R help - May 2008 - colorspace package does not compile on ubuntu 7.04 32 bit

Hi everyone, 
I am trying to install colorspace (needed as part of my favourite ggplot2)
on R v 2.7.0 running under ubuntu 7.04. The package is provided as source
files and the compilation fails as below.
I suspect this might be a problem with gcc v3/v4 incompatibility (or
anything else), but I don't really know how to resolve it. Any advice will
be appreciated - or perhaps somebody has got this package compiled and could
share the binaries?  
Many thanks!
Mikhail

----
Mikhail Spivakov, PhD
European Bioinformatics Institute
European Molecular Biology Laboratory
Germany/UK

* Installing *source* package 'colorspace' ...
** libs
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c colorspace.c -o
colorspace.o
In file included from colorspace.c:1:
/usr/share/R/include/R.h:28:20: error: stdlib.h: No such file or directory
/usr/share/R/include/R.h:29:19: error: stdio.h: No such file or directory
In file included from
/usr/lib/gcc/i486-linux-gnu/4.1.2/include/syslimits.h:7,
                 from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:11,
                 from /usr/share/R/include/R.h:30,
                 from colorspace.c:1:
/usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:122:61: error: limits.h:
No such file or directory
In file included from colorspace.c:1:
/usr/share/R/include/R.h:32:18: error: math.h: No such file or directory
/usr/share/R/include/R.h:33:19: error: errno.h: No such file or directory
In file included from /usr/share/R/include/R.h:50,
                 from colorspace.c:1:
/usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or
directory
In file included from colorspace.c:2:
/usr/share/R/include/Rinternals.h:770: error: expected declaration
specifiers or ?...? before ?FILE?
/usr/share/R/include/Rinternals.h:773: error: expected declaration
specifiers or ?...? before ?FILE?
colorspace.c: In function ?gtrans?:
colorspace.c:28: warning: implicit declaration of function ?pow?
colorspace.c:28: warning: incompatible implicit declaration of built-in
function ?pow?
colorspace.c: In function ?ftrans?:
colorspace.c:36: warning: incompatible implicit declaration of built-in
function ?pow?
colorspace.c: In function ?g?:
colorspace.c:92: warning: incompatible implicit declaration of built-in
function ?pow?
colorspace.c: In function ?LAB_to_XYZ?:
colorspace.c:106: warning: incompatible implicit declaration of built-in
function ?pow?
colorspace.c:114: warning: incompatible implicit declaration of built-in
function ?pow?
colorspace.c:117: warning: incompatible implicit declaration of built-in
function ?pow?
colorspace.c:123: warning: incompatible implicit declaration of built-in
function ?pow?
colorspace.c: In function ?f?:
colorspace.c:132: warning: incompatible implicit declaration of built-in
function ?pow?
colorspace.c: In function ?XYZ_to_LAB?:
colorspace.c:144: warning: incompatible implicit declaration of built-in
function ?pow?
colorspace.c: In function ?XYZ_to_HLAB?:
colorspace.c:170: warning: implicit declaration of function ?sqrt?
colorspace.c:170: warning: incompatible implicit declaration of built-in
function ?sqrt?
colorspace.c: In function ?LAB_to_polarLAB?:
colorspace.c:203: warning: implicit declaration of function ?atan2?
colorspace.c:203: warning: incompatible implicit declaration of built-in
function ?atan2?
colorspace.c:207: warning: incompatible implicit declaration of built-in
function ?sqrt?
colorspace.c: In function ?polarLAB_to_LAB?:
colorspace.c:216: warning: implicit declaration of function ?cos?
colorspace.c:216: warning: incompatible implicit declaration of built-in
function ?cos?
colorspace.c:217: warning: implicit declaration of function ?sin?
colorspace.c:217: warning: incompatible implicit declaration of built-in
function ?sin?
colorspace.c: In function ?HSV_to_RGB?:
colorspace.c:272: warning: implicit declaration of function ?floor?
colorspace.c:272: warning: incompatible implicit declaration of built-in
function ?floor?
colorspace.c: In function ?XYZ_to_LUV?:
colorspace.c:311: warning: incompatible implicit declaration of built-in
function ?pow?
colorspace.c: In function ?LUV_to_XYZ?:
colorspace.c:325: warning: incompatible implicit declaration of built-in
function ?pow?
colorspace.c: In function ?LUV_to_polarLUV?:
colorspace.c:342: warning: incompatible implicit declaration of built-in
function ?sqrt?
colorspace.c:343: warning: incompatible implicit declaration of built-in
function ?atan2?
colorspace.c: In function ?polarLUV_to_LUV?:
colorspace.c:354: warning: incompatible implicit declaration of built-in
function ?cos?
colorspace.c:355: warning: incompatible implicit declaration of built-in
function ?sin?
colorspace.c: In function ?CheckSpace?:
colorspace.c:373: warning: implicit declaration of function ?strcmp?
colorspace.c: In function ?CheckHex?:
colorspace.c:407: warning: implicit declaration of function ?strlen?
colorspace.c:407: warning: incompatible implicit declaration of built-in
function ?strlen?
colorspace.c:411: warning: implicit declaration of function ?isxdigit?
colorspace.c: In function ?hex_to_RGB?:
colorspace.c:1115: warning: passing argument 1 of ?decodeHexStr? discards
qualifiers from pointer target type
make: *** [colorspace.o] Error 1
ERROR: compilation failed for package 'colorspace'
** Removing '/home/mspivako/R/i486-pc-linux-gnu-library/2.7/colorspace'

