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Description
Hello,
I'm using the TCGAWorkflow package. My issue here is that I have an error that says that this package does not exist. I'm currently working with the 3.5.1 version of R and 3.7 of Bioconductor and I've tried to install the package through bioconductor and through github but I have an error on both commands.
Here are the errors:
-Through Bioconductor:
source("https://bioconductor.org/biocLite.R")
biocLite("TCGAWorkflow")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02).
Installing package(s) ‘TCGAWorkflow’
installing the source package ‘TCGAWorkflow’
trying URL 'https://bioconductor.org/packages/3.7/workflows/src/contrib/TCGAWorkflow_1.2.4.tar.gz'
Content type 'application/x-gzip' length 5181152 bytes (4.9 MB)
downloaded 4.9 MB
installing source package 'TCGAWorkflow' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called 'stringi'
ERROR: lazy loading failed for package 'TCGAWorkflow'
removing 'C:/Users/Ignasi/Documents/R/win-library/3.5/TCGAWorkflow'
In R CMD INSTALL
The downloaded source packages are in
‘C:\Users\Ignasi\AppData\Local\Temp\RtmpgbEJro\downloaded_packages’
installation path not writeable, unable to update packages: foreign, survival
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘TCGAWorkflow’ had non-zero exit status
library(TCGAWorkflow)
Error in library(TCGAWorkflow) :
there is no package called ‘TCGAWorkflow’
-Through github:
devtools::install_github('BioinformaticsFMRP/TCGAWorkflow')
Downloading GitHub repo BioinformaticsFMRP/TCGAWorkflow@master
from URL https://api.github.com/repos/BioinformaticsFMRP/TCGAWorkflow/zipball/master
Installing TCGAWorkflow
"C:/PROGRA1/R/R-351.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL
"C:/Users/Ignasi/AppData/Local/Temp/RtmpmWU4YM/devtools1dc43cb11a4d/BioinformaticsFMRP-TCGAWorkflow-93a30ee"
--library="C:/Users/Ignasi/Documents/R/win-library/3.5" --install-tests
installing source package 'TCGAWorkflow' ...
** R
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'
ERROR: lazy loading failed for package 'TCGAWorkflow'
removing 'C:/Users/Ignasi/Documents/R/win-library/3.5/TCGAWorkflow'
In R CMD INSTALL
Installation failed: Command failed (1)
I've done a little bit of research on this errors but I couldn't find anything and I don't know how to solve them.
PS: I'm new here and I wrote the same message at "package ‘TCGAWorkflow’ is not available #5", as a respond to the person that wrote the issue, not as a new issue.
Sorry.