[R] Problem installing Hmisc (more info)
Prof Brian Ripley
ripley at stats.ox.ac.uk
Sun Feb 6 08:50:39 CET 2005
On Sat, 5 Feb 2005, Michael Kubovy wrote:
> Following Brian Ripley's advice:
>
>> $ which g77
>> /sw/bin/g77
So I think you have fink.
> I then found Makeconf, in
> /Library/Frameworks/R.framework/Versions/2.0.1/Resources/etc
>
> I edited it according to Brian's advice. It had:
You didn't. You need to replace
L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 appropriately.
>
>> FLIBS = -L/usr/local/lib
>> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2
>> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -lfrtbegin
>> -lg2c -lSystem
> which now is:
>> FLIBS = -L/usr/local/lib
>> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2
>> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -L/sw/bin -lg2c
>> -lSystem
>
> Nevertheless the install failed just as below. But the console complaint was
> slightly different from before:
>> WARNING: ignoring environment value of R_HOME
>> * Installing *source* package 'Hmisc' ...
>> ** libs
>> g77 -fno-common -g -O2 -c cidxcn.f -o cidxcn.o
>> g77 -fno-common -g -O2 -c cidxcp.f -o cidxcp.o
>> g77 -fno-common -g -O2 -c hoeffd.f -o hoeffd.o
>> g77 -fno-common -g -O2 -c jacklins.f -o jacklins.o
>> g77 -fno-common -g -O2 -c largrec.f -o largrec.o
>> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
>> -I/usr/local/include -fno-common -g -O2 -c ranksort.c -o ranksort.o
>> g77 -fno-common -g -O2 -c rcorr.f -o rcorr.o
>> g77 -fno-common -g -O2 -c wclosest.f -o wclosest.o
>> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
>> Hmisc.so cidxcn.o cidxcp.o hoeffd.o jacklins.o largrec.o ranksort.o rcorr.o
>> wclosest.o -L/usr/local/lib
>> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2
>> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -L/sw/bin -lg2c
>> -lSystem -lcc_dynamic -framework R
>> ld: warning -L: directory name
>> (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2) does not exist
>> ld: warning -L: directory name
>> (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../..) does not exist
>> ld: can't locate file for: -lg2c
>> make: *** [Hmisc.so] Error 1
>> ERROR: compilation failed for package 'Hmisc'
>> ** Removing
>> '/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/Hmisc'
>> ** Restoring previous
>> '/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/Hmisc'
>
>> On Feb 5, 2005, at 4:59 PM, Prof Brian Ripley wrote:
>>
>>> On Sat, 5 Feb 2005, Michael Kubovy wrote:
>>>
>>>> Frank Harrell suggested I re-post with information about the version of
>>>> R
>>>
>>> Thanks, that starts to make sense. You appear to have g77 installed, but
>>> not in the place the person who prepared the binary install of R has it.
>>> Where do you have it installed? ('whereis g77' or 'which g77' should tell
>>> you.) Then you need to alter FLIBS in R_HOME/etc/Makeconf to point to it.
>>> (You can remove -lfrtbegin from FLIBS: it is not needed: your R_HOME looks
>>> to be /Library/Frameworks/R.framework/Versions/2.0.1.)
>>>
>>> However, I believe there is a more fundamental problem: because libg2c is
>>> a static library on current MacOS X, most packages using Fortran cannot be
>>> compiled there. That's presumably the case with Hmisc, as the automated
>>> package builder is not providing a binary build. (There is supposedly a
>>> check directory on CRAN, but it is not there at present.)
>>>
>>>>
>>>> Heres's the information:
>>>>>> version
>>>>> _
>>>>> platform powerpc-apple-darwin6.8
>>>>> arch powerpc
>>>>> os darwin6.8
>>>>> system powerpc, darwin6.8
>>>>> status
>>>>> major 2
>>>>> minor 0.1
>>>>> year 2004
>>>>> month 11
>>>>> day 15
>>>>> language R
>>>>
>>>> Here's what happens when I try to install:
>>>>>> install.packages("Hmisc")
>>>>> trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
>>>>> Content type `text/plain; charset=iso-8859-1' length 47565 bytes
>>>>> opened URL
>>>>> ==================================================
>>>>> downloaded 46Kb
>>>>>
>>>>> trying URL `http://cran.r-project.org/src/contrib/Hmisc_3.0-1.tar.gz'
>>>>> Content type `application/x-tar' length 453567 bytes
>>>>> opened URL
>>>>> ==================================================
>>>>> downloaded 442Kb
>>>>>
>>>>> Delete downloaded files (y/N)?
>>>>>
>>>>> The packages are in /tmp/Rtmp1911/Rinstdirfc4111
>>>>> Warning message:
>>>>> Installation of package Hmisc had non-zero exit status in:
>>>>> install.packages("Hmisc")
>>>>
>>>> Here's what the Console had to say:
>>>>> * Installing *source* package 'Hmisc' ...
>>>>> ** libs
>>>>> g77 -fno-common -g -O2 -c cidxcn.f -o cidxcn.o
>>>>> g77 -fno-common -g -O2 -c cidxcp.f -o cidxcp.o
>>>>> g77 -fno-common -g -O2 -c hoeffd.f -o hoeffd.o
>>>>> g77 -fno-common -g -O2 -c jacklins.f -o jacklins.o
>>>>> g77 -fno-common -g -O2 -c largrec.f -o largrec.o
>>>>> gcc -no-cpp-precomp
>>>>> -I/Library/Frameworks/R.framework/Resources/include
>>>>> -I/usr/local/include -fno-common -g -O2 -c ranksort.c -o ranksort.o
>>>>> g77 -fno-common -g -O2 -c rcorr.f -o rcorr.o
>>>>> g77 -fno-common -g -O2 -c wclosest.f -o wclosest.o
>>>>> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
>>>>> Hmisc.so cidxcn.o cidxcp.o hoeffd.o jacklins.o largrec.o ranksort.o
>>>>> rcorr.o wclosest.o -L/usr/local/lib
>>>>> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2
>>>>> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -lfrtbegin
>>>>> -lg2c -lSystem -lcc_dynamic -framework R
>>>>> ld: warning -L: directory name
>>>>> (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2) does not exist
>>>>> ld: warning -L: directory name
>>>>> (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../..) does not
>>>>> exist
>>>>> ld: can't locate file for: -lfrtbegin
>>>>> make: *** [Hmisc.so] Error 1
>>>>> ERROR: compilation failed for package 'Hmisc'
>>>>> ** Removing
>>>>> '/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/
>>>>> Hmisc'
>>>>> ** Restoring previous
>>>>> '/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/
>>>>> Hmisc'
>
> _____________________________
> Professor Michael Kubovy
> University of Virginia
> Department of Psychology
> USPS: P.O.Box 400400 Charlottesville, VA 22904-4400
> Parcels: Room 102 Gilmer Hall
> McCormick Road Charlottesville, VA 22903
> Office: B011 +1-434-982-4729
> Lab: B019 +1-434-982-4751
> Fax: +1-434-982-4766
> WWW: http://www.people.virginia.edu/~mk9y/
>
--
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
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