SubCellBarCode

[TanerArslan]

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[bioc-issue-bot]

Hi @TanerArslan

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: SubCellBarCode
Type: Package
Title: SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome
Version: 0.99.0
Author: Taner Arslan
Maintainer: Taner Arslan <taner.arslan@ki.se>
Description: Mass-Spectrometry based spatial proteomics have enabled the proteome-wide mapping of protein subcellular localization (Orre et al. 2019, Molecular Cell). SubCellBarCode R package robustly classifies proteins into corresponding subcellular localization.
License: GPL-2
Encoding: UTF-8
LazyData: true
Depends: R  (>= 3.5)
Suggests: knitr, 
    rmarkdown, BiocStyle
Imports:
    Rtsne, scatterplot3d, caret, e1071, ggplot2, gridExtra, networkD3, ggrepel, graphics, stats
biocViews: Proteomics, MassSpectrometry, Classification
RoxygenNote: 6.1.1
VignetteBuilder: knitr

[bioc-issue-bot]

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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]

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

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[bioc-issue-bot]

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

4a3299a Version bumped 0.99.1

[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.

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[nturaga]

Hi @TanerArslan ,

I will review your package only once the build report (http://bioconductor.org/spb_reports/SubCellBarCode_buildreport_20190303094835.html) is clean i.e , no ERROR or WARNING messages and as few as possible NOTE messages.

Please let me know once you have solved these problems as noted in the build report, saying you are ready for a review.

Best,

Nitesh

[bioc-issue-bot]

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

2cb0e3b hidden file deleted 3a900f8 Version bumped 0.99.2

[TanerArslan]

Hi @nturaga ,

Thank you for reviewing my package. Currently, i am working on issues and i will let you know when the package is ready for review.

Best.

/Taner

[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, TIMEOUT, 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]

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

b04e70c Subset data 71835fb intend fixed 6333009 Version Bumped 0.99.3

[bioc-issue-bot]

Dear Package contributor,

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

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

0b5d88f Example size reduced 03e2c25 Version Bumped 0.99.4

[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.

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[bioc-issue-bot]

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[TanerArslan]

Hi @nturaga , The package was built without errors or warnings. It is ready for the revision.

Looking forward to hear you soon.

Best, /Taner

[TanerArslan]

Hi Nitesh @nturaga ,

The package was ready for the last week. Since i did not hear from you, I hesitated whether i have done everything correct. Should i open a new issue or wait from you?

Thanks in advance.

/Taner

[nturaga]

I will take a look at it within the next few days. Thanks for the update.

Best,

Nitesh

On Mon, Mar 11, 2019 at 9:43 AM Taner Arslan notifications@github.com wrote:

Hi Nitesh @nturaga https://github.com/nturaga ,

The package was ready for the last week. Since i did not hear from you, I hesitated whether i have done everything correct. Should i open a new issue or wait from you?

Thanks in advance.

/Taner

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1030#issuecomment-471543167, or mute the thread https://github.com/notifications/unsubscribe-auth/ACnoS21huipABxmJVFwHWo8pNv9Rmq1cks5vVl1mgaJpZM4bYlNI .

[TanerArslan]

Thanks for the quick respond.

I am looking forward to hear you soon.

Cheers.

/Taner

[nturaga]

SubCellBarCode review

DESCRIPTION

ok

NAMESPACE

ok

man

ok

data

ok

vignette

• Title is missing in the vignette.

R

• In applyThresholdNeighborhood.R, you can just make a helper function instead of declaring a function replacePrediction within the main function. This would be much cleaner, if you make it an private function with (.replacePrediction). Similar with merge.probability.

• In calRowMean.R, the line,

  t.df <- data.frame(Proteins = names(t.df), Fr = unname(t.df))

  does not have to be in the lapply loop. Check in other places as well to see if you have code which doesn't need to be inside the loop (apply statements).

  There are some nested loops in probabilityThresholdCompartments.R which you can make more efficient very easily. Just move items which don't get effected by the loop, outside ot.

• This statement can be written more cleanly,

  if( is.data.frame(protein.data) == FALSE )
      stop('Input must be a data frame format! Type ?loadData')

  vs

  if (!is.data.frame(protein.data))
      ...

  Make similar changes everywhere. You don't need to test if something is TRUE as well. The if statement only ever enters if TRUE.

  if (! is.character(rownames(protein.data)) == TRUE)
      stop('Rownames must be character!')

  vs

  if (! is.character(rownames(protein.data)))
      ...

• Unless it's a vector of length > 1, you don't need to use sprintf for the message function. The vector is recycled only if the length is greater than 1.

  message(sprintf("Number of removed sample-wise proteins: %s",
              length(sample.removed.prot)))

  vs

  message("Number of removed sample-wise proteins: ",
              length(sample.removed.prot))

  Do this everywhere as needed. Make sure you are using an extra function like sprintf only if it's needed. In most places in your code it is not.

