I have been trying to install the ncdf R package. I have searched answers and attempted to solve the problem, but it looks like it's the time for me to ask for some help here.
I downloaded ncdf_1.6.5.tar.gz from this page ("https://cran.r-project.org/src/contrib/Archive/ncdf/), saved it in Download folder.
As it does not have a NAMESPACE file, I untar-ed the file and did the following
cd Downloads
cd ncdf
echo 'exportPattern( "." )' > NAMESPACE
cd ..
tar -zcf ncdf.tar.gz ncdf
Then I tried to install the package by this command
R CMD INSTALL -l /Users/xyc/Downloads/ncdf.tar.gz
It gave me this
ARGUMENT 'CDM' __ignor'e__
ARGUMENT 'INSTALL' __ignor'e__
AVIS : option inconnue '-l'
ARGUMENT 'ncdf.tar.gz' __ignor'e__
R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R est un logiciel libre livré sans AUCUNE GARANTIE.
Vous pouvez le redistribuer sous certaines conditions.
Tapez 'license()' ou 'licence()' pour plus de détails.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Tapez 'demo()' pour des démonstrations, 'help()' pour l'aide
en ligne ou 'help.start()' pour obtenir l'aide au format HTML.
Tapez 'q()' pour quitter R.
Obviously, this did not install the package.
I tried to install in RStudio by
install.packages("ncdf.tar.gz", lib = "/Users/xyc/Downloads", repos = NULL)
It showed me
* installing *source* package ‘ncdf’ ...
checking for nc-config... /opt/local/bin/nc-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
make: error: unable to find utility "make", not a developer tool or in PATH
ERROR: compilation failed for package ‘ncdf’
* removing ‘/Users/xyc/Downloads/ncdf’
* restoring previous ‘/Users/xyc/Downloads/ncdf’
Warning in install.packages :
installation of package ‘ncdf.tar.gz’ had non-zero exit status
Could someone help me here? Thank you very much.
UPDATE
Thank you for all your inputs. I downloaded Xcode 9 and a lower version of ncdf and did this
$ sudo xcode-select --switch /Users/xyc/Downloads/Xcode.app
$R CMD INSTALL ncdf_1.6.3.tar.gz
It gave me 96 warnings and 11 errors. The compilation failed again.
* installing to library ‘/Users/hhsieh/Library/R/3.4/library’
* installing *source* package ‘ncdf’ ...
checking for nc-config... /opt/local/bin/nc-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -
I/opt/local/include -I/usr/local/include -fPIC -Wall -g -O2 -c
._ncdf.c -o ._ncdf.o
._ncdf.c:1:1: warning: null character ignored [-Wnull-character]
<U+0000><U+0005><U+0016><U+0007><U+0000><U+0002><U+0000><U+0000>Mac OS
X <U+0000><U+0002><U+0000><U+0000>...
^
._ncdf.c:1:2: error: expected identifier or '('
<U+0000><U+0005><U+0016><U+0007><U+0000><U+0002><U+0000><U+0000>Mac OS
X <U+0000><U+0002><U+0000><U+0000>...
^
._ncdf.c:1:5: warning: null character ignored [-Wnull-character]
<U+0000><U+0005><U+0016><U+0007><U+0000><U+0002><U+0000><U+0000>Mac OS
X <U+0000><U+0002><U+0000><U+0000>...
^
._ncdf.c:1:7: warning: null character ignored [-Wnull-character]
<U+0000><U+0005><U+0016><U+0007><U+0000><U+0002><U+0000><U+0000>Mac OS
X <U+0000><U+0002><U+0000><U+0000>...
^
._ncdf.c:1:8: warning: null character ignored [-Wnull-character]
<U+0000><U+0005><U+0016><U+0007><U+0000><U+0002><U+0000><U+0000>Mac OS
X <U+0000><U+0002><U+0000><U+0000>...
^
._ncdf.c:1:25: warning: null character ignored [-Wnull-character]
<U+0000><U+0005><U+0016><U+0007><U+0000><U+0002><U+0000><U+0000>Mac OS
X <U+0000><U+0002><U+0000><U+0000>...
