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waldronlab / TCGAutils

Toolbox package for organizing and working with TCGA data
https://bioconductor.org/packages/TCGAutils
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depends on RTCGAToolbox 2.7.5 -- cannot find! #5

Closed vjcitn closed 7 years ago

vjcitn commented 7 years ago

Error in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘RTCGAToolbox’ 2.7.0 is being loaded, but >= 2.7.5 is required ERROR: lazy loading failed for package ‘TCGAutils’

maybe it is my lack of git strength? all i see in bioc is 2.7.0, devel branch

LiNk-NY commented 7 years ago

Hi Vince, @vjcitn Thanks creating this issue. The repo is located under:

BiocInstaller::biocLite("LiNK-NY/RTCGAToolbox")

I will add this note to the README in TCGAutils

lwaldron commented 7 years ago

Since your RTCGAToolbox is likely permanently disconnected from Mehmet's, and it is no longer actively maintained, would it be practical to put the relevant code in TCGAutils as non-exported functions and get rid of the dependency?

LiNk-NY commented 7 years ago

Hi Levi, @lwaldron The relevant code is integral to RTCGAToolbox. The improvements are mostly in naming consistency so to facilitate seamless extraction of data types. Please see: https://github.com/mksamur/RTCGAToolbox/compare/master...LiNk-NY:master for a difference between forks. It seems to me like these can be merged after a few improvements, namely removing @ from messages on my branch. Regards, Marcel

LiNk-NY commented 7 years ago

Update: It's possible that https://github.com/mksamur/RTCGAToolbox is out of sync with the Bioconductor repository. I have contacted Mehmet about this. More to follow. For now, the issue is closed.