[R-SIG-Mac] problems installing gstat
Raphael.Viscarra-Rossel at csiro.au
Raphael.Viscarra-Rossel at csiro.au
Wed Oct 29 10:12:25 CET 2014
Hello
I am wondering if anyone else is having problems installing gstat in R
3.1.1 on yosemite (and also mavericks)?
I looked for similar problems on the web but found very little on this.
I also installed XCODE and then tried installing form source but then
other errors.
sessionInfo and errors below.
HelpŠ. please?
Raphael.
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.1.1
##### BEFORE INSTALLING XCODE
> install.packages('gstat',type="source", repos='http://cran.csiro.au/')
Installing package into Œ/Users/vis010/Library/R/3.1/library¹
(as Œlib¹ is unspecified)
trying URL 'http://cran.csiro.au/src/contrib/gstat_1.0-19.tar.gz'
Content type 'application/x-gzip' length 2045717 bytes (2.0 Mb)
opened URL
==================================================
downloaded 2.0 Mb
* installing *source* package Œgstat¹ ...
** package Œgstat¹ successfully unpacked and MD5 sums checked
creating cache ./config.cache
checking for gcc... gcc
checking whether the C compiler (gcc ) works... no
configure: error: installation or configuration problem: C compiler cannot
create executables.
ERROR: configuration failed for package Œgstat¹
* removing Œ/Users/vis010/Library/R/3.1/library/gstat¹
* restoring previous Œ/Users/vis010/Library/R/3.1/library/gstat¹
The downloaded source packages are in
Œ/private/var/folders/zk/jzsww5w169g2zbl5hp260575y_7z7l/T/RtmpwsAqM6/downl
oaded_packages¹
Warning message:
In install.packages("gstat", type = "source", repos =
"http://cran.csiro.au/") :
installation of package Œgstat¹ had non-zero exit status
###### AFTER INSTALLING XCODE
Installing package into ‘/Users/vis010/Library/R/3.1/library’
(as ‘lib’ is unspecified)
trying URL 'http://cran.csiro.au/src/contrib/gstat_1.0-19.tar.gz'
Content type 'application/x-gzip' length 2045717 bytes (2.0 Mb)
opened URL
==================================================
downloaded 2.0 Mb
* installing *source* package ‘gstat’ ...
** package ‘gstat’ successfully unpacked and MD5 sums checked
creating cache ./config.cache
checking for gcc... gcc
checking whether the C compiler (gcc ) works... yes
checking whether the C compiler (gcc ) is a cross-compiler... no
checking whether we are using GNU C... yes
checking whether gcc accepts -g... yes
checking how to run the C preprocessor... gcc -E
checking for AIX... no
checking for minix/config.h... no
checking for POSIXized ISC... no
checking for ANSI C header files... yes
checking for working const... yes
checking whether time.h and sys/time.h may both be included... yes
checking for 8-bit clean memcmp... yes
checking for vprintf... yes
checking for strstr... yes
checking for strtod... yes
checking for strtol... yes
checking for drand48... yes
checking for gettimeofday... yes
checking whether byte ordering is bigendian... no
checking for memory.h... yes
checking for ANSI C header files... (cached) yes
checking for gcc option to accept ANSI C...
checking for function prototypes... yes
checking for working const... (cached) yes
checking for complex.h... yes
checking for malloc.h... no
checking for varargs.h... no
checking for size_t... yes
checking for working const... (cached) yes
checking whether byte ordering is bigendian... (cached) no
checking for u_int
computing machine epsilon(s)
gcc -o macheps ./src/meschach/dmacheps.c
./src/meschach/dmacheps.c:36:1: warning: type specifier missing, defaults
to 'int' [-Wimplicit-int]
main()
^~~~
1 warning generated.
gcc -o macheps ./src/meschach/fmacheps.c
./src/meschach/fmacheps.c:36:1: warning: type specifier missing, defaults
to 'int' [-Wimplicit-int]
main()
^~~~
1 warning generated.
computing M_MAX_INT
gcc -o maxint maxint.c
./src/meschach/maxint.c:28:1: warning: type specifier missing, defaults to
'int' [-Wimplicit-int]
main()
^~~~
1 warning generated.
