Here is my entire code:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.14")
BiocManager::install("rhdf5")
install.packages("devtools")
devtools::install_github("pachterlab/sleuth")
When I run just:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.14")
I get in the console:
if (!require("BiocManager", quietly = TRUE))
- install.packages("BiocManager")
BiocManager::install(version = "3.14")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for
details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.1.1/library
packages:
class, foreign, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
Old packages: 'cli'
Update all/some/none? [a/s/n]:
I type "a" into console and get:
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/cli_3.2.0.zip'
Content type 'application/zip' length 1257150 bytes (1.2 MB)
downloaded 1.2 MB
package ‘cli’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘cli’
Warning: restored ‘cli’
The downloaded binary packages are in
C:\Users\foste\AppData\Local\Temp\Rtmpy2Z9Er\downloaded_packages
Warning message:
In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\foste\Documents\R\win-library\4.1\00LOCK\cli\libs\x64\cli.dll to C:\Users\foste\Documents\R\win-library\4.1\cli\libs\x64\cli.dll: Permission denied
What in the world is going on? HELP! Thanks.