Problem with new version - CRASHES

[kokyriakidis]

It crashes when I try to open it. There are also several problems when I try to install it. I am using TCGAbiolingsGUI version 1.5.2 and TCGAbiolinks 2.7.6

edit: When it crashed this message appears in R: Error : package or namespace load failed for 'minfi' in inDL(x, as.logical(local), as.logical(now), ...): unable to load shared object 'C:/Users/Konstantinos/Documents/R/win-library/3.4/openssl/libs/x64/openssl.dll': `maximal number of DLLs reached...

[tiagochst]

The last version is using more DLLs due to the number of packages than the default accepted by R. You will need to inscrese the R_MAX_NUM_DLLS.

Increasing loaded DLL

If you receive this error message: maximal number of DLLs reached... You will need to increase the maximum number of DLL R can load wit the enriroment variable R_MAX_NUM_DLLS.

For MACOS please modify the file /Library/Frameworks/R.framework/Resources/etc/Renviron and add R_MAX_NUM_DLLS=120 in the end. Or you can run in R the following command: system(' echo "R_MAX_NUM_DLLS=150" >> /Library/Frameworks/R.framework/Resources/etc/Renviron')

For UBUNTU please modify the file /usr/local/lib/R/etc/Renviron and add R_MAX_NUM_DLLS=120 in the end. Or you can run in R the following command: system(' echo "R_MAX_NUM_DLLS=150" >> /usr/local/lib/R/etc/Renviron')

For other OS check https://stat.ethz.ch/R-manual/R-patched/library/base/html/Startup.html.

[kokyriakidis]

I fixed that but there is another problem now. It needs another package:

library(TCGAbiolinksGUI) Loading required package: shinydashboard Attaching package: ‘shinydashboard’ The following object is masked from ‘package:graphics’: box Error: package ‘TCGAbiolinksGUI.data’ required by ‘TCGAbiolinksGUI’ could not be found

When I try to download the package with this link: devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinksGUI.data")

it says:

devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinksGUI.data") Downloading GitHub repo BioinformaticsFMRP/TCGAbiolinksGUI.data@master from URL https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinksGUI.data/zipball/master Installing TCGAbiolinksGUI.data "C:/PROGRA~1/R/R-34~1.3PA/bin/x64/R" --no-site-file
--no-environ --no-save --no-restore --quiet CMD
INSTALL
"C:/Users/Konstantinos/AppData/Local/Temp/Rtmp46vdTT/devtools1df04ba03e67/BioinformaticsFMRP-TCGAbiolinksGUI.data-b740f23"
--library="C:/Users/Konstantinos/Documents/R/win-library/3.4"
--install-tests

ERROR: this R is version 3.4.3, package 'TCGAbiolinksGUI.data' requires R >= 3.5.0 In R CMD INSTALL Installation failed: Command failed (1)

what can I do?

[tiagochst]

I donwngraded the R version. Actually Bioconductor requested to use version 3.5 for the devel. Now devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinksGUI.data",ref = "R_3.4) should work.