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How do I download and install "RTCGA.clinical" package? I have tried the following command to no avail. if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("RTCGA.clinical")
Thanks ```
Please provide you output/error, since those lines of code work for me:
(note that I included
force=TRUE
because I had the package already installed, and this argument is needed for a reinstall).Thanks for the response. I am installing it for the first time. Could not break through with what you gave. Thanks anyway
It is not clear to me what you mean...
If you copy the code below, and paste it in a freshly opened R session, then the package should install. The remainder of my output was to show you that the installation procedure ran, and finally that the package could be loaded in the R session (by using
library(RTCGA.clinical)
) .if (!require("BiocManager", quietly = TRUE))
replacement repositories: CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01) Installing package(s) 'RTCGA.clinical' installing the source package ‘RTCGA.clinical’
trying URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/RTCGA.clinical_20151101.24.0.tar.gz' Content type 'application/x-gzip' length 14652323 bytes (14.0 MB) downloaded 14.0 MB
The downloaded source packages are in ‘C:\Users\HP\AppData\Local\Temp\Rtmp69JU9M\downloaded_packages’ Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.1.2/library packages: class, foreign, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial Old packages: 'fansi', 'glue', 'magrittr', 'rlang', 'survival' Update all/some/none? [a/s/n]:
Above is the output from the command you sent.
OK, note this error message:
It basically states the installed version of the package
rlang
does not meet the requirements, and you should update it.Next note this message:
This means you started R on your Win10 machine with insufficient user rights; or you did start R as a different user that installed R (that obviously had installation rights). Although R should be able to handle this types of setups, when i need to install or update packages, I always run R on my Win10 machine as local administrator.
Lastly, if you could solve the 2nd issue then you would simply say
a[ll]
to this (last) question (and then install the packageRTCGA.clinical
again):Thank you very much. Installation completed.
Thanks for the response. I am installing it for the first time. Could not break through with what you gave. Thanks anyway