hbc / bcbioRNASeq

R package for bcbio RNA-seq analysis.

https://bioinformatics.sph.harvard.edu/bcbioRNASeq

GNU Affero General Public License v3.0

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v0.2.5 #104

Closed mjsteinbaugh closed 6 years ago

mjsteinbaugh commented 6 years ago

@roryk This should work for testing bcbio integration.

Minor changes

Enable support bcbio integration, by modifying bcbioRNASeq() constructor to work with minimal bcbio test data.
Switched from internal usage of aes_() in favor of consistent usage of aes_string(). This will make the transition to [ggplot2][] v2.3.0 easier in a future update.

lintr-bot commented 6 years ago

R/AllClasses.R:645:1: style: Trailing blank lines are superfluous.

lintr-bot commented 6 years ago

R/AllClasses.R:645:1: style: Trailing blank lines are superfluous.

roryk commented 6 years ago

Looks like bioc-devel is failing

roryk commented 6 years ago

Maybe need to revert https://github.com/hbc/bcbioRNASeq/pull/104/commits/03ab682ec0858c33fa26a99625bee98143ee0258 ?

codecov[bot] commented 6 years ago

Codecov Report

Merging #104 into master will decrease coverage by 0.07%. The diff coverage is 95.91%.

@@            Coverage Diff             @@
##           master     #104      +/-   ##
==========================================
- Coverage    85.8%   85.72%   -0.08%     
==========================================
  Files          44       44              
  Lines        2254     2256       +2     
==========================================
  Hits         1934     1934              
- Misses        320      322       +2

Impacted Files	Coverage Δ
R/methods-plotExonicMappingRate.R	`91.66% <100%> (-0.23%)`	:arrow_down:
R/methods-plotIntronicMappingRate.R	`91.66% <100%> (-0.23%)`	:arrow_down:
R/AllClasses.R	`83.25% <95.74%> (-0.6%)`	:arrow_down:

Continue to review full report at Codecov.

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lintr-bot commented 6 years ago

R/AllClasses.R:645:1: style: Trailing blank lines are superfluous.

lintr-bot commented 6 years ago

R/AllClasses.R:645:1: style: Trailing blank lines are superfluous.

mjsteinbaugh commented 6 years ago

Okay this should be good to go now.

roryk commented 6 years ago

Appveyor still borked, looks like the issue is building against devel, can we just build against release?

mjsteinbaugh commented 6 years ago

Not easily – checking against Bioconductor release uses a super old version on AppVeyor. We can just disable the build checks for this for the moment

lintr-bot commented 6 years ago

R/AllClasses.R:645:1: style: Trailing blank lines are superfluous.

lintr-bot commented 6 years ago

R/AllClasses.R:645:1: style: Trailing blank lines are superfluous.

mjsteinbaugh commented 6 years ago

@roryk Okay Travis and AppVeyor should both be good to go now

roryk commented 6 years ago

Awesome! Thanks so much Mike.