SCM

[#269] Pre-compiled fails on Mac 10.4, source okay

Date:
2008-12-16 23:12
Priority:
2
State:
Closed
Submitted by:
Brian O'Meara (bcomeara)
Assigned to:
Jim Regetz (regetz)
Operating System:
MacOS X
Severity:
normal
Resolution:
None
Component:
None
Version:
None
URL:
Summary:
Pre-compiled fails on Mac 10.4, source okay

Detailed description
Installing the binary from R-forge fails on Mac OS 10.4. This is because the binary is built on 10.5 machines, evidently, and not cross-compiled (right term?) for 10.4 machines. See <http://lists.apple.com/archives/darwin-dev/2007/Nov/msg00107.html>. Building from source works on 10.4.

Here's the screen dump (the "_strtod$UNIX200" makes me think it's a 10.5 compilation thing, given the apple discussion above):

> install.packages("phylobase",repos="http://R-Forge.R-project.org";)
trying URL 'http://R-Forge.R-project.org/bin/macosx/universal/contrib/2.8/phylobase_0.4.tgz'
Content type 'application/x-gzip' length 624354 bytes (609 Kb)
opened URL
==================================================
downloaded 609 Kb


The downloaded packages are in
/tmp/Rtmp2iKH8s/downloaded_packages
> library(phylobase)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/Library/Frameworks/R.framework/Resources/library/phylobase/libs/i386/phylobase.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/phylobase/libs/i386/phylobase.so, 6): Symbol not found: _strtod$UNIX2003
Referenced from: /Library/Frameworks/R.framework/Resources/library/phylobase/libs/i386/phylobase.so
Expected in: /usr/lib/libSystem.B.dylib

Error in library(phylobase) : .First.lib failed for 'phylobase'
>

Comments:

Message  ↓
Date: 2010-04-01 20:23
Sender: Peter Cowan

I say we close it. 10.4 is 5 years old now and hasn't gotten an update from Apple in 3 years. Since it's release there have been two new operating systems.

Date: 2010-04-01 20:11
Sender: François Michonneau

What's the status of this bug? Does anybody have a Mac with 10.4 to test with our new approach of building NCL?

Date: 2009-08-26 18:55
Sender: Peter Cowan

Summary -- there's nothing we can do at this point.

According to the message Jim sent to the list, it appears that the package isn't being properly cross compiled by R-Forge. This may be related to our use of C++ code (NCL). There is hope that CRAN will compile this correctly. If so we should file a feature request with R-Forge.

Date: 2009-08-19 19:53
Sender: Jim Regetz

I have a machine to test this on as soon as R-Forge successfully builds the OS X binary.

Date: 2009-08-19 19:16
Sender: François Michonneau

I suspect R-forge only tries to build if it detects a change in the version number (and not in revision number). I committed the cleanup code after the building time yesterday so we can't test its effects on Mac.

I propose we now call 0.4.2 version in trunk to see if it solves the building issue.

Date: 2009-08-19 19:07
Sender: Ben Bolker

status? maybe fixed by François's "cleanup" code?

Date: 2009-08-13 18:32
Sender: François Michonneau

The check logs for the Mac build says:
** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -IRcppSrc -Incl/ncl -fPIC -mtune=core2 -g -O2 -c NCLInterface.cpp -o NCLInterface.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -IRcppSrc -Incl/ncl -fPIC -mtune=core2 -g -O2 -c ReadWithNCL.cpp -o ReadWithNCL.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o phylobase.so NCLInterface.o ReadWithNCL.o -LRcppSrc -lRcpp -Lncl/ncl/.libs -lncl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: library not found for -lncl
collect2: ld returned 1 exit status

The logs for the Windows build look ok though...

Date: 2009-08-13 18:21
Sender: Brian O'Meara

Can't check it, as there is no Mac binary on R-forge (see <https://r-forge.r-project.org/bin/macosx/universal/contrib/latest/phylobase_0.4.tgz>. Source still builds on OS 10.4 (on my Mac, at least). There's no windows binary on R-forge, either.

Date: 2009-08-13 17:46
Sender: Ben Bolker

bump: what is the status of this bug?

Date: 2008-12-18 03:57
Sender: Ben Bolker

should we contact R-forge admins on this one??

Attached Files:

Changes

Field Old Value Date By
status_idOpen2010-04-01 22:34francois
close_date2010-04-01 22:342010-04-01 22:34francois
assigned_toskembel2009-08-18 15:46skembel
assigned_tonone2009-08-18 15:45skembel
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