checking char \0 vs. float zeros
checking for bcopy... yes
checking for bzero... yes
checking for function prototypes
checking for function prototypes in structures
updating cache ./config.cache
creating ./config.status
creating makefile
sed: ./makefile.in: No such file or directory
creating src/config.h
creating src/machine.h
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c block.c -o block.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c chfactor.c -o chfactor.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c copy.c -o copy.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c data.c -o data.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c direct.c -o direct.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c err.c -o err.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c fit.c -o fit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c gcdist.c -o gcdist.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c getest.c -o getest.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c gls.c -o gls.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c glvars.c -o glvars.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c hsehldr.c -o hsehldr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c ivecop.c -o ivecop.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c lex.c -o lex.o
lex.l:352:7: warning: 'tmpnam' is deprecated: This function is provided
for compatibility reasons only. Due to security concerns inherent in the
design of tmpnam(3), it is highly recommended that you use mkstemp(3)
instead. [-Wdeprecated-declarations]
fn = tmpnam(NULL);
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Develo
per/SDKs/MacOSX10.10.sdk/usr/include/stdio.h:276:7: note: 'tmpnam' has
been explicitly marked deprecated here
char *tmpnam(char *);
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c lm.c -o lm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c lufactor.c -o lufactor.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c machine.c -o machine.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c mapio.c -o mapio.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c matop.c -o matop.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c meminfo.c -o meminfo.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c memory.c -o memory.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c msim.c -o msim.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c norm.c -o norm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c nsearch.c -o nsearch.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c parse.c -o parse.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c polygon.c -o polygon.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c pqueue.c -o pqueue.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c predict.c -o predict.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c pxop.c -o pxop.o
pxop.c:279:22: warning: passing 'u_int *' (aka 'unsigned int *') to
parameter of type 'int *' converts between pointers to integer types with
different sign [-Wpointer-sign]
numtransp = myqsort(px2->pe,px2->size);
^~~~~~~
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c qrfactor.c -o qrfactor.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c random.c -o random.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c read.c -o read.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c reml.c -o reml.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c s.c -o s.o
s.c:89:19: warning: unused variable 'VarName' [-Wunused-const-variable]
static const char VarName[] = "(R Data)";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c select.c -o select.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c sem.c -o sem.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c sim.c -o sim.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c solve.c -o solve.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c sparse.c -o sparse.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c sprow.c -o sprow.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c stat.c -o stat.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c submat.c -o submat.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c userio.c -o userio.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c utils.c -o utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c vario.c -o vario.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c vario_fn.c -o vario_fn.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c vario_io.c -o vario_io.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c vecop.c -o vecop.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
-fPIC -Wall -mtune=core2 -g -O2 -c version.c -o version.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined
dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib
-o gstat.so block.o chfactor.o copy.o data.o direct.o err.o fit.o gcdist.o
getest.o gls.o glvars.o hsehldr.o init.o ivecop.o lex.o lm.o lufactor.o
machine.o mapio.o matop.o meminfo.o memory.o msim.o norm.o nsearch.o
parse.o polygon.o pqueue.o predict.o pxop.o qrfactor.o random.o read.o
reml.o s.o select.o sem.o sim.o solve.o sparse.o sprow.o stat.o submat.o
userio.o utils.o vario.o vario_fn.o vario_io.o vecop.o version.o
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
installing to /Users/vis010/Library/R/3.1/library/gstat/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/Users/vis010/Library/R/3.1/library/xts/libs/xts.so':
dlopen(/Users/vis010/Library/R/3.1/library/xts/libs/xts.so, 6): Library
not loaded:
/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.2.dy
lib
Referenced from: /Users/vis010/Library/R/3.1/library/xts/libs/xts.so
Reason: image not found
ERROR: lazy loading failed for package ‘gstat’
* removing ‘/Users/vis010/Library/R/3.1/library/gstat’
* restoring previous ‘/Users/vis010/Library/R/3.1/library/gstat’
The downloaded source packages are in
‘/private/var/folders/zk/jzsww5w169g2zbl5hp260575y_7z7l/T/RtmpwsAqM6/downl
oaded_packages’
Warning message:
In install.packages("gstat", type = "source") :
installation of package ‘gstat’ had non-zero exit status
More information about the R-SIG-Mac
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