I have been trying to install the SDMTools package from github, using devtools, and have also tried to install from the Cran archive, below is the code for installing through github:
devtools::install_github("jjvanderwal/SDMTools")
this is then the code to try and install from Cran archive:
install.packages("https://cran.r-project.org/src/contrib/Archive/SDMTools/SDMTools_1.1-221.2.tar.gz", repos = NULL, type="source")
Both of these produce the same error,
* installing *source* package 'SDMTools' ...
** package 'SDMTools' successfully unpacked and MD5 sums checked
** using staged installation
** libs
Warning in system(cmd) : 'make' not found
ERROR: compilation failed for package 'SDMTools'
* removing 'C:/Users/micha/AppData/Local/R/win-library/4.2/SDMTools'
Warning in install.packages :
installation of package ‘C:/Users/micha/AppData/Local/Temp/Rtmps1CvqJ/downloaded_packages/SDMTools_1.1-221.2.tar.gz’ had non-zero exit status
If anyone would be able to help with any suggestions of what to try or any alternative methods, would be greatly appreciated!
I am currently working on version 4.2.1, (have also tried this on version 4.1.3).
Related
I am trying to install the RADammi package on R 3.6 using "devtools", however I receive this error:
Installing package into ‘C:/Users/taham/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
ERROR: dependencies 'Biostrings', 'IRanges' are not available for package 'RADami'
* removing 'C:/Users/taham/Documents/R/win-library/3.6/RADami'
Error: Failed to install 'unknown package' from URL:
(converted from warning) installation of package > ‘C:/Users/taham/AppData/Local/Temp/RtmpycMnQ2/remotes11246cb38f0/RADami’ had non-zero exit status.
It is an old package that has been removed from CRAN
https://rdrr.io/cran/RADami/
how should I install it?
update:
I finally could manage to install the two dependencies using below command:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Biostrings")
BiocManager::install("IRanges")
I have downloaded the zip archived RADami file and tried to install the package, I receive this fetal error again:
install.packages("C:/Users/taham/Downloads/RADami_1.1-2.tar.gz", repos = NULL, type = "source")
Installing package into ‘C:/Users/taham/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
installing source package 'RADami' ...
** package 'RADami' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: objects 'c.phylo', 'c.multiPhylo' are not exported by 'namespace:ape'
Execution halted
ERROR: lazy loading failed for package 'RADami'
removing 'C:/Users/taham/Documents/R/win-library/3.6/RADami'
Warning in install.packages :
installation of package ‘C:/Users/taham/Downloads/RADami_1.1-2.tar.gz’ had non-> zero exit status
I get the same error when using devtools
It sounds like you need to first install "IRanges" and "Biostrings" from BioConductor:
library(devtools)
install_bioc("IRanges")
install_bioc("Biostrings")
Though these have other dependencies such as "S4Vector" which you may need to install manually also.
Then you should be able to install RADami:
install_url("https://cran.r-project.org/src/contrib/Archive/RADami/RADami_1.0-3.tar.gz")
I also had this issue with installing from the CRAN archive, but was successfully able to install it from the developer's Github. In R:
library(devtools)
install_github("andrew-hipp/RADami")
I am trying to install an archived R package, SciencesPo, but it's not installing, even after installing the dependencies. The following is the code and the messages that follow
install.packages("C:\Users\Overman\Downloads\SciencesPo_1.4.1.tar.gz", repos = NULL, type = "source")
Installing package into ‘C:/Users/Overman/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
* installing source package 'SciencesPo' ...
** package 'SciencesPo' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
Warning in system(cmd) : 'make' not found
ERROR: compilation failed for package 'SciencesPo'
* removing 'C:/Users/Overman/Documents/R/win-library/3.5/SciencesPo'
In R CMD INSTALL
Warning in install.packages :
installation of package ‘C:/Users/Overman/Downloads/SciencesPo_1.4.1.tar.gz’ had non-zero exit status
Installing Rtools solved the problem.
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.
I have a serious problem about R package installation in windows where I haven't got the administrator priveleges. For example, to install ggplot2 I did :
install.packages("C:/Users/Rasengan/Downloads/ggplot2_1.0.0.tar.gz", repos = NULL, type="source")
I get this error message :
ERROR: dependencies 'plyr', 'gtable', 'reshape2', 'scales', 'proto' are not available for package 'ggplot2'
* removing 'C:/Program Files/R/R-3.1.1/library/ggplot2'
Warning messages:
1: running command '"C:/PROGRA~1/R/R-31~1.1/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.1.1\library" "C:/Users/Rasengan/Downloads/ggplot2_1.0.0.tar.gz"' had status 1
2: In install.packages("C:/Users/Rasengan/Downloads/ggplot2_1.0.0.tar.gz", :
installation of package ‘C:/Users/Rasengan/Downloads/ggplot2_1.0.0.tar.gz’ had non-zero exit status
So the problem come from the pakage which depends ggplot2, what I tried is to install the different packages ('plyr', 'gtable', 'reshape2', 'scales', 'proto') one by one but the process is endless because 'plyr' depended of many or packages ...
Please could you help me, because I need shiny, ggplot2 and rCharts for my work.
Thank you in advance!
PS: the proto package doesn't depend of an other package, so I installed it easly :
> install.packages("C:/Users/Rasengan/Downloads/proto_0.3-10.tar.gz", repos = NULL, type="source")
* installing *source* package 'proto' ...
** package 'proto' successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'proto.Rnw'
'protoref.Rnw'
** testing if installed package can be loaded
* DONE (proto)
I am trying to install the R package "colorspace" in Ubuntu Linux from local repository as follows:
install.packages("/home/colorspace_1.2-4.tar.gz", repos = NULL, type="source")
This throws the following error:
Installing package into '/home/vertica/R/x86_64-unknown-linux-gnu-library/3.0'
(as 'lib' is unspecified)
* installing *source* package 'colorspace' ...
** package 'colorspace' successfully unpacked and MD5 sums checked
** libs
sh: make: command not found
ERROR: compilation failed for package 'colorspace'
* removing '/home/vertica/R/x86_64-unknown-linux-gnu-library/3.0/colorspace'
Warning message:
In install.packages("/home/colorspace_1.2-4.tar.gz", :
installation of package '/home/colorspace_1.2-4.tar.gz' had non-zero exit
status
Could someone help me with this issue?
Thank you.
Ravi
Its saying it can't find "make", which makes me think you don't have all the compilers and so on that you need to build packages from source.
Install the "build-essential" package, something like:
sudo apt-get install build-essential
from your command line (not from R!)