(inactive) PhosMap

[ecnuzdd]

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[bioc-issue-bot]

Hi @ecnuzdd

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: PhosMap
Type: Package
Title: A Modular Analysis Package for Phosphoproteomic Data
Version: 1.1.1
Author: Dongdong Zhan
Maintainer: Dongdong Zhan <ecnuzdd@163.com>
Description: Functions summary:
    1. Extracting the confidence probability of phosphorylation sites at peptide level from identification results searched by Mascot.
    2. Generating the quality control file of phosphorylation sites based on score of sites from Mascot.
    3. Pre-processing phosphoproteomic data.
    4. Kinase substrate enrichment analysis.
    5. Motif enrichment analysis.
    6. Data visualization
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Date: 2018-11-07
Imports: graphics, stats, utils
Suggests: stringr, ggseqlogo, rmotifx, pheatmap, samr, limma, RankProd, ksea, e1071, ClueR, tourr

[mtmorgan]

This package does not have a vignette, and does not re-use standard Bioconductor classes and methods for interoperability, and is therefore not suitable for Bioconductor.

[ecnuzdd]

Hi, I have updated PhosMap, please help me reopen the issue to make it work.

[bioc-issue-bot]

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[bioc-issue-bot]

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[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.

[mtmorgan]

Your package can depend only on CRAN or Bioconductor packages.

[bioc-issue-bot]

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

4b64afa update

[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.

[ecnuzdd]

Does Bioconducor not support non-CRAN or non-Bioconductor packages? The rmotifx and ksea packages are not located on CRAN and Bioconductor. In DESCRIPTION file, I wrote that: Additional_repositories: https://github.com/omarwagih/rmotifx/,https://github.com/evocellnet/ksea/

[mtmorgan]

Packages must be on CRAN or Bioconductor, since these have at least minimal quality control and certainty of availability.

[ecnuzdd]

In proteome, kinase-substrate enrichment analysis (KSEA) and Motif enrichment analysis (rmotifx) are two general methods. For this case, how do I use the two packages? In DESCRIPTION file, if I modified them to "Suggests" labels, does it work? it is successful while executing 'R CMD build'.

[mtmorgan]

It's successful from R CMD build because you have the packages installed. The build system will not install them, and they cannot be in the Depends:, Imports:, or Suggests: fields. If these packages are central to the functionality of your own package, then it means that your package cannot be accepted to Bioconductor.

[ecnuzdd]

Thanks for your help.
They are not core functionality but a part of my package. I will update my package by separating their functions of external packages.

[bioc-issue-bot]

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

6525fb1 Update DESCRIPTION

[ecnuzdd]

Hello, I have seriously check the build report. All compiling is ok except that there is only one warning when running "R CMD check".

The warnning prompts "R CMD check exceeded 10 min requirement", this is because PhosMap needs to load reference library when applying it to process Phosphoproteomics data. In our examples, we put these large files on a FTP server, once the example is tested, it first grasp reference data from FTP. The process would take a few minutes, which finally result in the warning from package builder of Biocoductor .

So, could the warning be ignored? If not, please give me some suggestion about fixing it.

[ecnuzdd]

@bioc-issue-bot Hello, I have seriously check the build report. All compiling is ok except that there is only one warning when running "R CMD check".

The warnning prompts "R CMD check exceeded 10 min requirement", this is because PhosMap needs to load reference library when applying it to process Phosphoproteomics data. In our examples, we put these large files on a FTP server, once the example is tested, it first grasp reference data from FTP. The process would take a few minutes, which finally result in the warning from package builder of Biocoductor .

So, could the warning be ignored? If not, please give me some suggestion about fixing it.

[mtmorgan]

Have you thought of using BiocFileCache to download the data only once? Or better, to make your data available on AnnotationHub or the related ExperimentHub so that it is there even after you lose interested, and is automatically cached locally?