The downloaded packages are in
        /tmp/RtmpSxK3ea/downloaded_packages
Warning message:
In install.packages("colorspace") :
  installation of package 'colorspace' had non-zero exit status

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Hi again,

I have managed to solve this problem myself - indeed, the trouble was with
the package being incompatible with gcc v4. 

Here what I've done - perhaps it's going to be useful for someone else:

1) installed gcc v3.4: sudo apt-get install gcc-3.4
2) opened .../R/etc/Makeconf (changing its access rights so it's no longer
read-only first)
3) changed all instances of gcc to gcc-3.4

I realise that this was perhaps quite a drastic measure and I could have
created a Makefile for the colorspace package specifically instead. But the
v4/v3 incompatibility is such a common problem that I decided to change this
once and for all - until new packages utilising some v4 - specific C code
appear out there..

Cheers
Mikhail



Mikhail Spivakov wrote:
> 
> Hi everyone, 
> I am trying to install colorspace (needed as part of my favourite ggplot2)
> on R v 2.7.0 running under ubuntu 7.04. The package is provided as source
> files and the compilation fails as below.
> I suspect this might be a problem with gcc v3/v4 incompatibility (or
> anything else), but I don't really know how to resolve it. Any advice
will
> be appreciated - or perhaps somebody has got this package compiled and
> could share the binaries?  
> Many thanks!
> Mikhail
> 
> ----
> Mikhail Spivakov, PhD
> European Bioinformatics Institute
> European Molecular Biology Laboratory
> Germany/UK
> 
> * Installing *source* package 'colorspace' ...
> ** libs
> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c colorspace.c
> -o colorspace.o
> In file included from colorspace.c:1:
> /usr/share/R/include/R.h:28:20: error: stdlib.h: No such file or directory
> /usr/share/R/include/R.h:29:19: error: stdio.h: No such file or directory
> In file included from
> /usr/lib/gcc/i486-linux-gnu/4.1.2/include/syslimits.h:7,
>                  from
> /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:11,
>                  from /usr/share/R/include/R.h:30,
>                  from colorspace.c:1:
> /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:122:61: error:
> limits.h: No such file or directory
> In file included from colorspace.c:1:
> /usr/share/R/include/R.h:32:18: error: math.h: No such file or directory
> /usr/share/R/include/R.h:33:19: error: errno.h: No such file or directory
> In file included from /usr/share/R/include/R.h:50,
>                  from colorspace.c:1:
> /usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or
> directory
> In file included from colorspace.c:2:
> /usr/share/R/include/Rinternals.h:770: error: expected declaration
> specifiers or ?...? before ?FILE?
> /usr/share/R/include/Rinternals.h:773: error: expected declaration
> specifiers or ?...? before ?FILE?
> colorspace.c: In function ?gtrans?:
> colorspace.c:28: warning: implicit declaration of function ?pow?
> colorspace.c:28: warning: incompatible implicit declaration of built-in
> function ?pow?
> colorspace.c: In function ?ftrans?:
> colorspace.c:36: warning: incompatible implicit declaration of built-in
> function ?pow?
> colorspace.c: In function ?g?:
> colorspace.c:92: warning: incompatible implicit declaration of built-in
> function ?pow?
> colorspace.c: In function ?LAB_to_XYZ?:
> colorspace.c:106: warning: incompatible implicit declaration of built-in
> function ?pow?
> colorspace.c:114: warning: incompatible implicit declaration of built-in
> function ?pow?
> colorspace.c:117: warning: incompatible implicit declaration of built-in
> function ?pow?
> colorspace.c:123: warning: incompatible implicit declaration of built-in
> function ?pow?
> colorspace.c: In function ?f?:
> colorspace.c:132: warning: incompatible implicit declaration of built-in
> function ?pow?
> colorspace.c: In function ?XYZ_to_LAB?:
> colorspace.c:144: warning: incompatible implicit declaration of built-in
> function ?pow?
> colorspace.c: In function ?XYZ_to_HLAB?:
> colorspace.c:170: warning: implicit declaration of function ?sqrt?
> colorspace.c:170: warning: incompatible implicit declaration of built-in
> function ?sqrt?
> colorspace.c: In function ?LAB_to_polarLAB?:
> colorspace.c:203: warning: implicit declaration of function ?atan2?
> colorspace.c:203: warning: incompatible implicit declaration of built-in
> function ?atan2?
> colorspace.c:207: warning: incompatible implicit declaration of built-in
> function ?sqrt?
> colorspace.c: In function ?polarLAB_to_LAB?:
> colorspace.c:216: warning: implicit declaration of function ?cos?
> colorspace.c:216: warning: incompatible implicit declaration of built-in
> function ?cos?
> colorspace.c:217: warning: implicit declaration of function ?sin?
> colorspace.c:217: warning: incompatible implicit declaration of built-in
> function ?sin?
> colorspace.c: In function ?HSV_to_RGB?:
> colorspace.c:272: warning: implicit declaration of function ?floor?
> colorspace.c:272: warning: incompatible implicit declaration of built-in
> function ?floor?
> colorspace.c: In function ?XYZ_to_LUV?:
> colorspace.c:311: warning: incompatible implicit declaration of built-in
> function ?pow?
> colorspace.c: In function ?LUV_to_XYZ?:
> colorspace.c:325: warning: incompatible implicit declaration of built-in
> function ?pow?
> colorspace.c: In function ?LUV_to_polarLUV?:
> colorspace.c:342: warning: incompatible implicit declaration of built-in
> function ?sqrt?
> colorspace.c:343: warning: incompatible implicit declaration of built-in
> function ?atan2?
> colorspace.c: In function ?polarLUV_to_LUV?:
> colorspace.c:354: warning: incompatible implicit declaration of built-in
> function ?cos?
> colorspace.c:355: warning: incompatible implicit declaration of built-in
> function ?sin?
> colorspace.c: In function ?CheckSpace?:
> colorspace.c:373: warning: implicit declaration of function ?strcmp?
> colorspace.c: In function ?CheckHex?:
> colorspace.c:407: warning: implicit declaration of function ?strlen?
> colorspace.c:407: warning: incompatible implicit declaration of built-in
> function ?strlen?
> colorspace.c:411: warning: implicit declaration of function ?isxdigit?
> colorspace.c: In function ?hex_to_RGB?:
> colorspace.c:1115: warning: passing argument 1 of ?decodeHexStr? discards
> qualifiers from pointer target type
> make: *** [colorspace.o] Error 1
> ERROR: compilation failed for package 'colorspace'
> ** Removing
'/home/mspivako/R/i486-pc-linux-gnu-library/2.7/colorspace'
> 
> The downloaded packages are in
>         /tmp/RtmpSxK3ea/downloaded_packages
> Warning message:
> In install.packages("colorspace") :
>   installation of package 'colorspace' had non-zero exit status
> 
> 
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