search

Bioconductor / Contributions

Contribute Packages to Bioconductor
135 stars 33 forks source link

statTarget #88

Closed 13479776 closed 8 years ago

13479776 commented 8 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Confirm the following by editing each check box to '[x]'

I am familiar with the essential aspects of Bioconductor software management, including:

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

bioc-issue-bot commented 8 years ago

Hi @13479776

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: statTarget
Type: Package
Title: Statistical Analysis of Metabolite Profile
Version: 1.2.2
Date: 2016-07-014
Author: Hemi Luan
Maintainer: Hemi Luan <hemi.luan@gmail.com>
Depends: R (>= 3.3.0)
Imports:
        randomForest,plyr,pdist,pROC,utils,grDevices,graphics,stats,rrcov,pls,impute,gWidgets2,gWidgets2RGtk2
Suggests: testthat
Description: An easy to use tool provides a graphical user interface for quality control based signal correction, integration of metabolomic data from multiple batches, and the comprehensive statistic analysis for non-targeted and targeted approaches.
License: GPL (>= 2)
URL: https://github.com/13479776/statTarget
biocViews: Metabolomics, MassSpectrometry
RoxygenNote: 5.0.1
LazyData: true
NeedsCompilation: no
Packaged: 2016-07-20 00:18:52 UTC; Hees
Repository: CRAN
Date/Publication: 2016-07-20 09:46:08
bioc-issue-bot commented 8 years ago

Your package has been approved for building. Your package is now submitted to our queue.

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 commented 8 years ago

As a preliminary comment, I notice that this package is also on CRAN. Please be aware that if it is accepted in Bioconductor, it must be removed from CRAN.

bioc-issue-bot commented 8 years ago

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 following build report for more details:

http://bioconductor.org/spb_reports/statTarget_buildreport_20160820050938.html

vobencha commented 8 years ago

Please address the issues below from the single package builder output. Once these are fixed I'll do a full review.

Valerie

13479776 commented 8 years ago

Yes, I have checked and revised the required and recommended problems

vobencha commented 8 years ago

When you commit changes to your repo and bump the version, the single package builder should pick up and run a new build ... I'm not sure why it didn't. I'll check in with Lori and see if we can get a new build.

bioc-issue-bot commented 8 years ago

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: "abnormal". 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 following build report for more details:

http://bioconductor.org/spb_reports/statTarget_buildreport_20160824091502.html

vobencha commented 8 years ago

The DESCRIPTION file is malformed with merge conflicts (thanks Lori for finding this!). Tidy that up, bump the version and recommit.

bioc-issue-bot commented 8 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 8 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 8 years ago

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

dfa55ff statTarget_undate

bioc-issue-bot commented 8 years ago

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". 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 following build report for more details:

http://bioconductor.org/spb_reports/statTarget_buildreport_20160824214911.html

13479776 commented 8 years ago

Could anyone tell me how to remove the package from CRAN? Thanks

vobencha commented 8 years ago

You'll need to contact the CRAN maintainers at CRAN@R-project.org.

13479776 commented 8 years ago

Thanks! vobencha. By the way, moscato1 could not build the package. Do you have any idea?

bioc-issue-bot commented 8 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 8 years ago

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

efece58 Update DESCRIPTION

bioc-issue-bot commented 8 years ago

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 following build report for more details:

http://bioconductor.org/spb_reports/statTarget_buildreport_20160826055243.html

bioc-issue-bot commented 8 years ago

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

10633f5 Update DESCRIPTION

bioc-issue-bot commented 8 years ago

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". 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 following build report for more details:

http://bioconductor.org/spb_reports/statTarget_buildreport_20160826200517.html

bioc-issue-bot commented 8 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 8 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 8 years ago

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

34cead9 Update DESCRIPTION

bioc-issue-bot commented 8 years ago

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". 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 following build report for more details:

http://bioconductor.org/spb_reports/statTarget_buildreport_20160826203257.html

bioc-issue-bot commented 8 years ago

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

4497c50 Update DESCRIPTION

bioc-issue-bot commented 8 years ago

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". 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 following build report for more details:

http://bioconductor.org/spb_reports/statTarget_buildreport_20160826204142.html

bioc-issue-bot commented 8 years ago

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

f6df267 Update DESCRIPTION

bioc-issue-bot commented 8 years ago

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". 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 following build report for more details:

http://bioconductor.org/spb_reports/statTarget_buildreport_20160829101641.html

vobencha commented 8 years ago

Please stop checking in new versions. The only error in the SPB output is the 'package must be removed' from CRAN which will remain an 'error' throughout the review. I will review the package this week and you'll have comments by Friday.

