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mnem #805

Closed MartinFXP closed 5 years ago

MartinFXP commented 6 years ago

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bioc-issue-bot commented 6 years ago

Hi @MartinFXP

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: mnem
Type: Package
Title: mnem
Version: 0.99.0
Author: Martin Pirkl
Maintainer: Martin Pirkl <martin.pirkl@bsse.ethz.ch>
Description: Given a single cell populations from different perturbation experiments mnem infers sub populations with different states for a signaling pathway.
Depends: R (>= 3.4)
License: GPL-3
Encoding: UTF-8
LazyData: true
biocViews: Pathways, SystemsBiology, NetworkInference, Network, RNASeq, PooledScreens, SingleCell, CRISPR, ATACSeq, DNASeq
RoxygenNote: 6.0.1
Imports: cluster, nem, epiNEM, graph, Rgraphviz, flexclust, lattice, modeltools, naturalsort, snowfall, stats4, tsne, methods, graphics, grid, stats, utils
VignetteBuilder: knitr
Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit

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bioc-issue-bot commented 6 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

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 6 years ago

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

1f898a0 Deleted white space + version bump

bioc-issue-bot commented 6 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: "ABNORMAL". 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 build report for more details.

bioc-issue-bot commented 6 years ago

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

9fbb6f2 attended warnings and notes

bioc-issue-bot commented 6 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: "ABNORMAL". 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 build report for more details.

bioc-issue-bot commented 6 years ago

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

95d7163 reduced file size

bioc-issue-bot commented 6 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: "ABNORMAL". 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 build report for more details.

bioc-issue-bot commented 6 years ago

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

18c6a02 vignette bugfix

bioc-issue-bot commented 6 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: "ABNORMAL". 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 build report for more details.

bioc-issue-bot commented 6 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.

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bioc-issue-bot commented 6 years ago

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

17321b0 removed the devtools install and added bioconducto...

bioc-issue-bot commented 6 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 build report for more details.

hpages commented 5 years ago

Hi @MartinFXP,

Thanks for submitting the mnem package. Unfortunately it's almost impossible for me to use or review this package the way it's currently documented. The man pages and vignette are way too minimalist and cryptic. Please keep in mind that the purpose of contributing a package to Bioconductor is to share a tool that other people will be able to use.

Here are a few basic suggestions for improving the documentation and usability of the package:

Thanks, H.

bioc-issue-bot commented 5 years ago

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

4afec7e extended help file descriptions and vignette minor...

bioc-issue-bot commented 5 years ago

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

ba669de forgot to include plot.bootmnem help file

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 years ago

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

1a6e82e replaced last 1:... with seq_len

bioc-issue-bot commented 5 years ago

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

8ffd465 removed typo and added another

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 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 build report for more details.

MartinFXP commented 5 years ago

Dear @hpages,

Thanks for the feedback. I addressed all of your concrete points accordingly and made the vignette more user friendly.

Title of package should not be the same as its name.

Fixed.

Man pages have titles that are the same as description. The recommended practice is to use something different for the title and the description. The title is typically shorter and the description provides more details.

Extended descriptions.

The app dataset is a list of lists with a mysterious structure and content. The man page says "For details see the vignette" but AFAICT the vignette doesn't provide any detail about this data set. Please explain the structure and content of the data set. Also explain how it was generated.

Explanation of the data object added to vignette.

The vignette contains too much code and almost no explanation about what the code is doing. The code seems to be generating many plots and graphs but these are not explained either.

I added echo=FALSE for code which is either for experts or just a derivation of shown code (i.e. only an index has to be changed to get the other plots).

Check for typos e.g. "genens" instead of "genes" or "finde" instead of "find" etc... There are many!

Ran spell check.

Best, Martin

bioc-issue-bot commented 5 years ago

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

da725a8 fixed bug which occurs at random probability initi...

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 years ago

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

f0b6cf5 improved vignette

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 years ago

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

1351aad DISC: weights work; responsibilities need some wor...

bioc-issue-bot commented 5 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: "ABNORMAL". 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 build report for more details.

bioc-issue-bot commented 5 years ago

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

b7ab083 full support for discrete/binary data (alpha tests...

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 years ago

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

dec3376 added discrete example to vignette; improved table...

bioc-issue-bot commented 5 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.

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bioc-issue-bot commented 5 years ago

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

a715a02 vignette improvement: referenced paper instead of ...

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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

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

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bioc-issue-bot commented 5 years ago

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

bf98ad8 bump

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 years ago

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

3aeab99 edit figure captions; sim data explanation

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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

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

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bioc-issue-bot commented 5 years ago

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

d9789d6 removed typos; added nem references

bioc-issue-bot commented 5 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.

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bioc-issue-bot commented 5 years ago

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

f3cacdd updated citation; added multi knockout support; bu...

bioc-issue-bot commented 5 years ago

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

a95cc16 back to R >= 3.5

bioc-issue-bot commented 5 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.

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bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 years ago

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

8f08398 minor corrections to get the buzzards off my back

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 years ago

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

a4b3342 removed new last 1:...

bioc-issue-bot commented 5 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 build report for more details.