[R-SIG-Mac] problems installing gstat

Prof Brian Ripley ripley at stats.ox.ac.uk
Wed Oct 29 10:33:23 CET 2014


Come on, that's not the error you posted about a few minutes ago.

This time you are using the wrong build of xts, one built for Snow 
Leopard it seems using an earlier version of gfortran.

You need to use either the Snow Leopard or Mavericks CRAN distribution 
of R, and install all your packages under just that build.  You cannot 
mix-n-match.


On 29/10/2014 09:12, Raphael.Viscarra-Rossel at csiro.au wrote:
> 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
>
>
>
>
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org
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>


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK



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