[R-SIG-Mac] Build error - not sure where to look
Ben Madin
lists at remoteinformation.com.au
Sun Mar 4 06:33:48 CET 2012
Thanks David,
On 04/03/2012, at 12:58 PM, David Winsemius wrote:
>> sh: make: command not found
>> ERROR: compilation failed for package ‘surveillance’
>
> Because it says that make is not found it would suggest that you need to provide more details about which version and where the developer tools were installed. I'm wondering if the PATH for R may not include the proper location.
>
> This package also require package:spc. The one that was used when I just compiled from source on a Leopard machine was spc_0.4.1.
My lack of low-level understanding may well be at fault here by the path for r do you mean this result from the Sys.getenv() call
in the GUI: PATH "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin"
in which case - none of them have a make in the them. There are however 'make' commands in :
/Developer/usr/bin (the old Xcode)
and
/Applications/Xcode.app/Contents/Developer/usr (I'm guessing the new one for Lion)
In the terminal
PATH
"/Library/Frameworks/PROJ.framework/Programs:/Library/Frameworks/GDAL.framework/Programs:/Library/Frameworks/MapServer.framework/Programs:/usr/local/pgsql/bin:/usr/local/mysql/bin:/usr/local/zend/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/X11/bin:/Developer/usr/bin:."
Which I guess explains the different error messages: So I added the new Xcode location to the system path, and re-ran R in the terminal and tried again :
still no joy - still can't find stdlib.h etc. Is there something else I've missed?
cheers
Ben
> install.packages(c('/Users/benmadin/Desktop/rgeos_0.2-3.tar.gz'), type='source', configure.args = '--with-geos-config=/Library/Frameworks/GEOS.framework/unix/bin/geos-config', repos=NULL)
* installing *source* package ‘rgeos’ ...
** package ‘rgeos’ successfully unpacked and MD5 sums checked
geos-config: /Library/Frameworks/GEOS.framework/unix/bin/geos-config
GEOS: 3.3.2dev
./configure: line 1263: test: 332dev: integer expression expected
CPPFLAGS: -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include
LIBS: -L/Library/Frameworks/GEOS.framework/Versions/3/unix/lib -lgeos
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/sp/include" -fPIC -g -O2 -c init.c -o init.o
In file included from init.c:1:
/Library/Frameworks/R.framework/Resources/include/R.h:28:20: error: stdlib.h: No such file or directory
/Library/Frameworks/R.framework/Resources/include/R.h:29:73: error: stdio.h: No such file or directory
In file included from /Library/Frameworks/R.framework/Resources/include/R.h:30,
from init.c:1:
/Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h:15:25: error: limits.h: No such file or directory
In file included from init.c:1:
/Library/Frameworks/R.framework/Resources/include/R.h:31:18: error: math.h: No such file or directory
In file included from /Library/Frameworks/R.framework/Resources/include/R.h:44,
from init.c:1:
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:24:39: error: string.h: No such file or directory
In file included from init.c:2:
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:801: error: expected declaration specifiers or ‘...’ before ‘FILE’
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:804: error: expected declaration specifiers or ‘...’ before ‘FILE’
make: *** [init.o] Error 1
ERROR: compilation failed for package ‘rgeos’
* removing ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/rgeos’
Warning message:
In install.packages(c("/Users/benmadin/Desktop/rgeos_0.2-3.tar.gz"), :
installation of package ‘/Users/benmadin/Desktop/rgeos_0.2-3.tar.gz’ had non-zero exit status
Sys.getenv()
__CF_USER_TEXT_ENCODING
"0x1F5:0:15"
Apple_PubSub_Socket_Render
"/tmp/launch-zsxAK5/Render"
Apple_Ubiquity_Message
"/tmp/launch-7y6sZQ/Apple_Ubiquity_Message"
COMMAND_MODE
"unix2003"
DISPLAY
"/tmp/launch-kge8iE/org.x:0"
EDITOR
"vi"
HOME
"/Users/benmadin"
LANG
"en_AU.UTF-8"
LN_S
"ln -s"
LOGNAME
"benmadin"
MAKE
"make"
PAGER
"/usr/bin/less"
PATH
"/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin"
R_ARCH
"/x86_64"
R_BROWSER
"/usr/bin/open"
R_BZIPCMD
"/usr/bin/bzip2"
R_DOC_DIR
"/Library/Frameworks/R.framework/Resources/doc"
R_GUI_APP_REVISION
"6086"
R_GUI_APP_VERSION
"1.44"
R_GZIPCMD
"/usr/bin/gzip"
R_HOME
"/Library/Frameworks/R.framework/Resources"
R_INCLUDE_DIR
"/Library/Frameworks/R.framework/Resources/include"
R_LIBS_SITE
""
R_LIBS_USER
"~/Library/R/2.14/library"
R_PAPERSIZE
"a4"
R_PDFVIEWER
"/usr/bin/open"
R_PLATFORM
"x86_64-apple-darwin9.8.0"
R_PRINTCMD
"lpr"
R_QPDF
"/Library/Frameworks/R.framework/Resources/bin/qpdf"
R_RD4DVI
"ae"
R_RD4PDF
"times,inconsolata,hyper"
R_SESSION_TMPDIR
"/var/folders/sh/gwpnxgts1m9f3km36qr5wn600000gn/T//RtmpYZESBS"
R_SHARE_DIR
"/Library/Frameworks/R.framework/Resources/share"
R_SYSTEM_ABI
"osx,gcc,gxx,gfortran,?"
R_TEXI2DVICMD
"/usr/bin/texi2dvi"
R_UNZIPCMD
"/usr/bin/unzip"
R_ZIPCMD
"/usr/bin/zip"
SED
"/usr/bin/sed"
SHELL
"/bin/bash"
SSH_AUTH_SOCK
"/tmp/launch-nTCbsk/Listeners"
TAR
"/usr/bin/gnutar"
TMPDIR
"/var/folders/sh/gwpnxgts1m9f3km36qr5wn600000gn/T/"
USER
"benmadin"
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