  Take a look at : http://bioconductor.org/developers/how-to/coding-style/

  End-User messages
  
  message() communicates diagnostic messages (e.g., progress during lengthy computations) during code evaluation.
  warning() communicates unusual situations handled by your code.
  stop() indicates an error condition.
  cat() or print() are used only when displaying an object to the user, e.g., in a show method.

[TanerArslan]

Hi Nitesh @nturaga,

Thanks for the reviewing package.

I will make the changes as soon as possible.

/Taner

[bioc-issue-bot]

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

95bd7f4 helper functions added 7769d88 first revision c7f8ffa Version bumped 0.99.6

[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.

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Please see the build report for more details.

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

430ff98 redundacy deleted ee3db2b Version bumped 0.99.7

[bioc-issue-bot]

Dear Package contributor,

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

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

d3ad223 Example runtime decreased 8ad1457 Vignette updated ed57295 Version bumped 0.99.8

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

e5fed86 Version bumped 0.99.9

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

9aa1854 example errors fixed e1ecc73 Version bumped 0.99.10

[bioc-issue-bot]

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44ffa82 Example error fixed 192e435 Version Bumped 0.99.11

[bioc-issue-bot]

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

9c3be2c example size increased 3f62ba4 Version bumped 0.99.12

[bioc-issue-bot]

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[bioc-issue-bot]

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

bcd75df example size increased e0f6cab Version bumped 0.99.13

[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.

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[bioc-issue-bot]

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

4251387 Version bumped 0.99.14

[bioc-issue-bot]

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[TanerArslan]

Dear Nitesh @nturaga ,

I have done and made changes about your comment. Below you can see detailed information;

vignette

• Title is missing in the vignette.

As you can see the attached code chunk and SubCellBarCode.rmd, the title is not missing on my side and it is present in html output.

title: "SubCellBarCode: Integrated workflow for robust classification and visualization of spatial proteome" author: name: Taner Arslan affiliation: "Karolinska Institute, Stockholm, Sweden" name: Lukas Orre affiliation: "Karolinska Institute, Stockholm, Sweden" name: Mattias Vesterlund affiliation: "Karolinska Institute, Stockholm, Sweden" name: Yanbo Pan affiliation: "Karolinska Institute, Stockholm, Sweden" name: Janne Lehtiö affiliation: "Karolinska Institute, Stockholm, Sweden" date: "r Sys.Date()" output: BiocStyle::html_document: toc_fload: true BiocStyle::pdf_document: default
package: SubCellBarCode

Moreover, you have noticed the same problem in scMerge package that you have recently reviewed. I checked its code and it contains title in the rmd file. I wonder whether there is a compatibility issue?

R

• In applyThresholdNeighborhood.R, you can just make a helper function instead of declaring a function replacePrediction within the main function. This would be much cleaner, if you make it an private function with (.replacePrediction). Similar with merge.probability.

I removed all helper functions in applyThresholdNeighborhood.R and defined separate functions. Further, I have noticed that in probabilityThresholdNeighborhood.R possessed same issue and i defined separate functions for it, as well.

• In calRowMean.R, the line,

t.df <- data.frame(Proteins = names(t.df), Fr = unname(t.df))

does not have to be in the lapply loop. Check in other places as well to see if you have code which doesn't need to be inside the loop (apply statements).

I removed the t.df data frame in the loop.

• This statement can be written more cleanly,

  if( is.data.frame(protein.data) == FALSE ) stop('Input must be a data frame format! Type ?loadData')

vs

if (!is.data.frame(protein.data)) ...

I made the changes everywhere.

• Unless it's a vector of length > 1, you don't need to use sprintf for the message function. The vector is recycled only if the length is greater than 1.

message(sprintf("Number of removed sample-wise proteins: %s", length(sample.removed.prot)))

I removed all redundant sprintf in the package.

I looked end user messages and replaced for some cases.

Looking forward to hear you soon.

Taner.

[TanerArslan]

Dear Nitesh @nturaga, I just would like to kindly remind you that package is ready for 17 days for the second round revision. I really want it to be accepted before the new release and very sorry if i am poking you :)

[bioc-issue-bot]

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

96d19a0 Version bumped 0.99.15

[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.

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

48e883a Example fixed b37acec Version bumped 0.99.16

[bioc-issue-bot]

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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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[nturaga]

Update

Hi Taner,

• Depending on how big your matrices can get, checkout the packages matrixStats, use the functions like rowMeans , colMeans etc to make your code more efficient. These functions are highly optimized and work in a similar signature to the base R rowMeans as well.

Your package looks mostly ready. It can make the 24th deadline.

Best,

Nitesh

On Wed, Apr 17, 2019 at 5:49 AM bioc-issue-bot notifications@github.com wrote:

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 http://bioconductor.org/spb_reports/SubCellBarCode_buildreport_20190417054908.html for more details.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1030#issuecomment-484016337, or mute the thread https://github.com/notifications/unsubscribe-auth/ACnoS25-JFmHwgJ6nwVF-cJpUxfEX0wxks5vhu4cgaJpZM4bYlNI .

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

842e6a4 rowSums added a8b354f Version bumped 0.99.17

[bioc-issue-bot]

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

2175dfe Version bumped to 0.99.18

[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.