I am having problems to install the package lme4 in R.
Following the output. It looks like it can't open nlopt. Someone knows how to solve it?
I am in Linux 16.10
checking nlopt.h usability... no
checking nlopt.h presence... no
checking for nlopt.h... no
configure: Need to download and build NLopt
trying URL 'http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz'
Error in download.file(url = "http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz", :
cannot open URL 'http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz'
Execution halted
/bin/tar: This does not look like a tar archive
gzip: stdin: unexpected end of file
/bin/tar: Child returned status 1
/bin/tar: Error is not recoverable: exiting now
Warning message:
In untar(tarfile = "nlopt-2.4.2.tar.gz") :
'/bin/tar -xf 'nlopt-2.4.2.tar.gz'' returned error code 2
configure: Starting to install library to /tmp/Rtmp1o9ETL/R.INSTALL2a78412beb2/nloptr/nlopt-2.4.2
./configure: line 3325: cd: nlopt-2.4.2: No such file or directory
Briefly:
There is no such thing as "Linux 16.10'
There is Ubuntu 16.10
[Optional] On Ubuntu, see this README from CRAN on how to get R and some packages prebuilt from CRAN
Irregardless, and answered here before checking for nlopt.h... no is the hint: do sudo apt-get install libnlopt-dev and try again.
You can get both r-cran-nloptr and r-cran-lme4 from Ubuntu too but those may be older versions given that your OS is 16.04, ie from 2016.
Related
I am trying to install the R package sf. It mentions the system dependencies GDAL, GEOS and PROJ.4. I have installed all of these using
$sudo apt-get install libgdal-dev libgeos-dev libproj-dev proj-bin
However sf still complains that it is missing (something from?) the libraries:
$sudo R CMD INSTALL sf_0.6-3.tar.gz
[...]
configure: pkg-config proj exists, will use it
checking proj_api.h usability... yes
checking proj_api.h presence... yes
checking for proj_api.h... yes
configure: PROJ: 4.9.2
checking for pj_init_plus in -lproj... no
configure: error: libproj not found in standard or given locations.
ERROR: configuration failed for package ‘sf’
The same goes for using the install.packages("sf") command in R. I am using R version 3.5.0 on an Ubuntu 16.04 system, I managed to install the package on another computer with R version 3.4.3 but don't know what I did different to make it work then. Both apt and pkg-config --modversion proj say that the version is higher than needed (4.9.2) and i tried to find some info that could help me resolve the problem using pkg-config or on the internet but couldn't find anything. I did find the following line in /usr/include/proj_api.h (found using sudo apt-file search proj_api.h):
projPJ pj_init_plus(const char *);
which mentions the thing in the check not found, but I don't understand in what way it relates to this.
As a note, I do have two versions of R installed, I also have version 3.2.3 on the computer. Could this be a source of the problem? (I am sure, that the version I am installing the sf package to is 3.5)
EDIT
I have found another R package (proj4) with the libproj dependency and tried to install that one. While it did stop at the same error, this one gave a longer message:
>install.packages("proj4")
[...]
checking proj_api.h usability... yes
checking proj_api.h presence... yes
checking for proj_api.h... yes
checking for pj_init_plus in -lproj... no
configure: error: libproj and/or proj_api.h not found in standard search locations.
*** Install PROJ.4 and if necessary set PKG_CPPFLAGS/PKG_LIBS accordingly.
ERROR: configuration failed for package ‘proj4’
The PKG_CPPFLAGS/PKG_LIBS variables? are not found in R, and echo $PKG_LIBS showed nothing either. Might there be a way I could set these so that the packages can be installed?
I am thankful for any tips or hints as to what causes this.
Peter
I think you may be using older versions of libgdal-dev and you
the following question could be the issue you are seeing
Rgdal installation failed on ubuntu 16.04
sudo add-apt-repository -y ppa:ubuntugis/ubuntugis-unstable
sudo apt update
sudo apt install gdal-bin python-gdal python3-gdal libgdal1-dev
I attempt to install Cairo package in R under a Docker Ubuntu 18.04 container. Before installing the R Cairo package, I installed these packets in Ubuntu: libgtk2.0-dev, libcairo2-dev, xvfb, xauth, xfonts-base, r-base-dev, and libxt-dev.
However, when I installed Cairo package in R, I got the following error:
checking if R was compiled with the RConn patch... no
checking cairo.h usability... yes
checking cairo.h presence... yes
checking for cairo.h... yes
checking for PNG support in Cairo... yes
checking for ATS font support in Cairo... no
configure: CAIRO_LIBS=-lfreetype -lz -lpng16 -lz -lcairo -lXext -lXrender -lX11
checking for library containing deflate... no
checking whether Cairo programs can be compiled... configure: error: Cannot
compile a simple Cairo program. See config.log for details.
