[R-SIG-Mac] package-install problem on Mac OS X lion
Rob Goedman
robjgoedman at me.com
Fri Sep 23 02:33:41 CEST 2011
John,
If re-installing Xcode doesn't fix this, what version of Xcode are you using? On my system 'which make' shows below symbolic link and version info.
Initially I had all kind of issues after installing Lion, but since switching to a prerelease version of IOS + Xcode 4.2 development tools the issues disappeared. My Xcode version is below.
With that setup, both 1.7-1, which I use, and 1.7-0 versions of Rcmdr compile and install fine, so I doubt there is anything wrong with the C code.
The other thing I noticed in the install output (below) is that the arch (i386) differs, but it looks like your install doesn't even get that far.
I do install from within R.app. From the command line, below output shows Rcmdr will compile, but can't find package 'car' (I probably need to specify the default library path).
I use R-devel. The Sys.info() and R.Version() look similar (also below).
Regards,
Rob
----------make------------------------------------------------------
Robs-Intel:Downloads rob$ which make
/usr/bin/make
Robs-Intel:Downloads rob$ ls -lia /usr/bin/make
98707895 lrwxr-xr-x 1 root wheel 7 Aug 10 17:42 /usr/bin/make -> gnumake
Robs-Intel:Downloads rob$ make --v
GNU Make 3.81
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.
This program built for i386-apple-darwin11.0
----------Xcode---------------------------------------------------
Version 4.2 (4D151a)
-----------Installing source of Rcmdr in R.app--------------------------
trying URL 'http://R-Forge.R-project.org/src/contrib/Rcmdr_1.7-1.tar.gz'
Content type 'application/x-gzip' length 2963563 bytes (2.8 Mb)
opened URL
==================================================
downloaded 2.8 Mb
* installing *source* package ‘Rcmdr’ ...
** libs
*** arch - x86_64
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 ismdi.c -o ismdi.o
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Rcmdr.so ismdi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/rob/Library/R/2.14/library/Rcmdr/libs/x86_64
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
The Commander GUI is launched only in interactive sessions
* DONE (Rcmdr)
------Installing from command line-------------------------------
Robs-Intel:Downloads rob$ R_ARCH=/x86_64 R CMD INSTALL Rcmdr_1.7-0.tar.gz
* installing to library ‘/Users/rob/Library/R/2.14/library’
* installing *source* package ‘Rcmdr’ ...
** libs
*** arch - x86_64
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 ismdi.c -o ismdi.o
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Rcmdr.so ismdi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/rob/Library/R/2.14/library/Rcmdr/libs/x86_64
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Error : package ‘car’ required by ‘Rcmdr’ could not be found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/rob/Library/R/2.14/library/Rcmdr’
* restoring previous ‘/Users/rob/Library/R/2.14/library/Rcmdr’
------R.Version()------------------------------------------------
> R.Version()
$platform
[1] "x86_64-apple-darwin9.8.0"
$arch
[1] "x86_64"
$os
[1] "darwin9.8.0"
$system
[1] "x86_64, darwin9.8.0"
$status
[1] "Under development (unstable)"
$major
[1] "2"
$minor
[1] "14.0"
$year
[1] "2011"
$month
[1] "09"
$day
[1] "20"
$`svn rev`
[1] "57033"
$language
[1] "R"
$version.string
[1] "R Under development (unstable) (2011-09-20 r57033)"
> Sys.info()
sysname
"Darwin"
release
"11.1.0"
version
"Darwin Kernel Version 11.1.0: Tue Jul 26 16:07:11 PDT 2011; root:xnu-1699.22.81~1/RELEASE_X86_64"
nodename
"Robs-Intel.local"
machine
"x86_64"
login
"rob"
user
"rob"
effective_user
"rob"
On Sep 22, 2011, at 3:54 PM, John Fox wrote:
> Dear all,
>
> After upgrading my MacBook Pro to OS X lion, I find that I'm unable to check or install the Rcmdr package, getting the following error:
>
> ---------- snip ---------
>
> John-Foxs-MacBook-Pro:workspace jfox$ R CMD INSTALL Rcmdr
> * installing to library ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library’
> * installing *source* package ‘Rcmdr’ ...
> ** libs
> *** arch - i386
> sh: make: command not found
> ERROR: compilation failed for package ‘Rcmdr’
> * removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcmdr’
> * restoring previous ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcmdr’
>
> ---------- snip ---------
>
> I am able to install from source other packages that don't have any compiled code, and so I hypothesize that this is due to some C code in the Rcmdr package. The Rcmdr installs fine on my Windows system and is built without error on R-Forge. As well, I was able to install the package from source before the OS upgrade.
>
> I've installed the current development version of R 2.13.2, gfortran 4.2.3 (probably not relevant because there's no fortran code in the package), and Xcode for lion from the Apple app store.
>
> Here are some more details of my system:
>
> ---------- snip ---------
>
>> Sys.info()
> sysname
> "Darwin"
> release
> "11.1.0"
> version
> "Darwin Kernel Version 11.1.0: Tue Jul 26 16:07:11 PDT 2011; root:xnu-1699.22.81~1/RELEASE_X86_64"
> nodename
> "John-Foxs-MacBook-Pro.local"
> machine
> "x86_64"
> login
> "jfox"
> user
> "jfox"
>
>> R.Version()
> $platform
> [1] "x86_64-apple-darwin9.8.0"
>
> $arch
> [1] "x86_64"
>
> $os
> [1] "darwin9.8.0"
>
> $system
> [1] "x86_64, darwin9.8.0"
>
> $status
> [1] "beta"
>
> $major
> [1] "2"
>
> $minor
> [1] "13.2"
>
> $year
> [1] "2011"
>
> $month
> [1] "09"
>
> $day
> [1] "19"
>
> $`svn rev`
> [1] "57033"
>
> $language
> [1] "R"
>
> $version.string
> [1] "R version 2.13.2 beta (2011-09-19 r57033)"
>
> ---------- snip ---------
>
> Any help would be appreciated.
>
> Thanks,
> John
>
> ------------------------------------------------
> John Fox
> Sen. William McMaster Prof. of Social Statistics
> Department of Sociology
> McMaster University
> Hamilton, Ontario, Canada
> http://socserv.mcmaster.ca/jfox/
>
> _______________________________________________
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