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RamsinghLab / arkas

This is the kallisto package
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committing cleanup changes & coercions #38

Closed ttriche closed 8 years ago

ttriche commented 8 years ago

also see artemis diffs (for sloppy TSS-based collapseTpm, etc.) which is apparently where they got lost. May cherrypick those into this PR if I can do so

arcolombo commented 8 years ago

yes using rowRanges directly seems like a way to go. since the KallistoExperiment class contains RangedSummarizedExperiment then rowRanges is already accessible. I wasn't sure if we could just blow out features and use rowRanges, and was currently putting in a slot for rowRanges and was going to write an accessor method x@rowRanges to be the new features (identical to SummarizedExperiment). but this method makes alot of sense; just call rowRanges itself since Kexp is a child-class. duh.

arcolombo commented 8 years ago

this should be merged ...

ttriche commented 8 years ago

bingo

by the way, the coercions work, although if memory runs low I get a node stack overflow error. That still annoys me; there has to be a brute force solution to that problem, I just haven't figured it out yet

--t

On Sat, Aug 13, 2016 at 6:19 PM, Anthony R. Colombo < notifications@github.com> wrote:

this should be merged ...

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arcolombo commented 8 years ago

so I've pulled down @ttriche new commit and have solved 2 warnings.

Status: 2 WARNINGs, 5 NOTEs See ‘/home/arcolombo/Documents/github_repos/arkas.Rcheck/00check.log’ for details.

Probably some imports need to be declared in the NAMESPACE file.

so I want to merge this later on. need to do some clean up. and testing on my end. but I think I managed to reduce 2 WARNINGS that were causing me some grief in my spiritual and emotional life.

peace kindness repeat.

arcolombo commented 8 years ago

merging PR #38 because it uses aliases. I am creating a PR #39 that incorporates collapseTSS, and also reduces many warnings down to 2 final warnings about documentation and \usage commands (Seemingly very simple/trivial to solve). so this is going in. TRAVIS is puking, but oh well.

arcolombo commented 8 years ago

I have it down to 1 WARNING about documentation

Status: 1 WARNING, 5 NOTEs See ‘/home/arcolombo/Documents/github_repos/arkas.Rcheck/00check.log’ for details.

perhaps this week we can discuss submitting this to BioC.

ttriche commented 8 years ago

nice work!!

--t

On Sun, Aug 14, 2016 at 6:39 PM, Anthony R. Colombo < notifications@github.com> wrote:

I have it down to 1 WARNING about documentation

  • checking Rd cross-references ... OK
  • checking for missing documentation entries ... WARNING Undocumented code objects: ‘eff_length’ ‘kallistoVersion’ ‘tpm’ ‘transcriptomes’ Undocumented S4 methods: generic 'counts' and siglist 'KallistoExperiment' generic 'eff_length' and siglist 'KallistoExperiment' generic 'kallistoVersion' and siglist 'KallistoExperiment' generic 'mad' and siglist 'KallistoExperiment' generic 'pData' and siglist 'KallistoExperiment' generic 'pData<-' and siglist 'KallistoExperiment,DataFrame' generic 'tpm' and siglist 'KallistoExperiment' generic 'transcriptomes' and siglist 'KallistoExperiment' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
  • checking for code/documentation mismatches ... OK
  • checking Rd \usage sections ... OK
  • checking Rd contents ... OK
  • checking for unstated dependencies in examples ... OK
  • checking contents of ‘data’ directory ... OK
  • checking data for non-ASCII characters ... OK
  • checking data for ASCII and uncompressed saves ... OK
  • checking installed files from ‘inst/doc’ ... OK
  • checking files in ‘vignettes’ ... OK
  • checking examples ... OK
  • checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: ‘arkasData’
  • checking package vignettes in ‘inst/doc’ ... OK
  • checking running R code from vignettes ... ‘Repeat-CrossValidation.Rmd’ using ‘UTF-8’ ... OK ‘arkas.Rmd’ using ‘UTF-8’ ... OK ‘calculateTpms.Rmd’ using ‘UTF-8’ ... OK ‘crossModels.Rmd’ ... OK ‘example.Rmd’ using ‘UTF-8’ ... OK ‘geneWiseAnalysis.Rmd’ using ‘UTF-8’ ... OK ‘gwa-safeExit.Rmd’ using ‘UTF-8’ ... OK NONE
  • checking re-building of vignette outputs ... OK
  • checking PDF version of manual ... OK
  • DONE

Status: 1 WARNING, 5 NOTEs See ‘/home/arcolombo/Documents/github_repos/arkas.Rcheck/00check.log’ for details.

perhaps this week we can discuss submitting this to BioC.

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