I was trying to install the 'pmml' package in R using the install.packages('') option as well as from source. But keep getting errors both ways.
Trying from R
install.packages('pmml',dependencies=T)
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/home/PepperBoy/R/x86_64-pc-linux-gnu-library/3.2/XML’
ERROR: dependency ‘XML’ is not available for package ‘pmml’
* removing ‘/home/PepperBoy/R/x86_64-pc-linux-gnu-library/3.2/pmml’
Trying from source
> install.packages('pmml_1.4.2.tar.gz', repos = NULL, type="source")
Installing package into ‘/home/PepperBoy/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
ERROR: dependency ‘XML’ is not available for package ‘pmml’
* removing ‘/home/PepperBoy/R/x86_64-pc-linux-gnu-library/3.2/pmml’
Warning message:
In install.packages("pmml_1.4.2.tar.gz", repos = NULL, type = "source") :
installation of package ‘pmml_1.4.2.tar.gz’ had non-zero exit status
Trying using R CMD INSTALL
% R CMD INSTALL pmml_1.4.2.tar.gz
* installing to library ‘/home/PepperBoy/R/x86_64-pc-linux-gnu-library/3.2’
ERROR: dependency ‘XML’ is not available for package ‘pmml’
* removing ‘/home/PepperBoy/R/x86_64-pc-linux-gnu-library/3.2/pmml’
I have also tried install the xml library for R using these same methods, but keep getting similar errors like
ERROR: configuration failed for package ‘XML’
* removing ‘/home/PepperBoy/R/x86_64-pc-linux-gnu-library/3.2/XML’
You need to install the system library libxm2-dev to install the XML package (on which pmml depends). So, if you are on Debian or Ubuntu, just install it through:
sudo apt-get install libxml2-dev
and then proceed with the R packages installation. Be careful to check the SystemRequirements section in the home page of any R package you want to install (for XML, see here).
Related
hi i am trying to install package for experiment designs like this
install.packages("daewr", dependencies = T)
but it returns the following
configure: error: GNU MP not found, or not 4.1.4 or up, see http://gmplib.org
ERROR: configuration failed for package ‘gmp’
* removing ‘/home/yeferson/R/x86_64-pc-linux-gnu-library/4.0/gmp’
Warning in install.packages :
installation of package ‘gmp’ had non-zero exit status
ERROR: dependency ‘gmp’ is not available for package ‘partitions’
* removing ‘/home/yeferson/R/x86_64-pc-linux-gnu-library/4.0/partitions’
Warning in install.packages :
installation of package ‘partitions’ had non-zero exit status
ERROR: dependency ‘partitions’ is not available for package ‘DoE.base’
* removing ‘/home/yeferson/R/x86_64-pc-linux-gnu-library/4.0/DoE.base’
Warning in install.packages :
installation of package ‘DoE.base’ had non-zero exit status
ERROR: dependency ‘DoE.base’ is not available for package ‘FrF2’
* removing ‘/home/yeferson/R/x86_64-pc-linux-gnu-library/4.0/FrF2’
Warning in install.packages :
installation of package ‘FrF2’ had non-zero exit status
ERROR: dependency ‘FrF2’ is not available for package ‘daewr’
* removing ‘/home/yeferson/R/x86_64-pc-linux-gnu-library/4.0/daewr’
Warning in install.packages :
installation of package ‘daewr’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpB1bSe0/downloaded_packages’
so i decided to download the file from https://cran.r-project.org/web/packages/daewr/index.html
after trying to install it returns me
also installing the dependencies ‘gmp’, ‘partitions’, ‘DoE.base’, ‘FrF2.catlg128’
I try to install the first one but it asks for a Bessel package and it still gives me problems
I solved it by installing dependency one by one, many answer you install the dependencies but they do not say how I will explain them for the new ones in linux and in R to install the daerw package with the aforementioned problems, install the following in the linux console
sudo apt-get install libgsl-dev
with that install libraries now I can open R and install
install.packages('gsl')
then I opened the linux console again and installed
sudo apt-get install libgmp-dev
I go back to R and install
install.packages("gmp", dependencies = T)
now I can install the package without problems
install.packages("daewr", dependencies = T)
library(daewr)
I hope that any comment is welcome.
I'm trying to install the 'agricolae' package on R, but I get an error saying
configure: error: libproj not found in standard or given locations.
ERROR: configuration failed for package ‘sf’
* removing ‘/R/x86_64-pc-linux-gnu-library/3.6/sf’
Warning in install.packages :
installation of package ‘sf’ had non-zero exit status
ERROR: dependency ‘sf’ is not available for package ‘spdep’
* removing ‘/R/x86_64-pc-linux-gnu-library/3.6/spdep’
Warning in install.packages :
installation of package ‘spdep’ had non-zero exit status
ERROR: dependency ‘spdep’ is not available for package ‘agricolae’
* removing ‘/R/x86_64-pc-linux-gnu-library/3.6/agricolae’
Warning in install.packages :
installation of package ‘agricolae’ had non-zero exit status
I recently upgraded to Ubuntu 18.04.2 and R version 3.6.0 (2019-04-26) -- "Planting of a Tree" and that's when the problems started.
When I do
$ sudo apt-get install -y libproj-dev
I get:
libproj-dev is already the newest version (5.2.0-1~bionic0).
The error says that package 'sf' is not available for dependency 'spdep'. So you should be attempting to install pkg 'sf'. (I'm on the same OS as you and pkg:agricolae installed without problem just now. I have a more complete set of spatial R and system packages than you do.)