[ecnuzdd]

@mtmorgan Thanks for your reply. Maybe I don't describle the question clearly.

My question is that "R CMD check" would test examples written in each Rscript, the smooth execution of these partial examples is dependent on some libraries with large sizes (> 200 MB), whose loading time will result in the warnning "R CMD check exceeded 10 min requirement". These loading process does not matter where the library file exists or no matter how to cache them.

Of course, when users perform PhosMap in practice, all dependence libraries will cache locally for reusing.

I am sure that all Rscript is OK, the only warnning at the moment is "R CMD check" exceeds time while it does not come from performability of Rscript.

[mtmorgan]

Revise the evaluated code so that it remains comprehensive but evaluates within the specified time limit. It is not satisfactory to assume that the R scripts are ok -- they may be now, but changes in your package or packages that your package depends on can break them in the future. Instead of running code on very large data, create an example data set that is enough to illustrate the analysis and to test your code.

The bottom line is that your package must build and check within specified time limits.

[bioc-issue-bot]

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

11ba322 Update DESCRIPTION

[bioc-issue-bot]

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

1690823 update for R check cmd
fd8b1cf Delete PhosMap.Rproj

[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: "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]

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]

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

a4afa7b update_examples_for_R_CMD_check

[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: "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]

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

c51e0b0 update_examples_for_R_CMD_check_01

[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: "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]

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

e44271b update_examples_for_R_CMD_check_01

[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: "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]

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

152f691 Update DESCRIPTION

[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.

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

Please see the build report for more details.

[mtmorgan]

6 June, 2019

Sorry for my very slow review.

Generally, I'm concerned about the reliance on an ftp site for data in your package; past experience has been that the author does not maintain these sites in the long term, meaning that users cannot rely on package functionality. I'm also concerned about the efficiency of the code, especially the absence of vectorization and use of 'copy-and-append' as indicated below. Finally many of your examples do not evaluate because they have if(FALSE){}; this renders the examples useless and the examples should be revised so that they are fully evaluated, with only rare exceptions. Likely this means using small sample data included with the package, or data made available in ExperimentHub.

DESCRIPTION

• good

NAMESPACE

• Looks like this is a combination of roxygen and 'hand' generated; this is very confusing for those looking at your code. Use one style or the other.

NEWS

• Make sure your formatting can be parsed by utils::news()

vignettes

• All data used in your vignette must either be in your package, or in an ExperimentHub resource; it is not acceptable to download data from a private server or github

• wrap lines carefully in code chunks so that they do not spill over page bounds on output

• use fl <- tempfile(); dir.create(fl) rather than getwd(), ~/, or other directories in the user's file system.

• Provide more narrative text to help the user understand the inputs and outputs of your code chunks.

• Avoid large code chunks without intervening narrative text.

R (specific examples identified in the comments, but applicable throughout)

• analysis_deps_anova.R:75; extract_psites_score.R:90 and many other places: avoid 'copy-and-append' pattern; instead, vectorize (best) or 'pre-allocate and fill', see http://bioconductor.org/developers/how-to/efficient-code/

• analysis_deps_anova.R:33 use @import or @importFrom to make functions from other packages available in your package; avoid using requireNamespace().

• use stop(), warning(), message() to signal error or informative messages to the user; use cat() only to display an object in a print() or show() method.

  if(group_nlevels < 2){
      cat('\n', 'Not found pairwise comparison.', '\n')
      stop('')
  }
  

  should be

  if(group_nlevels < 2)
      stop('Not found pairwise comparison.')
  

• load_data_with_ftp.R:22 use BiocFileCache to manage data downloaded by the user

• get_aligned_seq_for_mea.R:90 this code chunk looks like it could be vectorized, and could be re-written using efficient the effiicent Biostrings pacakge.

man

• Wrap man page examples, including comment strings to 80 characters so that they display clearly in a standard console

• Do not try to avoid evaluating example code with if (FALSE) {}, \dontrun{} or \donttest{}; if (FALSE){} is never appropriate; the latter are appropriate when a limited section of the example cannot be run by the user interactively (e.g., over-writing files) or during check (e.g., requiring user interaction).