ERROR: configuration failed for package ‘Cairo’
* removing ‘/opt/conda/lib/R/library/Cairo’
The downloaded source packages are in
‘/tmp/RtmprETcPh/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("Cairo") :
installation of package ‘Cairo’ had non-zero exit status
I've checked /tmp/RtmprETcPh/downloaded_packages, and there is only a filed called Cairo_1.5-9.tar.gz. And I don't know where to find config.log for more compile details of compiling a simple Cairo program.
Please help me to resolve out this issue if anybody know how to resolve out this issue.
Thank you
You may need to install the x11 dev libs since the docker container is likely not running these.
Try
sudo apt-get install libx11-dev
Under ubuntu 20.04, after installing libx11-dev, trying to install Cairo gave the error X11/Intrinsic.h not found. This is in libxt-dev. After installing this, Cairo could be installed.
I have looked at the multiple sources to figure out how to install rgeos and rgdal on Mac OS X High Sierra in a way that works with Anaconda Navigator. I mention Anaconda because I want to be able to build static project-specific, package environments to ensure that my projects work 6 months from now when the dependent packages change. I have successfully installed and used both rgeos and rgdal on a couple other computers but seem to be having issues on a new computer. I want to launch Shiny apps from Anaconda Navigator's RStudio. None of the solutions I found, listed below, worked:
https://dyerlab.ces.vcu.edu/2015/03/31/install-rgeos-on-osx/
https://cran.rstudio.com/web/packages/rgeos/rgeos.pdf
http://tlocoh.r-forge.r-project.org/mac_rgeos_rgdal.html
https://anaconda.org/conda-forge/r-rgdal
Based on the above sources and my slow progression through a series of error messages, I tried the following:
Install GDAL 2.2 Complete [30.0 MiB] 2018-3-10 from http://www.kyngchaos.com/software/frameworks. This installs GDAL, GEOS, PROJ, SQLite and UnixImageIO frameworks.
The above installed without an error message. But attempting to install rgeos gave an error message:
configure: error: geos-config not found or not executable.
Consequently, either the install failed and didn't notify me, or there is some type of $PATH issue (?). On a blog, someone suggested to do the following in response to the aforementioned issue:
brew install geos
The above completed successfully. So I went into RStudio and tried the following, which resolved the former error but produced a new one:
install.packages("~/Downloads/rgeos_0.3-28.tar.gz", repos = NULL, type = "source")
installing source package ‘rgeos’ ...
configure: CC: x86_64-apple-darwin13.4.0-clang
configure: CXX: x86_64-apple-darwin13.4.0-clang++
configure: rgeos: 0.3-28
checking for /usr/bin/svnversion... yes
cat: inst/SVN_VERSION: No such file or directory
configure: svn revision:
checking for geos-config... /usr/local/bin/geos-config
checking geos-config usability... yes
configure: GEOS version: 3.6.2
checking geos version at least 3.2.0... yes
checking geos-config clibs... yes
checking geos_c.h presence and usability... no
configure: error: geos_c.h not found in standard or given locations.
ERROR: configuration failed for package ‘rgeos’
removing ‘/Users/aloha2018/anaconda2/lib/R/library/rgeos’
Warning in install.packages :
installation of package ‘/Users/aloha2018/Downloads/rgeos_0.3-28.tar.gz’ had non-zero exit status
Any ideas on what to try next?
Naturally, I already tried in an RStudio application launched from Anaconda Navigator:
install.packages("rgeos")
install.packages("rgdal")
both from CRAN and from tar.gz. But it seems like it is unable to find a file called geos_c.h, which does indeed exist on my computer at:
/Library/Frameworks/GEOS.framework/Versions/3B/Headers/geos_c.h
Is there a way to tell RStudio to look in the directory containing that file so my rgeos and rgdal installations work? Are there other errors I should expect to encounter and if so, how do I avoid/resolve them?
I also tried in a Terminal window:
conda install -c conda-forge r-rgdal
but that fails after spending a long time attempting to "solve environment":
Andrews-MacBook-Pro:~ aloha2018$ conda install -c conda-forge r-rgdal
Solving environment: failed
UnsatisfiableError: The following specifications were found to be in conflict:
- r-rgdal
- rstudio==1.1.423
Use "conda info <package>" to see the dependencies for each package.
