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MSstatsBig #3193

Closed mstaniak closed 8 months ago

mstaniak commented 9 months ago

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bioc-issue-bot commented 9 months ago

Hi @mstaniak

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: MSstatsBig
Type: Package
Title: MSstats Preprocessing for Larger than Memory Data
Version: 0.99.0
Authors@R: c(
  person("Mateusz", "Staniak", email = "mtst@mstaniak.pl", role = c("aut", "cre")),
  person("Devon", "Kohler", email = "kohler.d@northeastern.edu", role = "aut")) 
Description: MSstats package provide tools for preprocessing, summarization and
    differential analysis of mass spectrometry (MS) proteomics data. Recently, 
    some MS protocols enable acquisition of data sets that result in larger than
    memory quantitative data. MSstats functions are not able to process such data.
    MSstatsBig package provides additional converter functions that enable 
    processing larger than memory data sets.
License: Artistic-2.0
Encoding: UTF-8
RoxygenNote: 7.2.3
Imports: 
    arrow,
    DBI,
    dplyr,
    MSstats,
    MSstatsConvert,
    sparklyr
Suggests: 
    knitr,
    rmarkdown
VignetteBuilder: knitr
biocViews: MassSpectrometry, Proteomics, Software
bioc-issue-bot commented 9 months ago

Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

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bioc-issue-bot commented 9 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): MSstatsBig_0.99.0.tar.gz macOS 12.6.5 Monterey: MSstatsBig_0.99.0.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/MSstatsBig to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

mstaniak commented 9 months ago

Hi, we have 4 functions in this package, and 3 of them have runnable examples. Making an example for the remaining functions was a problem because we didn't have publicly available data for this purpose. Is an exception to the 80% example coverage rule an option or should I add the missing example?

bioc-issue-bot commented 9 months ago

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

mstaniak commented 8 months ago

Hi @DarioS, last week I described a reason for ERROR in check, is it OK or should I look for another data set that could be used for runnable examples?

DarioS commented 8 months ago

It might be O.K. But, is it possible to use any publicly available data to help identify when the function begins to fail over time?

mstaniak commented 8 months ago

@DarioS I updated the package, now it includes an example for this function. No errors or warnings now. Please let me know if there are any other required changes.

bioc-issue-bot commented 8 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ef83d3eb8a86b4d1b52657d2eef4dd20f2c7400f

bioc-issue-bot commented 8 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): MSstatsBig_0.99.2.tar.gz macOS 12.6.5 Monterey: MSstatsBig_0.99.2.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/MSstatsBig to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 8 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ec39383c8d7a1e75ce4e008802593af393fc9d66

bioc-issue-bot commented 8 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): MSstatsBig_0.99.3.tar.gz macOS 12.6.5 Monterey: MSstatsBig_0.99.3.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/MSstatsBig to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

DarioS commented 8 months ago

MSstasBig is a file handling library for very large files that do not fit into R.A.M. I noted some issues.

Could it also handle what seems to be the most popular software at the moment, DIA-NN? Also, what about SCIEX formats?

> getwd()
  "C:/"
> converted_data = BigFragPipetoMSstatsFormat(system.file("extdata", "fgexample.csv", package = "MSstatsBig"),
                                              "output_file.csv", backend="arrow")
Error: IOError: Failed to open local file 'C:/topN_output_file.csv'. Detail: [Windows error 5] Access is denied.

Once then, you can load the output file into memory, or collect the arrow file using the code below.

What does collecting the arrow file mean? Collection has many different meanings in computer science.

Once the converter is run the clasic MSstats workflow can be followed.

Don't assume that everyone who finds your package is an MSstats expert. Add explanation of the large code chunk.

Also, copying every parameter from a function manual page is not appropriate for a vignette.

image

Please include useful information which is not found elsewhere.

bioc-issue-bot commented 8 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c6a7cb041da866d0934f85579d4888ed887d57bb

bioc-issue-bot commented 8 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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.

The following are build products from R CMD build on the Bioconductor Build System: macOS 12.6.5 Monterey: MSstatsBig_0.99.4.tar.gz Linux (Ubuntu 22.04.2 LTS): MSstatsBig_0.99.4.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/MSstatsBig to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 8 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 455d6bfe844d9f9d164813633fd2db2c3d6524bf

mstaniak commented 8 months ago

Hi,

thank you for the review,

CamelCaps is used for functions. It should only be used for classes. Functions and parameters need to be camelCase.

I changed names of function that started with "Big". We can keep the names that start with "MSstats", right?

Assignment uses = but needs to use <-.

Is this required? Our other packages relied heavily on data.table package and followed its style, including '=' usage. We can change it for this package if really necessary, please let me know.

Could it also handle what seems to be the most popular software at the moment, DIA-NN? Also, what about SCIEX formats?

It can handle DIA-NN output for MSstats via MSstatsPreprocessBig function and other formats with minor pre-processing on user side, I will add information about this to our documentation.

The vignette attempts to write to disk in the current working directory. This is not permitted.

I changed this by using tempdir()

The vignette lacks sufficient explanation.

We will update the vignette as soon as possible.

bioc-issue-bot commented 8 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): MSstatsBig_0.99.5.tar.gz macOS 12.6.5 Monterey: MSstatsBig_0.99.5.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/MSstatsBig to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 8 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0121fb3d683288ae864143313b25aa8d7776344d

mstaniak commented 8 months ago

Hi @DarioS I removed redundant information from the vignette. Instead, I added a few sentences on MSstats workflow (+reference) and applicability to outputs of other tools. Please let me know if other changes are required.

bioc-issue-bot commented 8 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): MSstatsBig_0.99.6.tar.gz macOS 12.6.5 Monterey: MSstatsBig_0.99.6.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/MSstatsBig to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

DarioS commented 8 months ago

CamelCaps can stay. But MSstatsTMT uses <-, so changing all assignments to <- is necessary.

bioc-issue-bot commented 8 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 831fa8c77dcc886ef4240f35275b6a1cb1740f85

bioc-issue-bot commented 8 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): MSstatsBig_0.99.7.tar.gz macOS 12.6.5 Monterey: MSstatsBig_0.99.7.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/MSstatsBig to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

mstaniak commented 8 months ago

I fixed that, are we good to go?

DarioS commented 8 months ago

We are.

bioc-issue-bot commented 8 months ago

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lshep commented 8 months ago

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