Re: [R] Package Installation produces "linux/limits.h: No such file or directory" error when installing the lpSolve package

From: Basileis <sharwan.joram_at_gmail.com>
Date: Fri, 13 Jun 2008 05:36:20 -0700 (PDT)

Hi,

   I too had this same problem but it got resolved by installing two packages :

  1. kernel-headers
  2. kernel-devel

I hope this helps in your case.

Regards
Sharwan

Joe_K wrote:
>
> Dear Friends,
>
> I am trying to install a few packages in R and am receiving error
> messages. Since the error messages are different, I am posting them
> separately. The second error is with the installation of lpSolve.
>
> The core error message is:
> ========================================================================
> In file included from /usr/include/bits/posix1_lim.h:153,
> from /usr/include/limits.h:145,
> from
> /usr/lib64/gcc/x86_64-suse-linux/4.2.1/include/limits.h:122,
> from
> /usr/lib64/gcc/x86_64-suse-linux/4.2.1/include/syslimits.h:7,
> from
> /usr/lib64/gcc/x86_64-suse-linux/4.2.1/include/limits.h:11,
> from colamd.c:677:
> /usr/include/bits/local_lim.h:36:26
> error: linux/limits.h: No such file or directory
> make: *** [colamd.o] Error 1
> ERROR: compilation failed for package 'lpSolve'
> ========================================================================
>
> The first things that I tried was to figure out where linux/limits.h was.
> I discovered that there are seven versions of limits.h on the system and
> they are not identical.
>
> /usr/include/limits.h
> /usr/src/linux-2.6.22.13-0.3/Documentation/i2c/chips/limits.h
> /usr/include/c++/4.2.1/tr1/limits.h
> /usr/lib64/qt4/demos/qtdemo/xml/limits.h
> /usr/src/linux-2.6.22.13-0.3/include/linux/limits.h
> /usr/src/linux-2.6.22.13-0.3/include/asm-arm/limits.h
> /usr/src/linux-2.6.22.13-0.3/include/asm-arm26/limits.h
>
> Only one has "linux" immediately preceding it in the path:
> /usr/src/linux-2.6.22.13-0.3/include/linux/limits.h
>
> I assume that /usr/include/bits/local_lim.h is trying to use a relative
> path. The only line in local_lim.h with limits.h in it is:
>
> #include <linux/limits.h>
>
> So, I tried modifying the line to read:
>
> #include </usr/src/linux-2.6.22.13-0.3/include/linux/limits.h>
>
> That did not work, so I changed it back again. I guess my theory about it
> looking for a relative path was wrong.
>
> Since then, I have been Googling the issue all weekend and have found
> similar errors, but not exactly the same. Some are suggesting changing
> kernel headers and other files. Since the context of these other posts
> are dissimilar, I figured it best not to mess with kernel headers or some
> of the other radical solutions offered.
>
> There was one suggestion in a post to install glibc-headers, however, I
> cannot seem to find that for Suse 10.3. Is it something included in
> another package? Is it something that is now obsolete?
>
> CAN ANYONE HELP ME DEBUG THIS?
>
> I am running R version 2.6.1 (2007-11-26) on Suse Linux 10.3 64-bit x86_64
> on a Boxx Technologies computer with a TYAN Thunder K8WE S2895 Motherboard
> with 4Gb Ram and 2 dual CPUs (total of 4 CPUs). The CPUs are AMD Opteron.
> Hard Disk Usage is 4 150 Gb SATA drives array with a Com3 9550SX
> Controller set at RAID 5.
>
> The full error message received from Rkward upon the package installation
> attempt was:
> ========================================================================
> R version 2.6.1 (2007-11-26)
> Copyright (C) 2007 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.

>>

> options (repos=c (CRAN="http://lib.stat.cmu.edu/R/CRAN"))
>> install.packages (pkgs=c ("lpSolve"),
>> lib="/home/joe/R/x86_64-unknown-linux-gnu-library/2.6",
>> destdir="/home/joe/.rkward/package_archive", dependencies=TRUE)

> trying URL
> 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/lpSolve_5.5.8.tar.gz'
> Content type 'application/x-gzip' length 449804 bytes (439 Kb)
> opened URL
>
> downloaded 439 Kb
> /home/joe/R/x86_64-unknown-linux-gnu-library/2.6
> * Installing *source* package 'lpSolve' ...
> ** libs
> gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/lib64/R/include -I .
> -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL
> -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL
> -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c
> colamd.c -o colamd.o
> In file included from /usr/include/bits/posix1_lim.h:153,
> from /usr/include/limits.h:145,
> from
> /usr/lib64/gcc/x86_64-suse-linux/4.2.1/include/limits.h:122,
> from
> /usr/lib64/gcc/x86_64-suse-linux/4.2.1/include/syslimits.h:7,
> from
> /usr/lib64/gcc/x86_64-suse-linux/4.2.1/include/limits.h:11,
> from colamd.c:677:
> /usr/include/bits/local_lim.h:36:26
> error: linux/limits.h: No such file or directory
> make: *** [colamd.o] Error 1
> ERROR: compilation failed for package 'lpSolve'
> ** Removing '/home/joe/R/x86_64-unknown-linux-gnu-library/2.6/lpSolve'
> Warning message:
> In install.packages(pkgs = c("lpSolve"), lib =
> "/home/joe/R/x86_64-unknown-linux-gnu-library/2.6", :
> installation of package 'lpSolve' had non-zero exit status
>> q ()

> ========================================================================
>
>
-- 
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