[ecnuzdd]

Hi Martin， Thanks for your careful review and constructive suggestion. I will comply with these suggestion to perform point-by-point updating. As for your concern about the reliance on an ftp site for data, I want to state that I specially apply for the ftp site from our network center to store demo data and library data of PhosMap and provide users with more smooth experience. I promise we will continuously maintain it and guarantee it works. Your suggestion about R code is helpful for us, I will further standardize them. The if(FALSE){} is an inappropriate format, I will replace them with \donttest{} for check. Best regards! Dongdong Zhan The Institute of Biomedical Sciences East China Normal University 500 Dongchuan Road Shanghai 200241, China On 6/7/2019 05:43，Martin Morgan<notifications@github.com> wrote： 6 June, 2019 Sorry for my very slow review. Generally, I'm concerned about the reliance on an ftp site for data in your package; past experience has been that the author does not maintain these sites in the long term, meaning that users cannot rely on package functionality. I'm also concerned about the efficiency of the code, especially the absence of vectorization and use of 'copy-and-append' as indicated below. Finally many of your examples do not evaluate because they have if(FALSE){}; this renders the examples useless and the examples should be revised so that they are fully evaluated, with only rare exceptions. Likely this means using small sample data included with the package, or data made available in ExperimentHub. DESCRIPTION good NAMESPACE Looks like this is a combination of roxygen and 'hand' generated; this is very confusing for those looking at your code. Use one style or the other. NEWS Make sure your formatting can be parsed by utils::news() vignettes All data used in your vignette must either be in your package, or in an ExperimentHub resource; it is not acceptable to download data from a private server or github wrap lines carefully in code chunks so that they do not spill over page bounds on output use fl <- tempfile(); dir.create(fl) rather than getwd(), ~/, or other directories in the user's file system. Provide more narrative text to help the user understand the inputs and outputs of your code chunks. Avoid large code chunks without intervening narrative text. R (specific examples identified in the comments, but applicable throughout) analysis_deps_anova.R:75; extract_psites_score.R:90 and many other places: avoid 'copy-and-append' pattern; instead, vectorize (best) or 'pre-allocate and fill', see http://bioconductor.org/developers/how-to/efficient-code/ analysis_deps_anova.R:33 use @import or @importFrom to make functions from other packages available in your package; avoid using requireNamespace(). use stop(), warning(), message() to signal error or informative messages to the user; use cat() only to display an object in a print() or show() method. if(group_nlevels < 2){ cat('\n', 'Not found pairwise comparison.', '\n') stop('') } should be if(group_nlevels < 2) stop('Not found pairwise comparison.') load_data_with_ftp.R:22 use BiocFileCache to manage data downloaded by the user get_aligned_seq_for_mea.R:90 this code chunk looks like it could be vectorized, and could be re-written using efficient the effiicent Biostrings pacakge. man Wrap man page examples, including comment strings to 80 characters so that they display clearly in a standard console Do not try to avoid evaluating example code with if (FALSE) {}, \dontrun{} or \donttest{}; if (FALSE){} is never appropriate; the latter are appropriate when a limited section of the example cannot be run by the user interactively (e.g., over-writing files) or during check (e.g., requiring user interaction). — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub, or mute the thread.

[mtmorgan]

If your package is ready for further review, please be sure to increment the version to trigger a build.

[ecnuzdd]

Hi Martin，

Thanks for your kind reminders.

We are updating PhosMap. Its new version will be coming soon.

Best regards!

Dongdong

[mtmorgan]

I'll mark this package as inactive. Comment here when you are ready to resume the review process.

[bioc-issue-bot]

This issue is being closed because there has been no progress
for an extended period of time. You may reopen the issue when
you have the time to actively participate in the review /
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