^
._ncdf.c:1:27: warning: null character ignored [-Wnull-character]
...OS X <U+0000><U+0002><U+0000><U+0000><U+0000> <U+0000>
<U+0000><U+0000>2<U+0000><U+0000><U+0000><AC>...
^
._ncdf.c:1:28: warning: null character ignored [-Wnull-character]
...OS X <U+0000><U+0002><U+0000><U+0000><U+0000> <U+0000>
<U+0000><U+0000>2<U+0000><U+0000><U+0000><AC>...
^
(warnings and error cut from here)
96 warnings and 11 errors generated.
make: *** [._ncdf.o] Error 1
ERROR: compilation failed for package ‘ncdf’
* removing ‘/Users/xyc/Library/R/3.4/library/ncdf’
I also tried this
$R CMD INSTALL --configure-args="-with-netcdf_incdir=/usr/local/netcdf/4.1.1-gcc/include -with-netcdf_libdir=/usr/local/netcdf/4.1.1-gcc/lib" ncdf_1.6.3.tar.gz
which also gave me 96 warnings and 11 errors.
96 warnings and 11 errors generated.
make: *** [._ncdf.o] Error 1
ERROR: compilation failed for package ‘ncdf’
* removing ‘/Users/xyc/Library/R/3.4/library/ncdf’
It looks like I still have a problem with XCode.
All suggestions are highly appreciated and welcome.
Thank you...
I tried to install the package "kohonen" and that is the output when trying to lauchn it
> require(kohonen)
Le chargement a nécessité le package : kohonen
Error: package or namespace load failed for ‘kohonen’ in dyn.load(file, DLLpath = DLLpath, ...):
impossible de charger l'objet partagé '/home/sebastien/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/libs/Rcpp.so':
~/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/libs/Rcpp.so: symbol _ZTTNSt7__cxx1118basic_stringstreamIcSt11char_traitsIcESaIcEEE, version GLIBCXX_3.4.21 not defined in file libstdc++.so.6 with link time reference
I tried to figure out what is going but I didn't find how to fix it. I'm on Ubuntu 14.04
I saw it may be fixed by downgrading gcc to 4.x (maybe 4.2, since the package sucessfully installed on my latpopo with this gcc version)
Current version is:
$ gcc --version
gcc (Homebrew gcc 5.4.0) 5.4.0
I saw you can have several gcc versions installed, but I dont know how to specify the gcc used by R.
EDIT
I tried using gcc 4.8 and R uses it. But it didn't solve my problem...
EDIT 2
It may be due to GLIBCXX_3.4.21 and libstdc++.so.6 with
But I have GLIBCC3.4.21
sebastien#sebastien-LABOFARM-HP-Z640-Workstation:~/.R$ strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
sebastien#sebastien-LABOFARM-HP-Z640-Workstation:/usr/lib/x86_64-linux-gnu$ ll libstdc*
lrwxrwxrwx 1 root root 19 août 20 21:01 libstdc++.so.6 -> libstdc++.so.6.0.24*
-rwxr-xr-x 1 root root 1114368 août 20 21:15 libstdc++.so.6.0.24*
I finally checked my laptop where the kohonen package works and i found this:
-rwxr-xr-x 1 root wheel 1471104 12 mar 2016 libstdc++.6.0.9.dylib
lrwxr-xr-x 1 root wheel 21 28 oct 2015 libstdc++.6.dylib -> libstdc++.6.0.9.dylib
lrwxr-xr-x 1 root wheel 17 28 oct 2015 libstdc++.dylib -> libstdc++.6.dylib
So basicallyI think my issue is libstdc++ is older so the package won't work.
I have tried to update gcc but it doesn't update libstdc++
Ok now some of my R packages cannot be load any more.
The error is the same; I'm lost
Ok so it seems my last error fix the original errors.
I just deleted every user installed R packages.
And then I reinstall some packages, including kohonen and it works.
