mnem

[MartinFXP]

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• Repository: https://github.com/cbg-ethz/mnem

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6e78c38 full multi knockdown support + vignette update

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349bc67 minor corrections in the vignette and trying to ge...

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916132d improved some help files with return value lists

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[MartinFXP]

Dear @hpages

I think this is now somewhat the finalised version. Unless of course I or other users find any bugs...

I hope/think the vignette now gives a good overview of what to do with this package. The warning stems from the 7+ minutes runtime of the check on the windows machine, which seems to be (not always) quite a bit slower than its mac and linux colleagues (~3 minutes). I don't think it is trivial to account for that on my end.

Thanks again for your time and all the best, Martin

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25da374 speed increased: vignette + examples

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48c48c9 fixed discrete and improved some help files

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[hpages]

Hi @MartinFXP

Thanks for the much improved vignette!

2 things still need your attention:

• Your man page titles are still the same as their description. For example opening the man page for getIC (e.g. with ?getIC) displays a 4-line title that repeats the entire Description section.

• I still don't know how the app data set was generated. The Data Generation section of the vignette says:

  The R code for generating the data object ‘app’ is shown in the accompanying R file.

  What is the "accompanying R file"? Where is it? Note that the primary documentation for any function or data set defined in an R package is its man page so any information about how the app data set was generated should appear there.

Thanks, H.

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603e535 separated title and description include=TRUE for d...

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c63805f changed returned 1:... to seq_len(...

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368eb62 corrected line indent

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

7bc0f9f 3rd time's the cha...

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[MartinFXP]

Dear @hpages

• Your man page titles are still the same as their description. For example opening the man page for getIC (e.g. with ?getIC) displays a 4-line title that repeats the entire Description section.

Fixed.

• I still don't know how the app data set was generated. The Data Generation section of the vignette says:

  The R code for generating the data object ‘app’ is shown in the accompanying R file.

  What is the "accompanying R file"? Where is it? Note that the primary documentation for any function or data set defined in an R package is its man page so any information about how the app data set was generated should appear there.

I included the relevant R code into the vignette.

Thanks again for your time to help improve the quality of the package.

Best, Martin

[hpages]

Martin,

Throwing 400+ lines of non-evaluated, hard to read, and impossible to run, code in your vignette is a very bad idea. The proper way to do these things is to put the code in a script that you include in your package. The script should be organized/structured/commented and with most of the code put inside functions, typically 1 function per major step but defining some other smaller helper functions is also a good idea and encouraged. The input of the script should be explained. Right now the 1st lines of the code is:

data <- read.csv("GSE92872_CROP-seq_Jurkat_TCR.digital_expression.csv", stringsAsFactors = FALSE)

Then hundreds lines later:

load(paste0(dataset, "_kegg.rda"))
load(paste0(dataset, "_llr.rda"))

However since we don't know anything about those files, we're back to square one, that is, we still have no idea how the app data set was generated. Bioconductor takes reproducibility very seriously (as it should be).

Thanks for understanding and sorry for the inconvenience,

H.

[bioc-issue-bot]

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

cffcdc4 added function to recreate app data; added hierarc...

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[bioc-issue-bot]

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

74226fc a lot of code cleaning; speed improvements

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[MartinFXP]

Dear @hpages

I cleaned and thinned out the code and put it in a function. I also did a test run to make sure it works as I totally agree, that reproducibility is very important.

app <- createApp()
?createApp # can be run with different parameters for testing; even then still takes a very long time

I don't know why I am not registered as a subscriber to the bioc-devel mailing list. I tried to register again, but nothing happened.

The other two errors look like they are out of my control.

Best, Martin

[bioc-issue-bot]

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

f1cb5df Warshall's algorithm for transitive closure; adjus...

[bioc-issue-bot]

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

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[hpages]

Hi @MartinFXP ,

Thanks again for all the improvements you've made to mnem.

As indicated by the build report (see output of R CMD BiocCheckGitClone) the package source tree contains the following compilation products: src/mm.o, src/RcppExports.o, src/mnem.so

This is likely to be related to the compilation error you get on Windows. Generally speaking, compilation products should never be committed to git.

The error we see on Mac looks like a problem on our side. Let's ignore it.

Best, H.

[bioc-issue-bot]

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

6ac916f cleaned src

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146c068 added precluster init; fixed null node for respons...

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

65dbe2d general improvements; added accuracy function; fix...

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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.

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[bioc-issue-bot]

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

a5b1af7 added full cluster init

[bioc-issue-bot]

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 build report for more details.

[MartinFXP]

Dear @hpages

regarding the last remaining error (on my side). I was subscribed to the mailing list before and for some reason and without my doing was unsubscribed. Several attempts of me to subscribe again were unsuccessful. I just get the note in the browser, that my request to subscribe was successful and I should get a notification mail once the request has been dealt with. But nothing happened. How should I go on about this?

Best, Martin

[lshep]

Have you checked your spam or filtered emails folder? Sometimes the email gets marked as spam.