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

Fri Jun 13 14:36:20 CEST 2008

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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