[#1343] Installing binary packages with Fortran code in MacOS

Date:
2011-04-05 12:59 Priority:
3

State:
Closed

Submitted by:
Jari Oksanen (jarioksa) Assigned to:
Nobody (None)

Hardware:
Macintosh Operating System:
None

Severity:
enhancement

URL:

Summary:
Installing binary packages with Fortran code in MacOS

Detailed description
Dear R-Forge maintainers, I have been informed recently that installation of binary package from R-Forge fails in MacOS. I don't have this problem, but other users have. This is the error they get when they try to load the package after seemingly successful installation: Loading required package: vegan Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.12/Resources/library/vegan/libs/x86_64/vegan.so': dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/library/vegan/libs/x86_64/vegan.so, 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib Referenced from: /Library/Frameworks/R.framework/Versions/2.12/Resources/library/vegan/libs/x86_64/vegan.so Reason: image not found The problem seems to missing Fortran runtime library. This issue seems to be discussed in R-MacOSX-FAQ section 5.4 which tells how to change the the package.so file to point to a fortran runtime library in the MacOSX R installation instead of the runtime used to build the package (and they say they do this in CRAN). Could it be possible to get this operation also in R-Forge so that users without similar Fortran compilers could be able to use R-Forge binaries. URL of the appropriate section in R-MacOSX-FAQ is http://cran.R-project.org/bin/macosx/RMacOSX-FAQ.html#Building-universal-package Best wishes, Jari Oksanen

Comments:

Message
Date: 2012-03-07 23:08 Sender: Clem Wang I'm not sure why this bug is closed... In any case, I read elsewhere that a work-around is to restart R and then try loading the library. That worked for me.
Date: 2012-03-02 01:58 Sender: Clem Wang Has any progress been made on making a good Mac binary for this package? When I try to load the library in R, I get an unhelpful error message: > install.packages("lme4") > library(lme4) Error in get(Info[i, 1], envir = env) : internal error -3 in R_decompress1 When I tried the instructions in the MacOSX-FAQ (mentioned in this thread to fix the problem), I got the error message using the Unix command line: $ for lib in `ls lme4/libs//.so`; do install_name_tool -change /usr/local/lib/libgfortran.2.dylib \ /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib \ $lib done install_name_tool: can't map file: lme4/libs/i386/lme4.so.dSYM (Invalid argument) install_name_tool: can't map file: lme4/libs/ppc/lme4.so.dSYM (Invalid argument) install_name_tool: can't map file: lme4/libs/x86_64/lme4.so.dSYM (Invalid argument) Or should I be doing something else? I'm using 2.14.2, on Mac OSX 10.6.8 on Intel Core i5 Many thanks in advance
Date: 2011-12-19 14:53 Sender: Stefan Theussl Dear Jari, thanks for this note. this is currently in testing stage. Will go online later today and hopefully fixes this issue. Best, Stefan
Date: 2011-12-18 15:52 Sender: Jari Oksanen I have had several user queries of vegan binaries failing in Mac. In one case I successfully followd instructions in http://cran.R-project.org/bin/macosx/RMacOSX-FAQ.html#Building-universal-package -- so I can confirm that this works- Could it be possible to have this kind of fixing of binary packages also in R-Forge so that the MacOS binaried offerred in R-Forge would work in Macs without Fortran installation? Cheers, Jari Oksanen

Attached Files:

Changes

Field	Old Value	Date	By
status_id	Open	2011-12-19 14:53	stefan7th
close_date	2011-12-19 14:53	2011-12-19 14:53	stefan7th