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AUCell #320

Closed s-aibar closed 7 years ago

s-aibar commented 7 years ago

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

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bioc-issue-bot commented 7 years ago

Hi @s-aibar

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: AUCell
Type: Package
Title: AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g.
    identify cells with specific gene signatures)
Version: 0.7.3
Date: 2017-03-14
Author: Sara Aibar, Stein Aerts. Laboratory of Computational Biology. VIB-KU
    Leuven Center for Brain & Disease Research. Leuven, Belgium
Maintainer: Sara Aibar <sara.aibar@kuleuven.vib.be>
Description: AUCell allows to identify cells with active gene sets (e.g.
    signatures, gene modules...) in single-cell RNA-seq data.
URL: http://scenic.aertslab.org
Imports:
    data.table,
    mixtools,
    BiocGenerics
Enhances: doMC, doRNG
Suggests:
    Biobase,
    GEOquery,
    DT,
    NMF,
    plotly,
    BiocStyle,
    knitr,
    rmarkdown,
    testthat
License: file LICENSE
biocViews: SingleCell,  GeneSetEnrichment, Transcriptomics, Transcription, GeneExpression
LazyData: TRUE
VignetteBuilder: knitr
RoxygenNote: 5.0.1
bioc-issue-bot commented 7 years ago

Your package has been approved for building. Your package is now submitted to our queue.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170314121438.html

bioc-issue-bot commented 7 years ago

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

aca8d67 Update version to 0.99.0

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170314161543.html

bioc-issue-bot commented 7 years ago

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

77bf72f 0.99.1: Do not load doMC on vignette. It is not av...

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170314162504.html

bioc-issue-bot commented 7 years ago

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

df97f42 0.99.1: Do not load doMC on vignette. It is not av... c4696a0 Merge branch 'master' of https://github.com/aertsl...

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170314163508.html

bioc-issue-bot commented 7 years ago

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

bf939c1 Update DESCRIPTION

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170315181322.html

bioc-issue-bot commented 7 years ago

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

3fa68eb Update DESCRIPTION

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170315183316.html

mtmorgan commented 7 years ago

19 March, 2017

DESCRIPTION

vignette

R

mtmorgan commented 7 years ago

The deadline for addition of packages to the next Bioconductor release is this Friday. If you'd like your package to be considered, please update your package and provide a written response to the review comments above.

s-aibar commented 7 years ago

Hello,

Thank you for reviewing the package and the heads-up about the deadline. We are working on the points mentioned on the review, but we are not expecting to be included in the next release of Bioc. We will push the new version to Github when it is ready -probably within a few weeks-.

Thank you, Sara Aibar

bioc-issue-bot commented 7 years ago

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

2689603 Update to version 0.99.3: - Improved selection of ... f762bd9 Merge branch 'master' of https://github.com/aertsl...

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170418090616.html

mtmorgan commented 7 years ago

It looks like development on this package has stalled. I will close the issue. Feel free to re-open it when you are ready to continue.

bioc-issue-bot commented 7 years ago

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

7ad1130 v 0.99.6

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, WARNINGS, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170808142034.html

bioc-issue-bot commented 7 years ago

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

b304c9f v 0.99.7

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170809084253.html

bioc-issue-bot commented 7 years ago

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

f0f64f0 v 0.99.8

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170809085642.html

s-aibar commented 7 years ago

Dear @mtmorgan ,

I have submitted a new version which addresses your comments. (Thank you for the suggestions, some of them were very useful!)

R CMD check and BiocCheck also run without error or warnings, except this one (which I'm not sure how to address):

Warning: replacing previous import SummarizedExperiment::shift by data.table::shift when loading AUCell

Thank you, Sara Aibar

PS: I think I cannot re-open the issue...

mtmorgan commented 7 years ago

In the NAMESPACE, instead of importing the entire package import(data.table) import only the things that you want importFrom(data.table, foo, bar) or import(data.table, except=shift).

bioc-issue-bot commented 7 years ago

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

be899b2 v 0.99.9 (Remove R CMD check warning)

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170809181339.html

bioc-issue-bot commented 7 years ago

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

f6193fc v 0.99.10 (small vignette fixex)

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170810082506.html

bioc-issue-bot commented 7 years ago

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

5e7729c v0.99.11 (Code cleaning)

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170810083822.html

bioc-issue-bot commented 7 years ago

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

f8efc7c v0.99.12

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170810164602.html

bioc-issue-bot commented 7 years ago

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

35f3038 v0.99.12 732619e Merge branch 'master' of https://github.com/aertsl...

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170810170246.html

bioc-issue-bot commented 7 years ago

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

568aa71 (version bump)

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170811094023.html

mtmorgan commented 7 years ago

Thanks very much for your revisions, which are mostly in line with the original comments. Unfortunately...

DESCRIPTION

bioc-issue-bot commented 7 years ago

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

dfb7304 v0.99.15: Change lisence & minor changes

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170925121246.html

bioc-issue-bot commented 7 years ago

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

ebdf893 v 0.99.16 eed8066 Merge branch 'master' of https://github.com/aertsl...

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170925122630.html

bioc-issue-bot commented 7 years ago

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

ebf08d8 v 0.99.17

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170926083923.html

bioc-issue-bot commented 7 years ago

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

db434ef 0.99.18

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/AUCell_buildreport_20170926085306.html

s-aibar commented 7 years ago

Hello,

We have changed the License to GPL-3 (plus a couple minor improvements). Please, let me know if everything is in order now.

Regards, Sara Aibar

bioc-issue-bot commented 7 years ago

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be sent to the maintainer email address in the next several days.

Thank you for contributing to Bioconductor!