evanbiederstedt commented 4 years ago

I'm making the following PR, as I noticed this discussion: https://github.com/JEFworks/MUDAN/pull/4 CC @slowkow

I think there's some misunderstanding, as the biocViews: within the DESCRIPTION is used for devtools.

One can see this with the travis builds, e.g.

The downloaded source packages are in
    ‘/tmp/RtmpSvLVpx/downloaded_packages’
Installing R packages from GitHub: JEFworks/MUDAN
$ Rscript -e 'remotes::install_github(c("JEFworks/MUDAN"))'
Using bundled GitHub PAT. Please add your own PAT to the env var `GITHUB_PAT`
Downloading GitHub repo JEFworks/MUDAN@master
sva          (NA -> 3.36.0  ) [CRAN]
...

Installing 47 packages: sva, irlba, RANN, igraph, Rtsne, ROCR, entropy, BiocGenerics, AnnotationDbi, annotate, Biobase, XML, DBI, xtable, RCurl, IRanges, RSQLite, S4Vectors, bitops, bit64, blob, memoise, pkgconfig, Rcpp, BH, plogr, bit, rlang, vctrs, ellipsis, glue, futile.logger, snow, lambda.r, futile.options, formatR, limma, locfit, gtools, gdata, caTools, genefilter, BiocParallel, matrixStats, edgeR, magrittr, gplots
Installing packages into ‘/home/travis/R/Library’
(as ‘lib’ is unspecified)
trying URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/sva_3.36.0.tar.gz'
Content type 'application/x-gzip' length 441903 bytes (431 KB)
==================================================
downloaded 431 KB
...
etc.

codecov-commenter commented 4 years ago

Codecov Report

Merging #9 into master will not change coverage. The diff coverage is n/a.

@@           Coverage Diff           @@
##           master      #9    +/-   ##
=======================================
  Coverage    0.00%   0.00%            
=======================================
  Files           2       2            
  Lines         732     583   -149     
=======================================
+ Misses        732     583   -149

Impacted Files	Coverage Δ
R/mudan.R	`0.00% <0.00%> (ø)`
R/mudan_object.R	`0.00% <0.00%> (ø)`

Continue to review full report at Codecov.

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JEFworks commented 4 years ago

Thanks for the fix Evan! Appreciate it.

JEFworks / MUDAN

add biocViews to the DESCRIPTION #9

Codecov Report