tradeSeq - Githubissues

koenvandenberge commented 5 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Repository: https://github.com/statOmics/tradeSeq

Confirm the following by editing each check box to '[x]'

[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

I am familiar with the essential aspects of Bioconductor software management, including:

[x] The 'devel' branch for new packages and features.
[x] The stable 'release' branch, made available every six months, for bug fixes.
[x] Bioconductor version control using Git (optionally via GitHub).

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bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

433c80d fix earlyDETest, #14

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

cd20f5c fixed warnings on the splinfun function

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

af25ec4 correct documentation for S4 objects

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

74256ae bug in vignette

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

5796673 Update DESCRIPTION

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

56a4ace simplify code to return pairwise diffEndTest resul...

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

118c990 plotSmoothers now allows a white border around mea...

bioc-issue-bot commented 5 years ago

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bfad492 update docs

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

5917791 better way to have a smaller vignette

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

b58e1de removed accent on my name, see if that create an i...

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

4a6a717 fitGAM returns NA if mgcv gam did not fit

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

a371074 better checking whether mgcv fitting failed

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

eacf58b pairwise diffEndTest now also returns logFC

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

6aeb487 add FC output for diffEndTest if models are a list

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

a374277 add testing against fc cutoff for pairwise diffEnd...

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

697a7b8 set Wald stat to 0 if FC threshold not met

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

19339cb update R requirements

bioc-issue-bot commented 5 years ago

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5398359 version bump

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bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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koenvandenberge commented 5 years ago

Dear @Kayla-Morrell

We have now fixed all errors and warnings, except for one warning, which is related to our usage of set.seed in the code. We require this for reproducibility purposes, since we perform a multinomial sampling to assign cells to lineages in a trajectory. Note, that the seed can be passed as an argument to the fitGAM function, hence it is not hard coded in the package.

It would be great to get feedback concerning the submission of tradeSeq to Bioconductor.

Best, Koen

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

abefe3a add SD to authors

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7ab37eb fix single lineage issues, assocTest and startVsEn...

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bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

5f71651 few more pkg tests

Bioconductor / Contributions

tradeSeq #1157