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")
Related
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).
it seems that the package "geoR" was removed from the repository.
So after trying to install it manually with:
install.packages(file.choose(), repos=NULL, type="source")
Installing package into "geoR_1.8-1.zip"(as ‘lib’ is unspecified)package 'geoR' successfully unpacked and MD5 sums checkedError in utils:::unpackPkgZip(pkg, pkg_name, lib, libs_only, lock, reuse_lockdir = reuse_lockdir) :package 'geoR' not installed because it is not built for UCRTWarning in install.packages :installation of package ‘geoR_1.8-1.zip’ had non-zero exit status
I have the latest version of R (4.2.0).
So I've tried another command:
install.packages("geoR_1.8-1.zip", repos = NULL, type = "win.binary")
Installing package into ‘libpath’(as ‘lib’ is unspecified)package ‘geoR’ successfully unpacked and MD5 sums checkedError in install.packages : package ‘geoR’ not installed because it is not built for UCRT
So how do I make it work?
I've already tried to uninstall R, Rstudio, Rtools42 and all the folders associated...
After a long try, I came up with this:
If I try to install an older version of geoR,
install.packages("geoR_1.7-5.2.tar.gz", repos = NULL, type = "source")
Installing package into ‘C:/Users/.../AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
ERROR: dependencies 'splancs', 'RandomFields' are not available for package 'geoR'
* removing 'C:/Users/..../AppData/Local/R/win-library/4.2/geoR'
Warning in install.packages :
installation of package ‘geoR_1.7-5.2.tar.gz’ had non-zero exit status
So this seems a dependancies issue, and after installing splancs correctly, RandomFields (manually because there is no repository for it) give me this output after a long string (maybe the compilation):
make: *** [C:/PROGRA~1/R/R-42~1.0/etc/x64/Makeconf:257: brownresnick.o] Error 1
ERROR: compilation failed for package 'RandomFields'
* removing 'C:/Users/.../AppData/Local/R/win-library/4.2/RandomFields'
Warning message:
In install.packages(file.choose()) :
installation of package ‘C:/Users/rmish/Downloads/RandomFields_3.3.tar.gz’ had non-zero exit status
Somebody wants to help me?
Thanks in advance, I'm really stuck.
Both RandomFields and geoR are no longer available on CRAN, so you'll have to download their respective tar files. You'll also need to install the splancs package, which is available on CRAN.
install.packages("splancs")
Download the two other packages here:
http://www2.uaem.mx/r-mirror/src/contrib/RandomFields_2.0.66.tar.gz
https://cran.r-project.org/src/contrib/Archive/geoR/geoR_1.8-1.tar.gz
Install RandomFields first:
install.packages("C:/path/to/RandomFields_2.0.66.tar.gz", repos = NULL, type = "source")
And then geoR:
install.packages("C:/path/to/geoR_1.8-1.tar.gz", repos = NULL, type = "source")
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 boot up a clean instance of R Studio. I don't save my environments and I don't use an Rprofile file. I tried both commands:
install.packages("viridis")
install.packages("viridis", dependencies = TRUE)
and I get this error:
installing source package ‘viridis’ ...
** package ‘viridis’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading Error : object ‘cividis’ is not exported by 'namespace:viridisLite' ERROR: lazy loading failed for
package ‘viridis’
removing ‘/home/stackinator/Rlibs/viridis’ Warning in install.packages : installation of package ‘viridis’ had non-zero exit status
Try the following:
if (!require("devtools")) install.packages("devtools")
devtools::install_github("sjmgarnier/viridis")
I am not sure why downloading it from CRAN didn't work, but devtools::install_github() downloads the source package from the repository rather than the bundled package that you get from CRAN with install.packages()
For more, check out this discussion from R Packages book:
http://r-pkgs.had.co.nz/package.html
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)