Whenever I try to install a new package I'm getting this error:
source("http://bioconductor.org/biocLite.R")
Warning in install.packages :
package ‘BiocInstaller’ is not available (for R version 3.0.2 RC)
Installing package into ‘/home/hd-master/R/x86_64-unknown-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)
trying URL 'http://www.bioconductor.org/packages/2.13/bioc/src/contrib/BiocInstaller_1.12.0.tar.gz'
Content type 'application/x-gzip' length 13509 bytes (13 Kb)
opened URL
==================================================
downloaded 13 Kb
Error in library(BiocInstaller) :
there is no package called 'BiocInstaller'
Execution halted
Install R-3.0.2 (not RC).
Try starting R as follows: R --vanilla
See if you are pointing to a weird mirror. What is the output of getOption("repos")?
Try this: install.packages("BiocInstaller", repos="http://bioconductor.org/packages/2.13/bioc")
Related
I am trying to use a function in the R package adegenet
It seems like it will install fine, but then when i call the package i get an error.
> install.packages("adegenet")
Installing package into ‘/Users/j2/Library/R/4.1/library’
(as ‘lib’ is unspecified)
trying URL 'https://mirrors.nics.utk.edu/cran/bin/macosx/contrib/4.1/adegenet_2.1.5.tgz'
Content type 'application/x-gzip' length 2830546 bytes (2.7 MB)
==================================================
downloaded 2.7 MB
The downloaded binary packages are in
/var/folders/p9/cy6q_pk935z1dfplsjrts30h0000gr/T//RtmpZXEMHg/downloaded_packages
> library(adegenet)
Error in value[[3L]](cond) :
Package ‘adegenet’ version 2.1.4 cannot be unloaded:
Error in unloadNamespace(package) : namespace ‘adegenet’ is imported by ‘adephylo’ so cannot be unloaded
I'm not sure if the problem is with the install or calling the library. Any advice would be appreceated.
Thanks!
I was using glmmTMB on a cluster. It was working for several weeks. I logged on today and it says I need to install glmmTMB. So, I tried that, but R is giving me the error below.
The main part says: failed to lock directory.
Thanks for any advice.
Installing package into ‘/home/xxxxxx/R/x86_64-redhat-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/glmmTMB_1.1.2.3.tar.gz'
Content type 'application/x-gzip' length 3910643 bytes (3.7 MB)
==================================================
downloaded 3.7 MB
ERROR: failed to lock directory ‘/home/xxxxxx/R/x86_64-redhat-linux-gnu-library/4.0’ for modifying
Try removing ‘/home/xxxxxx/R/x86_64-redhat-linux-gnu-library/4.0/00LOCK-glmmTMB’
Warning in install.packages :
installation of package ‘glmmTMB’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpYJgfa7/downloaded_packages’
I can't install.package("BatchGetSymbols") for some reason.
I am just doing this:
install.packages('BatchGetSymbols')
library(BatchGetSymbols)
and i am getting this:
> install.packages('BatchGetSymbols')
Installing package into ‘/home/rstudio/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
dependency ‘XML’ is not available
trying URL 'https://cran.rstudio.com/src/contrib/BatchGetSymbols_2.5.7.tar.gz'
Content type 'application/x-gzip' length 181321 bytes (177 KB)
==================================================
downloaded 177 KB
ERROR: dependency ‘XML’ is not available for package ‘BatchGetSymbols’
* removing ‘/home/rstudio/R/x86_64-pc-linux-gnu-library/3.6/BatchGetSymbols’
Warning in install.packages :
installation of package ‘BatchGetSymbols’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpAhaAos/downloaded_packages’
> library(BatchGetSymbols)
Error in library(BatchGetSymbols) :
there is no package called ‘BatchGetSymbols’
Does anyone understand why there is a problem??
Install the latest version of R before
Commands to install: https://cloud.r-project.org/bin/linux/
Choose the version of your system and run the commands
After that try to install the library.
I am trying to install 'gplots' in R 3.4.4, however I keep getting the following error:
install.packages("gplots")
Installing package into ‘/home/u1983390/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
Warning: dependency ‘caTools’ is not available
trying URL 'https://cloud.r-project.org/src/contrib/gplots_3.0.3.tar.gz'
Content type 'application/x-gzip' length 516153 bytes (504 KB)
==================================================
downloaded 504 KB
ERROR: dependency ‘caTools’ is not available for package ‘gplots’
* removing ‘/home/u1983390/R/x86_64-pc-linux-gnu-library/3.4/gplots’
The downloaded source packages are in
‘/tmp/Rtmplw9pSu/downloaded_packages’
Warning message:
In install.packages("gplots") :
installation of package ‘gplots’ had non-zero exit status
> install.packages('caTools')
Installing package into ‘/home/u1983390/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
Warning message:
package ‘caTools’ is not available (for R version 3.4.4)
I believe this can be solved by installing a version of caTools compatible with R 3.4.4 following this method. However, I cannot find where older versions of caTools are (I have looked in the CRAN archive).
Would anybody be able to direct me to an earlier version, or does anyone know a different method for instaling gplots?
Cheers,
Jamie
I'm attempting to install a package in R (v3.4 on Linux (64-bit)) and am being told that the execution was halted.
I attempted to log out of R and clear out my History and Environment. Below is the cod and the output I am getting:
> install.packages('zip')
Installing package into ‘/home/clang/R/x86_64-redhat-linux-gnu-library/3.4’ (as ‘lib’ is
unspecified) trying URL
'http://cran.rstudio.com/src/contrib/zip_1.0.0.tar.gz' Content type
'application/x-gzip' length 60823 bytes (59 KB)
================================================== downloaded 59 KB
Error: 1:7: unexpected '/' 1: setwd(/
^ Execution halted Warning in install.packages : installation of package ‘zip’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpaFlNP9/downloaded_packages’