R help - Nov 2011 - building biOps on macports, and configure--vars

All,

the MacOSX binary build of the biOps package is broken on cran, so I am trying
to compile from source. I am very close; the trick is apparently that this
package depends on fftw3, libjpeg and libtiff. My fftw3 is in /usr/local/, but
my libjpeg and libtiff are in /opt/local/ since i got them through macports. In
general, I'd like to keep as many of my third-party libraries as I can in
the macports system, which means that I need to point R CMD INSTALL to
/opt/local. Here is the problem I am running into:

This is my current command-line:
sudo R CMD INSTALL --configure-vars='LIBS=-L/opt/local/lib
CPPFLAGS=-I/opt/local/include/'
--configure-args='--includedir=/opt/local/include
--libdir=/opt/local/include' biOps_0.2.1.1.tar.gz

I found that by using the configure--vars argument i can get the
'configure' script to finish (without the configure--vars argument, the
'configure' script of course fails to find libjpeg and libtiff, and
exits).

However, after 'configure' runs, when the installer actually tries to
build the biOps package, it fails as follows:

gcc-4.2 -arch x86_64 -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include
-fPIC  -g -O2 -c jpegio.c -o jpegio.o
jpegio.c:36:21: error: jpeglib.h: No such file or directory
pegio.c: In function ?read_jpg_img_info?:
jpegio.c:52: error: storage size of ?cinfo? isn?t known
jpegio.c:53: error: storage size of ?jerr? isn?t known
[[... about 30 lines of this follow...]]
make: *** [jpegio.o] Error 1
ERROR: compilation failed for package ?biOps?

The problem is, obviously, that the gcc call is missing
"-I/opt/local/include", even though I put that in both
--configure-vars and --configure-args! I also note, that the
'--configure-args' seems to have no effect at all. It's
'--configure-vars' that allows the 'configure' script to finish
successfully.

I've searched and read various docs, but I don't know what else I can do
at this point (i'd like to avoid copying my libraries into /usr/local if at
all possible, and it does seem that the point of the configure--foo arguments is
to let me do that). Am I missing a necessary argument? Is it a bug in the biOps
package? Is there any solution/workaround that doesn't involve copying stuff
into /usr/local? Thanks for any help.


Yours,

Timothy Teravainen

Please don't ask non-R programming questions on R-help.

This is best asked on R-sig-mac, including details of how you built 
your R.  But the short answer is not to mix macports with the CRAN 
build of R.  And there are matching libs for CRAN's build at
http://r.research.att.com/libs/

On Thu, 17 Nov 2011, Timothy Teravainen wrote:
>
> All,
>
> the MacOSX binary build of the biOps package is broken on cran, so I am
trying to compile from source. I am very close; the trick is apparently that
this package depends on fftw3, libjpeg and libtiff. My fftw3 is in /usr/local/,
but my libjpeg and libtiff are in /opt/local/ since i got them through macports.
In general, I'd like to keep as many of my third-party libraries as I can in
the macports system, which means that I need to point R CMD INSTALL to
/opt/local. Here is the problem I am running into:
>
> This is my current command-line:
> sudo R CMD INSTALL --configure-vars='LIBS=-L/opt/local/lib
CPPFLAGS=-I/opt/local/include/'
--configure-args='--includedir=/opt/local/include
--libdir=/opt/local/include' biOps_0.2.1.1.tar.gz
>
> I found that by using the configure--vars argument i can get the
'configure' script to finish (without the configure--vars argument, the
'configure' script of course fails to find libjpeg and libtiff, and
exits).
>
> However, after 'configure' runs, when the installer actually tries
to build the biOps package, it fails as follows:
>
> gcc-4.2 -arch x86_64 -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include
-fPIC  -g -O2 -c jpegio.c -o jpegio.o
> jpegio.c:36:21: error: jpeglib.h: No such file or directory
> pegio.c: In function ?read_jpg_img_info?:
> jpegio.c:52: error: storage size of ?cinfo? isn?t known
> jpegio.c:53: error: storage size of ?jerr? isn?t known
> [[... about 30 lines of this follow...]]
> make: *** [jpegio.o] Error 1
> ERROR: compilation failed for package ?biOps?
>
> The problem is, obviously, that the gcc call is missing
"-I/opt/local/include", even though I put that in both
--configure-vars and --configure-args! I also note, that the
'--configure-args' seems to have no effect at all. It's
'--configure-vars' that allows the 'configure' script to finish
successfully.
>
> I've searched and read various docs, but I don't know what else I
can do at this point (i'd like to avoid copying my libraries into /usr/local
if at all possible, and it does seem that the point of the configure--foo
arguments is to let me do that). Am I missing a necessary argument? Is it a bug
in the biOps package? Is there any solution/workaround that doesn't involve
copying stuff into /usr/local? Thanks for any help.
>
>
> Yours,
>
> Timothy Teravainen
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595