So I try:
conda r-rgdal
But there is no output:
Andrews-MacBook-Pro:~ aloha2018$ conda info r-rgdal
Andrews-MacBook-Pro:~ aloha2018$
I've had a similar issue. I first solved it by installing everything using conda using the following environment.yml configuration
name: london-crime-r
channels:
- conda-forge
- conda
dependencies:
- gdal
- geos
- r-base
- r-rcpp
- r-irkernel
- r-mass
- r-dplyr
- r-rgdal
- r-rgeos
- r-raster
- rstudio
However, after updating conda, resolving dependencies did not finish within the 10 hours so I went the traditional route:
Use brew to install geos and gdal. It takes 40 minutes to build on my machine.
brew install geos gdal
Once that has been achieved, install R packages in this sequence.
install.packages('sp', type='source')
install.packages("rgeos", repos="http://R-Forge.R-project.org", type="source")
require(rgeos)
install.packages("rgdal", repos="http://R-Forge.R-project.org", type="source")
require(rgdal)
Subsequently, the packages below are ok with the plain install.
libraries <- c("rgdal",
"rgeos",
"raster",
"spdep",
"spatstat")
install.packages(libraries)
I'm having trouble getting a package that I have written to install (on a Windows 10 machine).
I'm running R CMD build packagename (no errors), then R CMD check packagename_0.1.0.tar.gz (or R CMD INSTALL packagename)
After a number of successful log entries, the output reads
* checking whether package 'packagename' can be installed ...Warning: running command '"C:/PROGRA~1/R/R-3.4.0/bin/x64/Rcmd.exe" INSTALL -l
"C:/Work/parsimony_inapp/packagename.Rcheck" --no-html
"C:\Work\PARSIM~1\packagename.Rcheck\00_pkg_src\packagename"' had status 1
ERROR
Installation failed.
00install.out reports the error:
C:/MinGW/bin/gcc -shared -s -static-libgcc -o packagename.dll tmp.def fitch.o reorder.o -Ld:/Compiler/gcc-4.9.3/local330/lib/x64 -Ld:/Compiler/gcc-
4.9.3/local330/lib -LC:/PROGRA~1/R/R-3.4.0/bin/x64 -lR
C:/PROGRA~1/R/R-3.4.0/bin/x64/R.dll: file not recognized: File format not
recognized
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'packagename'
Oddly, I can install the package from GitHub using devtools::github_install('path/to/package').
Advice I've found elsewhere doesn't help:
setwd() in Rprofile - not present
Set R_WIN_NO_JUNCTIONS - no effect
I've updated to the latest version of R (3.4.0), RTools (34) and Cygwin, and checked that my PATH environment variable contains (in order) C:\Rtools\bin; C:\Rtools\mingw_32\bin; C:\Program Files\R\R-3.4.0\bin; C:\Program Files\R\R-3.4.0\bin\x64.
I've tried including and excluding C:\cygwin64\bin and C:\MinGW\msys\1.0\bin from the path, and have tried installations of Rtools with and without the Cygwin dlls, and have tried uninstalling Cygwin completely.
Installing statnet on mac 10.10.3 with R 3.2.x (RStudio 0.99.441).
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [latentnet.so] Error 1
ERROR: compilation failed for package ‘latentnet’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/latentnet’
Warning in install.packages :
installation of package ‘latentnet’ had non-zero exit status
ERROR: dependency ‘latentnet’ is not available for package ‘statnet’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/statnet’
Warning in install.packages :
installation of package ‘statnet’ had non-zero exit status
I tried updating XCode/Command Line Tools. Also tried not installing dependencies. I have been able to install other packages, such as ergm and sna.
It looks like the install is looking for the GCC folder and not finding it.
whereis gcc
reveals that my gcc is in /usr/bin/gcc
It looks like the install is looking for it in /usr/local/lib/gcc/
Is there a way to fix this?
This is a compilation error that you only get if you are trying to install packages from source, or when a package requires a library to be compiled from source. Normally, if you don’t use the latest version of R, you can install statnet from binary and thus R won’t have to compile the source package.
The version you are mentioning at the beginning of your message (0.99.441) is the version of your R-Studio, and not R. The version of your R is 3.2.x (Hence its address in the Library folder: /Library/Frameworks/R.framework/Versions/3.2/Resources…). Before trying to fix the compilation error you may want to try to roll back your R to a version like 3.1.2 or 3.1.3 on which you can probably download and install statnet in binary format.
For the compiler, my guess is that even if you fix the address of your gcc with a symlink, you will still get an error about gfortran or the version of gcc. Once I solved this issue by installing R and the right version of gcc through Homebrew, but right now I don’t have the possibility to try the solution and tell you exactly how.
My experience (on Yosemite) is that if you use 3.1.2 or 3.1.3, even if there is need for compilation, the error with gcc won’t occur.
sudo mkdir /usr/bin/lib && sudo ln -s /usr/bin/gcc /usr/bin/lib/gcc
Creates a new directory in /usr/bin called `lib' and creates a symbolic link to gcc in that new directory.
If that doesn't fix the error, you can undo it with:
sudo rm -i /usr/bin/lib/gcc && sudo rm -id /usr/bin/lib