I am setting up ordination packages on my R platform and have
questions for installing the PCNM package. I am running an older
platform: iBook G3 (PPC processor), Mac OS 10.4.11, with R ver.
2.10.1 (installed from universal binary). I also have X-Code (ver.
3.4) installed. I tried to build some of the packages in the Darwin
terminal and run into some problems with AEM installation via the
PCNM compilation:
ibook:~ ambein$ R CMD build --binary AEM
* checking for file 'AEM/DESCRIPTION' ... OK
* preparing 'AEM':
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
Copyleft F. Guillaume Blanchet
Standardizable: FALSE
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building binary distribution
* installing *source* package 'AEM' ...
** libs
** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/
Resources/include -I/Library/Frameworks/R.framework/Resources/
include/i386 -I/usr/local/include -fPIC -g -O2 -c
buildbinary.c -o buildbinary.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-
headerpad_max_install_names -mmacosx-version-min=10.4 -undefined
dynamic_lookup -single_module -multiply_defined suppress -L/usr/
local/lib -o AEM.so buildbinary.o -F/Library/Frameworks/
R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/
Resources/include -I/Library/Frameworks/R.framework/Resources/
include/ppc -I/usr/local/include -fPIC -g -O2 -c buildbinary.c
-o buildbinary.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-
headerpad_max_install_names -mmacosx-version-min=10.4 -undefined
dynamic_lookup -single_module -multiply_defined suppress -L/usr/
local/lib -o AEM.so buildbinary.o -F/Library/Frameworks/
R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** preparing package for lazy loading
Attaching package: 'ade4'
The following object(s) are masked from package:base :
within
Loading required package: sp
Loading required package: boot
Loading required package: Matrix
Loading required package: lattice
Attaching package: 'lattice'
The following object(s) are masked from package:boot :
melanoma
Loading required package: MASS
Loading required package: nlme
Loading required package: maptools
Loading required package: foreign
Loading required package: deldir
deldir 0.0-12
Please note: The process for determining duplicated points
has changed from that used in version 0.0-9 (and previously).
Loading required package: coda
Loading required package: spam
Package 'spam' is loaded. Spam version 0.15-5 (2009-09-13).
Type demo( spam) for some demos, help( Spam) for an overview
of this package.
Help for individual functions is optained byadding the
suffix '.spam' to the function name, e.g. 'help(chol.spam)'.
Attaching package: 'spam'
The following object(s) are masked from package:Matrix :
norm
The following object(s) are masked from package:base :
backsolve,
forwardsolve
Attaching package: 'spdep'
The following object(s) are masked from package:ade4 :
mstree
** help
*** installing help indices
** building package indices ...
packaged installation of 'AEM' as AEM_0.2-6_R_powerpc-apple-
darwin8.11.1.tar.gz
* DONE (AEM)
ibook:~ ambein$ R CMD build --binary PCNM
Error: cannot change to directory 'PCNM'
ibook:~ ambein$ R CMD build --binary PCNM
* checking for file 'PCNM/DESCRIPTION' ... OK
* preparing 'PCNM':
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
copyleft
Standardizable: FALSE
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building binary distribution
* installing *source* package 'PCNM' ...
** R
** data
** inst
** preparing package for lazy loading
Attaching package: 'ade4'
The following object(s) are masked from package:base :
within
Loading required package: spdep
Loading required package: sp
Loading required package: boot
Loading required package: Matrix
Loading required package: lattice
Attaching package: 'lattice'
The following object(s) are masked from package:boot :
melanoma
Loading required package: MASS
Loading required package: nlme
Loading required package: maptools
Loading required package: foreign
Loading required package: deldir
deldir 0.0-12
Please note: The process for determining duplicated points
has changed from that used in version 0.0-9 (and previously).
Loading required package: coda
Loading required package: spam
Package 'spam' is loaded. Spam version 0.15-5 (2009-09-13).
Type demo( spam) for some demos, help( Spam) for an overview
of this package.
Help for individual functions is optained byadding the
suffix '.spam' to the function name, e.g. 'help(chol.spam)'.
Attaching package: 'spam'
The following object(s) are masked from package:Matrix :
norm
The following object(s) are masked from package:base :
backsolve,
forwardsolve
Attaching package: 'spdep'
The following object(s) are masked from package:ade4 :
mstree
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/Library/Frameworks/R.framework/
Resources/library/AEM/libs/ppc/AEM.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/AEM/libs/
ppc/AEM.so, 6): no suitable image found. Did find:
/Library/Frameworks/R.framework/Resources/library/AEM/libs/
ppc/AEM.so: incompatible cpu-subtype
Error : package 'AEM' could not be loaded
ERROR: lazy loading failed for package 'PCNM'
* removing '/private/tmp/Rinst49133202/PCNM'
ERROR
* installation failed
From a previous attempt to install PCNM (before I installed XCode),
I ran into these errors:
ibook:~ ambein$ R CMD build --binary PCNM
* checking for file 'PCNM/DESCRIPTION' ... OK
* preparing 'PCNM':
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
copyleft
Standardizable: FALSE
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building binary distribution
* installing *source* package 'PCNM' ...
** R
** data
** inst
** preparing package for lazy loading
[...snip...]
[attached dependent packages successfully until:]
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/Library/Frameworks/R.framework/
Resources/library/AEM/libs/ppc/AEM.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/AEM/libs/
ppc/AEM.so, 6): no suitable image found. Did find:
/Library/Frameworks/R.framework/Resources/library/AEM/libs/
ppc/AEM.so: incompatible cpu-subtype
Error : package 'AEM' could not be loaded
ERROR: lazy loading failed for package 'PCNM'
* removing '/private/tmp/Rinst124078213/PCNM'
ERROR
* installation failed
So then I attempted to build AEM first:
ibook:~ ambein$ R CMD build --binary AEM
* checking for file 'AEM/DESCRIPTION' ... OK
* preparing 'AEM':
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
Copyleft F. Guillaume Blanchet
Standardizable: FALSE
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building binary distribution
* installing *source* package 'AEM' ...
** libs
** arch - i386
sh: line 1: make: command not found
ERROR: compilation failed for package 'AEM'
* removing '/private/tmp/Rinst134861442/AEM'
ERROR
* installation failed
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