As an fyi, best practice is to make your changes to a local checkout and run R CMD build, R CMD check and R CMD BiocCheck locally. See the BiocCheck vignette for details:

http://www.bioconductor.org/packages/3.4/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html locally.

Bump the version and check into master after the package passes these checks locally.

Valerie

vobencha commented 8 years ago

Hi,

Please see comments below. Let me know if you have questions.

(1) XQuarts What role does this play in the GUI? Why are Mac users instructed to download https://www.xquartz.org? If statTarget has system dependencies they must be listed in SystemRequirements in DESCRIPTION.

(2) Format all code to be a max of 80 characters wide.

(3) Description From the 'Description' it's not clear what the package actually does:

 An easy to use tool provide graphical user interface for quality
 control based signal correction, integration of metabolomic data
 from multiple batches, and the comprehensive statistic analysis
 for non-targeted and targeted approaches.

I don't understand what 'integration of metabolomic data from multiple batches' means. Are we modifying datasets? What is a non-targeted vs targeted approach? Please break the Description into multiple sentences and clarify what some of the terms mean.

(4) vignette

Remove all of this:

\subsection{For Mac OS users} \noindent 1 - Install \texttt{XQuartz} from \texttt{ https://www.xquartz.org} \noindent 2 - Copy this code into R. \noindent > source("https://bioconductor.org/biocLite.R") \noindent >biocLite("impute") \noindent >install.packages("statTarget")

\subsection{For Windows users} \noindent 1 - Copy this code into R \noindent > source("https://bioconductor.org/biocLite.R") \noindent > biocLite("impute") \noindent > install.packages("statTarget")

Replace it with this:

Load the package with biocLite(): source("https://bioconductor.org/biocLite.R") biocLite("statTarget")

(5) When I library(statTarget) the GUI pops up. Nothing (other than a startup message) should happen when a package is loaded. Please remove the if (interactive()) from zzz.R. The GUI should be started by the user invoking statTarget.gui().

(6) function names

The dot '.' is used in S3 method dispatch - functions named in this manner can be confusing to novice users. Since none of your functions are S3 methods, please rename them with an underscore or camelCase, e.g., aucROC() instead of auc.ROC().

(7) exported functions and man pages

Not all functions in a package need to be exported in the NAMESPACE. If they are exported, they must have a complete man page. A complete man page includes an \example section with a runnable example. If the example can't be run in the background it can be wrapped in

if (interactive()) {
  ....
}

Decide which functions you need to export (i.e., which functions the user needs access to) and complete the man pages. Currently none of the man pages are complete. They are not descriptive and do not have \example sections. There are many examples of complete man pages in the repository, see GenomicRanges, GenomicAlignments, pRolocGUI, MSGFgui, etc.

Valerie

bioc-issue-bot commented 8 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 8 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 8 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 8 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 8 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 8 years ago

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

ab41d39 Update DESCRIPTION

bioc-issue-bot commented 8 years ago

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". 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 following build report for more details:

http://bioconductor.org/spb_reports/statTarget_buildreport_20160908060438.html

vobencha commented 8 years ago

When you're ready for me to look at the package again please include a message explaining what changes have been made. Valerie

bioc-issue-bot commented 8 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

13479776 commented 8 years ago

Dear all

I have changed the package according to your comments as the follows. Thank you very much!

(1) XQuarts What role does this play in the GUI? Why are Mac users instructed to download https://www.xquartz.org? If statTarget has system dependencies they must be listed in SystemRequirements in DESCRIPTION.

Response: For mac PC, the package "statTarget" requires X11 support being installed. I have added this clarification in the vignette.

(2) Format all code to be a max of 80 characters wide.

Response: Thanks, it have been revised.

(3) Description From the 'Description' it's not clear what the package actually does:

An easy to use tool provide graphical user interface for quality control based signal correction, integration of metabolomic data from multiple batches, and the comprehensive statistic analysis for non-targeted and targeted approaches.

I don't understand what 'integration of metabolomic data from multiple batches' means. Are we modifying datasets? What is a non-targeted vs targeted approach? Please break the Description into multiple sentences and clarify what some of the terms mean.

Response: The description have been revised. “An easy to use tool provide a graphical user interface for quality control based shift signal correction, integration of metabolomic data from multi-batch experiments, and the comprehensive statistic analysis in non-targeted or targeted metabolomics.”

