package ‘TCGAWorkflow’ is not available

[RobertBakaric]

The downloaded source packages are in
‘/common/tmp/RtmplmKhxH/downloaded_packages’
Warning message:
package ‘TCGAWorkflow’ is not available (for R version 3.4.4)

The downloaded source packages are in
‘/common/tmp/RtmplmKhxH/downloaded_packages’
Warning message:
package ‘TCGAWorkflow’ is not available (for R version 3.4.3)

The downloaded source packages are in
‘/common/tmp/RtmplmKhxH/downloaded_packages’
Warning message:
package ‘TCGAWorkflow’ is not available (for R version 3.2.0)

For which version is this available ? and for which bioconductor version ... Bioconductor 3.2 ?

[tiagochst]

Hello,

You will need Bioconductor >= 3.6 and R >= 3.4.

For Bioconductor 3.7 you can install with:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TCGAWorkflow")

For Bioconductor 3.6 you can install with:

source("http://bioconductor.org/workflows.R")
workflowInstall("TCGAWorkflow")

You can also install from github:

source("https://bioconductor.org/biocLite.R")
deps <- c("pathview","clusterProfiler","ELMER", "DO.db","GO.db", 
          "ComplexHeatmap","EDASeq", "TCGAbiolinks","AnnotationHub",
          "gaia","ChIPseeker","minet","BSgenome.Hsapiens.UCSC.hg19",
          "MotifDb","MotIV", "rGADEM", "motifStack","RTCGAToolbox")
for(pkg in deps)  if (!pkg %in% installed.packages()) biocLite(pkg, dependencies = TRUE)
deps <- c("devtools","DT","pbapply","readr","circlize")
for(pkg in deps)  if (!pkg %in% installed.packages())  install.packages(pkg,dependencies = TRUE)
devtools::install_github("BioinformaticsFMRP/TCGAWorkflowData")
devtools::install_github("BioinformaticsFMRP/TCGAWorkflow", dependencies = TRUE)

[IgnasiCI97]

Hello,

I'm also 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:

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.