DEqMS

[yafeng]

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• Repository: https://github.com/yafeng/DEqMS

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[bioc-issue-bot]

Hi @yafeng

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: DEqMS
Version: 0.99.0
Date: 2018/05/01
Title: Differential protein expression analysis for quantitative MS data
Author: Yafeng Zhu
Maintainer: Yafeng Zhu <yafeng.zhu@ki.se>
Depends: R (>= 3.4.2), methods,limma
Suggests: plyr, stats, matrixStats, reshape2, ggplot2,farms, knitr
LazyLoad: yes
Description:  Data analysis, differential protein expression analysis for quantitative MS data.
License: LGPL
biocViews: Proteomics, Mass Spectrometry, Preprocessing, Statistics, DifferentialExpression, MultipleComparisons
VignetteBuilder: knitr
Packaged: Tue May 1 20:19:39 2018; yafeng

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[bioc-issue-bot]

A reviewer has been assigned to your package Learn what to expect during the review process.

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.

[mtmorgan]

@nturaga will review your package. In your vignette, please use system.file(..., package="DEqMS") rather than hard-coded file paths. Consider also how you can increase the utility of your package by using core Bioconductor classes as inputs and outputs to your functions.

[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: "ERROR, 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.

[yafeng]

Hi, thanks for the evaluation of my package! I have modified the package accordingly. I think I have fixed the errors and warnings. I am still working on the documentation files.

[nturaga]

Hi, please check your build report. You still have errors, issue a version bump to rebuild your package.

[nturaga]

Hi @yafeng ,

Please fix the following.

[REQUIRED] Fix NAMESPACE

~/D/b/DEqMS ❯❯❯ git diff                                                                                    
diff --git a/NAMESPACE b/NAMESPACE
index 7530b4f..e3916ee 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,7 +2,8 @@
 exportPattern("^[^\\.]")

 importFrom("graphics", "boxplot", "lines", "plot")
-importFrom("limma::topTable")
-importFrom("plyr::ddply")
-importFrom("stats", "loess", "matrixStats", "na.omit", "nls", "p.adjust", "predict", "pt","ggplot2")
-
+importFrom("limma","topTable")
+importFrom("plyr","ddply")
+importFrom("stats", "loess", "na.omit", "nls", "p.adjust", "predict", "pt")
+import("matrixStats")
+import("ggplot2")

[REQUIRED] your package passes R CMD build, R CMD check, R CMD INSTALL.

[REQUIRED] When your package builds, make sure to fix any NOTEs, WARNINGs you may have in the build report.

[nturaga]

HI @yafeng ,

Please acknowledge that you are still working on the package and the required changes. I'm giving you a 2 week notice to respond, after which I will close the issue. We can reopen the issue once you have done so, and have fixed the errors.

If you have already fixed the issues, you'd need to issue a build report by bumping your package version. You also need to explicitly reply stating that you'd like another review, and describe the changes you made.

Best,

Nitesh

[yafeng]

Hi, I have fixed the NAMESPACE and documentation files except for two functions median_polish and farms.method that won't be seen by users. Do you know how to change the exportPattern() not to export this two methods?

[nturaga]

Instead of exportPattern() just use export() for each function explicitly. That makes it a lot easier to have control over what functions you export and exclude the ones you don't want users to have access to. You should also use more consistent naming of your functions and follow a coding style (http://bioconductor.org/developers/how-to/coding-style/).

Function names

Use camelCaps: initial lower case, then alternate case between words.
Do not use ‘.’ (in the S3 class system, some(x) where x is class A will dispatch to some.A).
Prefix non-exported functions with a ‘.’.

[yafeng]

@nturaga Thanks! I have now changed the function names accordingly.

[nturaga]

Please issue a version bump

[yafeng]

This is my first time to submit a package, what is a version bump -_- what should l do? should I change the version number in DESCRIPTION file from 0.99.0 to 0.99.1 ?

[nturaga]

Hi @yafeng , Yes, that is what you need to do.

The initial package submission process has a checklist which you marked as read. It includes https://bioconductor.org/developers/package-submission/ where we outline the process carefully.

Packages must satisfy the following checklist:

...
Set Version: 0.99.0 in the DESCRIPTION. Subsequent versions created during the review process 
will be numbered 0.99.1, 0.99.2, etc. When released, your package’s version number will be 
automatically incremented to 1.0.0.
...

Please be sure to take a look at the Package guidelines and package submission process as suggested above.

[yafeng]

OK, I have issued a version bump, and also looked through the guidelines. I created a empty NEWS file, I should update the NEWS file whenever there is new version release, right?

[nturaga]

@yafeng I think your webhook to the builder has failed, please try to reset it https://github.com/Bioconductor/Contributions#adding-a-web-hook. If you haven't set it up, you would need to do it. I think reading through package submission guidelines and checklist above will be helpful.

[yafeng]

OK, done.

[nturaga]

Please issue another version bump now to get your package to build.

[bioc-issue-bot]

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

68321c3 make an issue bump

[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.

[bioc-issue-bot]

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

a2b0169 fix error in NAMESPACE

[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: "ERROR, 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:

3d3563e remove not required dependencies in NAMESPACE

[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: "ERROR, 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:

389adc2 fix error in 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.

On one or more platforms, the build results were: "ERROR, 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:

07e003c fix error in NAMESPACE

[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.

[bioc-issue-bot]

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

b378e67 fix aes error

[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: "ERROR, 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:

91982c4 fix documentation files

[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.

[bioc-issue-bot]

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

c9a05af fix error in vignette

[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: "ERROR, 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:

cedf9e5 fix error in Rd files

[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: "ERROR, 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:

40fb747 fix farmsSummary.Rd

[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: "ERROR, 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.

[nturaga]

Hi @yafeng, Please respond when your package builds and checks cleanly with no artifacts (NOTES, WARNINGS, ERRORS) in the build report. I will proceed and review your package once you have done that.

[nturaga]

Hi @yafeng ,

Your package still has significant errors in it which need to be fixed as shown in the build report.

ERROR count: 1
WARNING count: 3
NOTE count: 6

Please acknowledge that you are still working on the package and the required changes. I'm giving you a 2 week notice to respond, after which I will close the issue. We can reopen the issue once you have done so, and have fixed the errors.

Best,

Nitesh

[bioc-issue-bot]

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

910b174 fix error in medpolish fun a9f4c16 limit row in 80 char

[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: "ERROR, 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:

1a9a935 fix error in doc file

[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: "ERROR, 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:

5ada8c9 fix error in docs

[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: "ERROR, 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.

[yafeng]

Can you help me on this warning, which I don't know how to fix.

WARNING: Import graphics, stats in DESCRIPTION as well as NAMESPACE.

[nturaga]

Hi,

You need to import the right functions in your namespace so your package can see it. There is extensive documentation on how NAMESPACES and DESCRIPTION files work.

http://r-pkgs.had.co.nz/namespace.html

http://r-pkgs.had.co.nz/description.html

[yafeng]

The wierd thing is that I already imported graphics, stats in DESCRIPTION as well as NAMESPACE. I don't understand why it was complaining that.

[bioc-issue-bot]

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

cf4921f fix warninngs from build test