Edit: There have been reports that it was necessary in addressing this problem to create an environment link to the location of your libraries:
$ export LD_LIBRARY_PATH=/lib:/usr/lib:/usr/local/lib
(From: https://stat.ethz.ch/pipermail/r-sig-geo/2018-August/026740.html which in turn linked to https://gis.stackexchange.com/questions/157059/repairing-broken-gdal-and-proj-4-on-ubuntu, which has so further debugging options mentioned.)
I'm running R 3.4.2 and R Studio 1.0.153. I want to install the prob package in R. The prob package in an archived file. It is located here. I am trying to install the prob_1.0-0.tar.gz package. I have no problem downloading and opening the package archive file. The code is below, it seems I need to install the fAsianOptions package.
ERROR: dependency 'fAsianOptions' is not available for package 'prob'
* removing 'C:/Users/blake_000/Documents/R/win-library/3.4/prob' Warning in install.packages : running command
'"C:/PROGRA~1/R/R-34~1.2/bin/x64/R" CMD INSTALL -l
"C:\Users\blake_000\Documents\R\win-library\3.4"
"C:/Users/BLAKE_~1/GOOGLE~1/Life/CSUEB/FALL20~1/6204-P~1/RCODE~1/prob_1.0-0.tar.gz"'
had status 1 Warning in install.packages : installation of package
‘C:/Users/BLAKE_~1/GOOGLE~1/Life/CSUEB/FALL20~1/6204-P~1/RCODE~1/prob_1.0-0.tar.gz’
had non-zero exit status
Unfortunately, the fAsianOptions package is also archived. It is located here and I downloaded version fAsianOptions_3010.79.tar.gz. There were a number of dependencies but I installed the required packages (timeDate, timeSeries, etc.)
However, the fAsianOptions package is not installing. The error code reads as follows:
install.packages("C:/Users/blake_000/Google Drive/Life/CSUEB/Fall
2017/6204- Probability/R Code/fAsianOptions_3010.79.tar.gz", repos =
NULL, type = "source") Installing package into
‘C:/Users/blake_000/Documents/R/win-library/3.4’ (as ‘lib’ is
unspecified)
* installing source package 'fAsianOptions' ...
** package 'fAsianOptions' successfully unpacked and MD5 sums checked
** libs
*** arch - i386 Warning: running command 'make -f "Makevars" -f "C:/PROGRA~1/R/R-34~1.2/etc/i386/Makeconf" -f
"C:/PROGRA~1/R/R-34~1.2/share/make/winshlib.mk"
SHLIB="fAsianOptions.dll" SHLIB_LIBADD='$(FLIBS)'
OBJECTS="EBMAsianOptions.o GammaFunctions.o
HypergeometricFunctions.o"' had status 127 ERROR: compilation failed
for package 'fAsianOptions'
* removing 'C:/Users/blake_000/Documents/R/win-library/3.4/fAsianOptions' Warning
in install.packages : running command
'"C:/PROGRA~1/R/R-34~1.2/bin/x64/R" CMD INSTALL -l
"C:\Users\blake_000\Documents\R\win-library\3.4"
"C:/Users/BLAKE_~1/GOOGLE~1/Life/CSUEB/FALL20~1/6204-P~1/RCODE~1/fAsianOptions_3010.79.tar.gz"'
had status 1 Warning in install.packages : installation of package
‘C:/Users/BLAKE_~1/GOOGLE~1/Life/CSUEB/FALL20~1/6204-P~1/RCODE~1/fAsianOptions_3010.79.tar.gz’
had non-zero exit status
I'm hoping that someone can help me to install the fAsianOptions dependency so I can install the prob package. Or, if there's an easier way, please let me know!
I had the same problem. I solved it by installing lower version of R -2.9. prob is available in repository for this version.
ERROR: dependencies ‘rJava’, ‘Rserve’ are not available for package ‘RHive’
* removing ‘/root/R/x86_64-redhat-linux-gnu-library/3.2/RHive’
How do I fix this?
I am trying to run:
R CMD INSTALL RHive_2.0-0.10.tar.gz
Directly uploading RHive to
R/x86_64-redhat-linux-gnu-library/3.2
gives
Error in library(RHive) : ‘RHive’ is not a valid installed package
I could run Rserve only by using
/usr/lib64/R/bin/R CMD /home/rstudio/R/x86_64-redhat-linux-gnu-library/3.2/Rserve/libs//Rserve
I was trying to install the devtools package in Rstudio by install.packages("devtools") but failed. The error messages are:
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Could not find libxml2. Please install libxml2-devel (rpm) or libxml2-dev (deb).
ERROR: configuration failed for package ‘xml2’
* removing ‘/home/xwang/R/x86_64-pc-linux-gnu-library/3.1/xml2’
Warning in install.packages :
installation of package ‘xml2’ had non-zero exit status
ERROR: dependency ‘xml2’ is not available for package ‘rversions’
* removing ‘/home/xwang/R/x86_64-pc-linux-gnu-library/3.1/rversions’
Warning in install.packages :
installation of package ‘rversions’ had non-zero exit status
ERROR: dependency ‘rversions’ is not available for package ‘devtools’
* removing ‘/home/xwang/R/x86_64-pc-linux-gnu-library/3.1/devtools’
Warning in install.packages :
installation of package ‘devtools’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpYccDpT/downloaded_packages’
Looks like it has trouble finding libxml-2.0. Does anyone know an easy fix to this? I'm using R version 3.1.2.
Eventually I fixed the problem by:
sudo apt-get install libxml2-dev
Then another problems popped up:
Error : object ‘curl_fetch_memory’ is not exported by 'namespace:curl'
which can be solved by installing the curl package:
install.packages("curl")
You just need to update to the newest version of R (R version 3.2.1)
It require some developer libraries (sources): curl developer, xml2 developer as dependecy.
so install it with the package repository (yum, dnf, apt-get) and retry to install the devtools package in R.