[R] Problems with updating R-packages

Martin Maechler maechler at stat.math.ethz.ch
Sat Dec 31 15:24:29 CET 2005

>>>>> "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


    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

    Jon> -- Jonathan Baron, Professor of Psychology, University
    Jon> of Pennsylvania Home page:
    Jon> http://www.sas.upenn.edu/~baron

    Jon> ______________________________________________
    Jon> R-help at stat.math.ethz.ch mailing list
    Jon> https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do
    Jon> read the posting guide!
    Jon> http://www.R-project.org/posting-guide.html

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