Maybe some packages (dependencies from kohonen) were compiled with different gcc version compiler and it brokes everything
I would like to use the R package brms, but I get an error that I do not manage to interpret. It might have to do with Rtools, which is however installed on my computer.
This is an example from the brms package:
fit1 <- brm(count ~ log_Age_c + log_Base4_c * Trt_c
+ (1|patient) + (1|visit) + (1|obs),
data = epilepsy, family = poisson(),
prior = c(set_prior("student_t(5,0,10)", class = "b"),
set_prior("cauchy(0,2)", class = "sd")))
And this is the error I get:
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created!
c:/Rtools/mingw_64/bin/g++: not found
make: *** [file202834c75e9.o] Error 127
Warning message:
l'exécution de la commande 'make -f "C:/PROGRA~1/R/R-33~1.0/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-33~1.0/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="file202834c75e9.dll" WIN=64 TCLBIN=64 OBJECTS="file202834c75e9.o"' renvoie un statut 2
In addition: Warning message:
running command 'C:/PROGRA~1/R/R-33~1.0/bin/x64/R CMD SHLIB file202834c75e9.cpp 2> file202834c75e9.cpp.err.txt' had status 1
Thanks for your help
Indeed, it is a problem with Rtools. What does system("g++ -v") give you? If it is status 127, Rtools cannot be found by R. Most likely, you haven't checked the box during Rtools installation where you were asked to amend the system path. I suggest that you unintall Rtools and install it again making sure to check the box. Please also verify that you are using the correct version of Rtools compatible with your R version.
I had a similar problem with my installation of rstan. The problem occurred with RTools33. Installing RTools34 seemed to fix the problem, although I now get the following warning:
In find_rtools() :
WARNING: Rtools 3.4 found on the path at c:/Rtools is not compatible with R 3.3.1.
Please download and install Rtools 3.3 from http://cran.r-project.org/bin/windows/Rtools/, remove the incompatible version from your PATH, then run find_rtools().
So far this warning appears benign.
If none of the other answers solve this issue, go into your R distribution and open
R-{version}\etc\x64\Makeconf
and change BINPREF on line 19 to whatever the path to your mingw_64\bin directory is.
To fix this error:" c:/Rtools/mingw_64/bin/g++: not found" I located RBuildTools folder on the C: drive, found the g++ file in the bin folder, copied the mingw_64 folder (or wherever your g++ file is located), created an Rtools folder on C: and pasted the mingw_64 folder. This will create the C:/Rtools/mingw_64/bin/ path you need to compile R code using the stan( ) function.
I followed the rStan wiki here on Windows Configuration.
Also instead of hacking Makevars in c:\ you can create your personal by following the instruction here.
In my %HOM%\.R\Makevars.win64 file I have
CXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function
BINPREF="H:/RTools/mingw_64/bin/"
This resolved my issue.
I am trying intall "R programing course" from the package Swirl with the function `install_from_swirl("R Programming").When I typed the function it returns this error
Error en handle_setopt(h, ...) : no se pudo encontrar la función "anyNA"
How I can solve this problem?
I think that problem it's caused for the package Curl.
My R version is 3.0.2 (2013-09-25)
I'm having trouble trying to install rstan at my server running R (version 3.0.1) using Windows 7 (64-bits).
I installed Rcpp and inline, and I got "* DONE (rstan)". However, when I run
fit <- stan(model_code = schools_code, data = schools_dat,iter = 1000, chains = 4)
I get the followig error:
Erreur dans compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! cygwin warning:
MS-DOS style path detected: C:/PROGRA~1/R/R-30~1.2/etc/x64/Makeconf
Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-30~1.2/etc/x64/Makeconf
CYGWIN environment variable option "nodosfilewarning" turns off this warning.
De plus : Message d'avis :
l'exécution de la commande 'C:/PROGRA~1/R/R-30~1.2/bin/x64/R CMD SHLIB file16bc2e56893.cpp 2> file16bc2e56893.cpp.err.txt' renvoie un statut 1
Does any of you know what to do?
My understanding is that Windows users are advised to use RTools rather than Cygwin compilers. Search with "RTools windows r" and also read the "R Extensions Manual".