NestLink (package type - Experiment Data )

cpanse commented 5 years ago

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lshep commented 5 years ago

So is there a reason for using the fig.retina=3 in the code that produces the large image sizes? Is it possible to remove this or is it really necessary for resolution?
Also keep in mind when doing the git cleaning code http://bioconductor.org/developers/how-to/git/remove-large-data/ you will need to change the argument to the java command to be the file size appropriate for cleaning (the default is 100Mb but I don't know the sizes of the files you had generated maybe 3Mb or 10Mb is more appropriate)

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lshep commented 5 years ago

Thank you for your submission. A few initial comments below:

README

[ ] eventually update to have Bioconductor installation instructions for your package.
For What its worth: BiocManager::install also can install package from github so it can't hurt to update this either if you wanted to keep the call to install from github as the development version of your package vs the bioconductor release version of your package

DESCRIPTION:

[ ] Use Authors@R or Author/Maintainer fields but not both
[ ] Remove LazyData=TRUE we find it actaully slows building and installation

INST/Scripts

[ ] make-data.R can you describe in text/sudo code/or code how the data list in metadat.csv was created. It can be text indicating download from website with specific settings or parameters etc... or accepted is what you have for the RData showing the code run to save the object ... There is currently no real indication how these files were made neither here nor in the man files

Vignettes: I reran all displayed code manually:

In simulateFlycodes.Rmd:

[ ] Compute Hydrophobicity value using SSRC


ssrc <- sapply(peptideStd, function(x){ssrc(x$peptideSequence)})
rt <- unlist(lapply(peptideStd, function(x){x$rt}))
plot(ssrc, rt); abline(ssrc.lm <- lm(rt ~ ssrc), col='red'); 
legend("topleft", paste("spearman", round(cor(ssrc, rt, method='spearman'),2)))

Doesn't run. I get

ssrc <- sapply(peptideStd, function(x){ssrc(x$peptideSequence)}) Error in sapply(peptideStd, function(x) { : object 'peptideStd' not found

[ ] At the end
```
the plots graph a LC-MS map.
```
What makes these plots? I don't see plotting code?

In summaryFASTA.Rmd

[ ] Import Data into R I believe you moved the WU160118.RData to EH and removed from extdata so this is no longer valid system.file("extdata/WU160118.RData", package = "NestLink").

In SupplementaryNote1.Rmd

[ ] Camera ready summary table When I try to run the plotting

rv <-lapply(unique(P$ConcGr), function(q){
pairs((P[P$ConcGr == q ,c('coli1', 'coli2', 'smeg1', 'smeg2')]),
  pch=16, col=rgb(0.5,0.5,0.5,alpha = 0.3),
  lower.panel = panel.cor,
  asp=1,
  main=q)
})
Error in pairs.default((P[P$ConcGr == q, c("coli1", "coli2", "smeg1",  : 
object 'panel.cor' not found

There is also a call later on in the code that also fails with panel.cor not found.

Man pages:

[ ] In general the documentation could be expanded on to provide more detail for all pages but in particular:
[ ] You have three compose functions for creating an AA sequence but there is no indication of how these 3 functions are different.
[ ] It seems like getNB and getFC are wrappers around getting predefined data - this should be better explained.

When finished with these updates please make sure there is a valid version bump and new build and comment back here when you are ready for re-review.
Cheers and I look forward to working with you to get your package accepted.

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bioc-issue-bot commented 5 years ago

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cpanse commented 5 years ago

@lshep We address all the [x] items. Thanks.

Thank you for your submission. A few initial comments below:

README
* [x]  eventually update to have Bioconductor installation instructions for your package.
  For What its worth:
  BiocManager::install also can install package from github so it can't hurt to update this either if you wanted to keep the call to install from github as the development version of your package vs the bioconductor release version of your package
DESCRIPTION:
* [x]  Use Authors@R  or Author/Maintainer fields but not both

* [x]  Remove LazyData=TRUE we find it actaully slows building and installation
INST/Scripts

replaced by a make-data.Rmd vignette

[x] make-data.R can you describe in text/sudo code/or code how the data list in metadat.csv was created. It can be text indicating download from website with specific settings or parameters etc... or accepted is what you have for the RData showing the code run to save the object ... There is currently no real indication how these files were made neither here nor in the man files

Vignettes: I reran all displayed code manually:

In simulateFlycodes.Rmd:
* [x]  Compute Hydrophobicity value using SSRC
ssrc <- sapply(peptideStd, function(x){ssrc(x$peptideSequence)})
rt <- unlist(lapply(peptideStd, function(x){x$rt}))
plot(ssrc, rt); abline(ssrc.lm <- lm(rt ~ ssrc), col='red'); 
legend("topleft", paste("spearman", round(cor(ssrc, rt, method='spearman'),2)))
Doesn't run. I get
> ssrc <- sapply(peptideStd, function(x){ssrc(x$peptideSequence)})
Error in sapply(peptideStd, function(x) { : object 'peptideStd' not found
the corresponding R code is now visible
* [x]  At the end
the plots graph a LC-MS map.
What makes these plots? I don't see plotting code?

