| I am using following R under Ubuntu - Linux:
| platform = "i386-pc-linux-gnu"
| arch = "i386"
| os = "linux-gnu"
| system = "i386, linux-gnu"
| major = "2"
| minor = "2.1"
[...]
So did you manage to compile R 2.2.1, but you cannot compile R packages?
Interesting.
| I would be really thankful if anyone could give me explanation of what I
| am doing wrong and how can I make update.
Well, you did get a _very_ specific error message of crti.o missing. So
let's
look for crti.o:
edd at joe:~$ locate crti.o
/usr/lib/crti.o
edd at joe:~$
and then figure out where that package belongs:
edd at joe:~$ dpkg -S `locate crti.o`
libc6-dev: /usr/lib/crti.o
So Jon Baron was spot-on: libc6-dev is what you need.
Now, a useful search page for Debian is at
http://www.debian.org/distrib/packages
where the search at the bottom allows you to search all Debian package
listings -- that would allow you to identify crti.o as part of libc6-dev
given that it cannot be found by the locate command on your machine.
Lastly, and as an aside, Ubuntu does rebuilds of the packages we maintain for
Debian. Running 'apt-cache policy r-cran-design' shows 2.0.11 being
available
for Ubuntu breezy. Debian itself has 2.0.12 in testing and unstable. So this
particular one you could also install as a package.
--
Hell, there are no rules here - we're trying to accomplish something.
-- Thomas A. Edison
Thanks to the detailed help with previous error message, I managed to update Design package. However, when I tried to update Matrix and lme4 I received an error message again: ...> /usr/bin/ld: cannot find -lblas-3 > collect2: ld returned 1 exit status > make: *** [Matrix.so] Error 1 > ERROR: compilation failed for package 'Matrix' > ** Removing '/usr/lib/R/site-library/Matrix' > ** Restoring previous '/usr/lib/R/site-library/Matrix'... When I tried to search for lblas-3, following instruction of professor Jonathan Baron, Dirk Eddelbuettel and Martin Maechler, I could not find it. With:> dpkg -S lblas-3and> dpkg -S *-lblas-3*I received:> dpkg: *-lblas-3* not found.Without Matrix, it is not possible to have lme4 updated. Also, I would like to have nlme and some other packages. The question is how should I procees and not be tedious with questions to the Mailing list?>>>>> "Jon" == Jonathan Baron <baron at psych.upenn.edu> >>>>> on Sat, 31 Dec 2005 08:08:49 -0500 writes:Jon> You may need to install glibc-devel or glibc-dev, Jon> depending on how Ubuntu works and depending on how you Jon> installed it. (For Fedora, these are called "devel".) Jon> You may be missing a great many "devel" rpms, such as Jon> readline-devel, blas-devel, and so on, which you will Jon> need for other packages. Jon> I'm not sure how you are supposed to know this, if it Jon> is true, although you must of course start by looking Jon> at the error message itself, which tells you that the Jon> problem is not finding crti.o. Jon> Appendix C1 of the installation and administration Jon> guide does mention the need for "dev(el)," but does not Jon> mention glibc in particular. Jon> When these things happen to me, I search for the Jon> missing file, in this case crti.o, on Google or on some Jon> repository of rpms, such as http://rpm.pbone.net. In Jon> this case, there is a lot of discussion on Google about Jon> the very error message you got, although it is Jon> probabaly all misleading. Jon> You can also see whether you actually have the file Jon> somewhere by saying Jon> slocate crti.o Jon> If you find it, you can discover which rpm it is part Jon> of by using its full path, e.g., Jon> rpm -qf /usr/lib/crti.o In Ubuntu (which is a Debian derivative), I directly search for the file in the installed (debian) packages by dpkg -S crti.o which returns libc6-dev: /usr/lib/crti.o So with ubuntu/debian, you need the libc6-dev package, which you install by e.g., apt-get install libc6-dev Martin