[R-SIG-Mac] problems installing gstat
Raphael.Viscarra-Rossel at csiro.au
Raphael.Viscarra-Rossel at csiro.au
Wed Oct 29 10:49:28 CET 2014
Dear Brian,
I am sorry for the confusion - I was trying everything and so the
mix-nmatch. My bad.
Thank you for your help though. Your suggestion worked and I now have
gstat installed.
Have not used it yet, but at least the library loaded fine.
Cheers!
Raphael.
On 29/10/2014 8:33 pm, "Prof Brian Ripley" <ripley at stats.ox.ac.uk> wrote:
>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/dow
>>nl
>> 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/Deve
>>lo
>> 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/dow
>>nl
>> 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
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>
>
>--
>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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