on typing
install.packages("ggplot2")
i get the following result:
Installing package into ‘/home/suraj/R/x86_64-pc-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Warning: dependency ‘plyr’ is not available
also installing the dependencies ‘reshape2’, ‘scales’
ERROR: dependency ‘plyr’ is not available for package ‘reshape2’
* removing ‘/home/suraj/R/x86_64-pc-linux-gnu-library/3.0/reshape2’
ERROR: dependency ‘plyr’ is not available for package ‘scales’
* removing ‘/home/suraj/R/x86_64-pc-linux-gnu-library/3.0/scales’
ERROR: dependencies ‘plyr’, ‘reshape2’, ‘scales’ are not available for package ‘ggplot2’
* removing ‘/home/suraj/R/x86_64-pc-linux-gnu-library/3.0/ggplot2’
The downloaded source packages are in
‘/tmp/RtmpSWlplq/downloaded_packages’
Warning messages:
1: In install.packages("ggplot2") :
installation of package ‘reshape2’ had non-zero exit status
2: In install.packages("ggplot2") :
installation of package ‘scales’ had non-zero exit status
3: In install.packages("ggplot2") :
installation of package ‘ggplot2’ had non-zero exit status
when i tried to install 'plyr' package by first downloading the plyr package and the using
install.packages("plyr_1.8.2.tar.gz",repos=NULL,type="source")
i get the following message:
Installing package into ‘/home/suraj/R/x86_64-pc-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)
ERROR: this R is version 3.0.2, package 'plyr' requires R >= 3.1.0
Warning message:
In install.packages("plyr_1.8.2.tar.gz", repos = NULL, type = "source") :
installation of package ‘plyr_1.8.2.tar.gz’ had non-zero exit status
install.packages("plyr_1.8.2.tar.gz",repos=NULL)
Installing package into ‘/home/suraj/R/x86_64-pc-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)
ERROR: this R is version 3.0.2, package 'plyr' requires R >= 3.1.0
Warning message:
In install.packages("plyr_1.8.2.tar.gz", repos = NULL) :
installation of package ‘plyr_1.8.2.tar.gz’ had non-zero exit status
plase can anyone guide me in this matter!
Install version 1.8.1 of plyr from http://cran.r-project.org/src/contrib/Archive/plyr
and everything works like a charm thanks to #nicola for helping me on this one
For Windows, the appropriate version of plyr can be found in the R 3.0 Windows Package Archive.
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 had used this to try to install the car package:
install.packages("car", dependencies=TRUE, INSTALL_opts = c('--no-lock'))
but received this error:
ERROR: dependency ‘openxlsx’ is not available for package ‘rio’
* removing ‘/home/dan-laptop/R/x86_64-pc-linux-gnu-library/3.2/rio’
Warning in install.packages :
installation of package ‘rio’ had non-zero exit status
ERROR: dependency ‘rio’ is not available for package ‘car’
* removing ‘/home/dan-laptop/R/x86_64-pc-linux-gnu-library/3.2/car’
Warning in install.packages :
installation of package ‘car’ had non-zero exit status
ERROR: dependency ‘car’ is not available for package ‘alr4’
* removing ‘/home/dan-laptop/R/x86_64-pc-linux-gnu-library/3.2/alr4’
Warning in install.packages :
installation of package ‘alr4’ had non-zero exit status
I tried installing the dependencies individually with no luck. Any help would be greatly appreciated. Thanks.
I am currently using RStudio for R right now. I am trying to use the broom::tidy function but am unable to install the broom package.
install.packages("broom")
generates the error:
ERROR: dependency ‘nlme’ is not available for package ‘psych’
* removing ‘/home/gherr/R/x86_64-pc-linux-gnu-library/3.2/psych’
Warning in install.packages :
installation of package ‘psych’ had non-zero exit status
ERROR: dependencies ‘psych’, ‘nlme’ are not available for package ‘broom’
* removing ‘/home/gherr/R/x86_64-pc-linux-gnu-library/3.2/broom’
Warning in install.packages :
installation of package ‘broom’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpwPtSkh/downloaded_packages’
install.packages("nlme")
generates this error:
Installing package into ‘/home/gherr/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘nlme’ is not available (for R version 3.2.3)
It appears that I am only unable to install the 'nlme' package and the other two installs are failing because it is a dependency.
I am using R 3.2.2 on a UNIX server (this is installed to my HOME).
Any package that I try to install returns an error message like this:
install.packages('knitr')
Warning: unable to access index for repository
https://cran.rstudio.com/src/contrib
Warning message:
package ‘knitr’ is not available (for R version 3.2.2)
I've also tried downloading the package source and installing manually, but that doesn't work:
install.packages('/home/baker/knitr_1.11.tar.gz',repos= NULL,type='source')
ERROR: dependencies ‘evaluate’, ‘digest’, ‘formatR’, ‘highr’, ‘markdown’, ‘stringr’, ‘yaml’ are not available for package ‘knitr’
* removing ‘/home/baker/R/lib64/R/library/knitr’
Warning message:
In install.packages("/home/baker/knitr_1.11.tar.gz", repos = NULL, :
installation of package ‘/home/baker/knitr_1.11.tar.gz’ had non-zero exit status
This is obviously a super frustrating problem...any ideas? I'm at a total loss.
I cannot install package useR2013, I try all possible commands from bioconductor web site and nothing. All the time I get the same message from R. Can You give any tips?
output of sessionInfo():
> install.packages("useR2013", repos=NULL, type="source")
Warning in install.packages :
package ‘useR2013’ is not available (for R version 3.0.1)
Installing package into ‘C:/Users/Bartek/Documents/R/win-library/3.0’
(as ‘lib’ is unspecified)
Ostrzeżenie: błędny pakiet 'useR2013'
BŁĄD: BŁĄD: nie określono pakietów
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-30~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Bartek\Documents\R\win-library\3.0" "useR2013"' had status 1
Warning in install.packages :
installation of package ‘useR2013’ had non-zero exit status
OR
> source("http://bioconductor.org/biocLite.R")
> install.packages("useR2013")
Warning in install.packages :
package ‘useR2013’ is not available (for R version 3.0.1)
Installing package into ‘C:/Users/Bartek/Documents/R/win-library/3.0’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘useR2013’ is not available (for R version 3.0.1)