(4) vignette

• Use the BiocStyle package to format your vignette. Vignettes on this page have details and examples:

http://www.bioconductor.org/packages/3.4/bioc/html/BiocStyle.html

Look at the source code for packages that use BiocStyle to get implementation ideas, e.g., http://www.bioconductor.org/packages/3.4/bioc/html/GenomicTuples.html

• Loading the package

You shouldn't need separate instructions for different platforms. The impute package is listed in 'imports' in DESCRIPTION which should be sufficient. If it needs to be attached to the search path move impute to 'depends'. Do not instruct the user to separately load impute.

Remove all of this:

\subsection{For Mac OS users} \noindent 1 - Install \texttt{XQuartz} from \texttt{ https://www.xquartz.org} \noindent 2 - Copy this code into R. \noindent > source("https://bioconductor.org/biocLite.R") \noindent >biocLite("impute") \noindent >install.packages("statTarget")

\subsection{For Windows users} \noindent 1 - Copy this code into R \noindent > source("https://bioconductor.org/biocLite.R") \noindent > biocLite("impute") \noindent > install.packages("statTarget")

Replace it with this:

Load the package with biocLite(): source("https://bioconductor.org/biocLite.R") biocLite("statTarget")

• The vignette should walk the user through an an analysis example. The general idea is to select some data - maybe from one of the experimental data packages here:

http://www.bioconductor.org/packages/release/BiocViews.html#___ExperimentData

import the data, manipulate, then apply your method. Explain why someone should want to use the package and what it might offer above and beyond the other 1000+ packages in Bioconductor.

• Add a Table of Contents with sections something like -

Background GUI overview -- what does it offer statistically -- highlight primary functions Analysis example -- use real data or a subset -- walk through an analysis or QC example -- conclusions

NOTE: Section 3.0 is not an effective way to introduce users to the package functions. Examples should be evaluated if possible. If you can't evaluate examples, include a few more screenshots. You may want to use this vignette as an example, http://www.bioconductor.org/packages/release/bioc/vignettes/MSGFgui/inst/doc/Using_MSGFgui.html

Response: I have undated the vignette according to the guide. The HTML file and new load code was added. The table of Contents was also undated.

Thanks!

(5) When I library(statTarget) the GUI pops up. Nothing (other than a startup message) should happen when a package is loaded. Please remove the if (interactive()) from zzz.R. The GUI should be started by the user invoking statTarget.gui().

Response: I have deleted the method.The package will start by statTargetGUI().

(6) function names

The dot '.' is used in S3 method dispatch - functions named in this manner can be confusing to novice users. Since none of your functions are S3 methods, please rename them with an underscore or camelCase, e.g., aucROC() instead of auc.ROC().

Response: I have changed these codes.

(7) exported functions and man pages

Not all functions in a package need to be exported in the NAMESPACE. If they are exported, they must have a complete man page. A complete man page includes an \example section with a runnable example. If the example can't be run in the background it can be wrapped in

if (interactive()) { .... }

Decide which functions you need to export (i.e., which functions the user needs access to) and complete the man pages. Currently none of the man pages are complete. They are not descriptive and do not have \example sections. There are many examples of complete man pages in the repository, see GenomicRanges, GenomicAlignments, pRolocGUI, MSGFgui, etc.

Response: I have revised the man files.

Sincerely yours, Hemi

bioc-issue-bot commented 8 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

vobencha commented 8 years ago

Please bump the version so a new build is triggered. Thanks. Valerie

bioc-issue-bot commented 8 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 8 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 8 years ago

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

5858788 Update DESCRIPTION

bioc-issue-bot commented 8 years ago

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 following build report for more details:

http://bioconductor.org/spb_reports/statTarget_buildreport_20160928093408.html

13479776 commented 8 years ago

Dear Mention,

   The error was happened. I am not understand the meaning of this problems. Do i have to delete the .Rnw and . tex files?

   Thank you very much!

<<
creating vignettes ...Error in find_vignette_product(name, by = "weave", dir = docdir, engine = engine) : Located more than one weave output file (by engine utils::Sweave) for vignette with name statTarget: statTarget.html, statTarget.pdf, statTarget.tex Execution halted

Best wishes, Hemi

在 2016年9月28日，上午1:25，vobencha notifications@github.com 写道：

Please bump the version so a new build is triggered. Thanks. Valerie

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

vobencha commented 8 years ago
bioc-issue-bot commented 8 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.