In summaryFASTA.Rmd
* [x]   Import Data into R
  I believe you moved the WU160118.RData to EH and removed from extdata so this is no longer valid `system.file("extdata/WU160118.RData", package = "NestLink").`
In SupplementaryNote1.Rmd
* [x]  Camera ready summary table
  When I try to run the plotting
rv <-lapply(unique(P$ConcGr), function(q){
pairs((P[P$ConcGr == q ,c('coli1', 'coli2', 'smeg1', 'smeg2')]),
      pch=16, col=rgb(0.5,0.5,0.5,alpha = 0.3),
      lower.panel = panel.cor,
      asp=1,
      main=q)
})
Error in pairs.default((P[P$ConcGr == q, c("coli1", "coli2", "smeg1",  : 
  object 'panel.cor' not found
There is also a call later on in the code that also fails with panel.cor not found.

Man pages:
* [x]  In general the documentation could be expanded on to provide more detail for all
  pages but in particular:

* [x]  You have three compose functions for creating an AA sequence but there is no
  indication of how these 3 functions are different.

* [x]  It seems like getNB and getFC are wrappers around getting predefined data - this
  should be better explained.
When finished with these updates please make sure there is a valid version bump and new build and comment back here when you are ready for re-review. Cheers and I look forward to working with you to get your package accepted.

lshep commented 5 years ago

I apologize for the delay - I was out on holiday.

A few last things to clean up or respond to:

Description:

[ ] Please remove Maintainer field and use the designation 'cre' in the Authors@R to designate maintainer

Vignettes:

summaryFASTA

[ ] Import Data into R - I'm confused why you included the code snippet concerning the extracting data - users wouldn't know what ~/Download/444589.Rdata is or contains so the clip iteself does not seem useful, only confusing. I would either expand more details on the background or remove this snippet and only include the shipped data component.

cmpPredictedMeasuredFlyCodees

[ ] Why not include this as a function with the package rather than showing the code? Its fine as is but just curious.

R/man

runNGSAnalysis

[ ] Would a user know what valid input param are? Should there be a list or helper of some sort describing the acceptable values for this param list and what the values mean? Can a param list be missing one of those input params (i.e is there a default?)

compose.R

[ ] Would there be a case to use the getFC or getNB with a user provided file rather than the provided experimentHub file? Are the files in ExperimentHub processed and unique that these function only provide a wrapper to retrieving the data or does these function provide utility for converting files of a particular format to a usable format for your functions?

Again, I apologize for the delay. As before please make changes and when ready do a version bump to kick off a new build and respond here addressing the above concerns.

Cheers, ~L

cpanse commented 5 years ago

@lshep Please find our answers in line with your message.

I apologize for the delay - I was out on holiday.

A few last things to clean up or respond to:

Description:

* [x]  Please remove Maintainer field and use the designation 'cre' in the Authors@R to designate maintainer

Vignettes:

summaryFASTA

* [x]   Import Data into R -  I'm confused why you included the code snippet   concerning the extracting data - users wouldn't know what   `~/Download/444589.Rdata` is or contains so the clip iteself does not seem   useful, only confusing.  I would either expand more details on the background or remove this snippet and only include the shipped data component.

text bucket was moved that part to make-data.Rmd vignette and added more information.

cmpPredictedMeasuredFlyCodees

* [x]  Why not include this as a function with the package rather than showing the code? Its fine as is but just curious.

is now a function.

R/man

runNGSAnalysis

* [x]  Would a user know what valid input param are? Should there be a list or helper of some sort describing the acceptable values for this param list and what the values mean? Can a param list be missing one of those input params (i.e is there a default?)

added description for all parameter and set default values if no parameter is provided.

compose.R

* [x]  Would there be a case to use the getFC or getNB with a user provided file rather than the provided experimentHub file?  Are the files in ExperimentHub processed and unique that these function only provide a wrapper to retrieving the data or does these function provide utility for converting files of a particular format to a usable format for your functions?

generalized that function to make it also work for additional files.

Thank you for fruitful recommendations,

Lennart and Christian

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mtmorgan commented 5 years ago

I'm a little confused about this package. The 'Maintainer' (cre in Authors@R) is different from the owner of the repository contributing the package. Who's in charge?

cpanse commented 5 years ago

I am in charge. We have had two cre roles at the beginning, but it did pass the R CMD check. I fix that. Sorry for the confusion. Best wishes, Christian

On Mon, Jan 14, 2019 at 6:20 PM Martin Morgan notifications@github.com wrote:

I'm a little confused about this package. The 'Maintainer' (cre in Authors@R) is different from the owner of the repository contributing the package. Who's in charge?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/931#issuecomment-454086946, or mute the thread https://github.com/notifications/unsubscribe-auth/AErMY6ONwZh6A8Yk0Ad7oK8x5DuD1rwuks5vDLxVgaJpZM4YSyWF .

mtmorgan commented 5 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/cpanse.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

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(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("NestLink"). The package 'landing page' will be created at

https://bioconductor.org/packages/NestLink

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

Bioconductor / Contributions

NestLink (package type - Experiment Data ) #931