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CVE #26

Closed andreasmock closed 7 years ago

andreasmock 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 @andreasmock

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: CVE
Title: Cancer Variant Explorer
Version: 0.99.0
Authors@R: person("Andreas", "Mock", email = "mock.science@gmail.com", role = c("aut", "cre"))
Author: Andreas Mock [aut, cre]
Maintainer: Andreas Mock <mock.science@gmail.com>
Description: Shiny app for interactive variant prioritisation in precision cancer medicine.
Depends:
    R (>= 3.2.1),
    shiny,
    ConsensusClusterPlus
Imports:
    WGCNA,
    plyr,
    rmarkdown,
    GO.db,
    RColorBrewer,
    ggplot2,
    ape,
    jsonlite,
    gplots,
    limma,
    phytools,
    GOstats,
    GSEABase,
    impute,
    preprocessCore
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
Suggests: knitr,
    rmarkdown
VignetteBuilder: rmarkdown
biocViews: BiomedicalInformatics
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.

lshep commented 8 years ago

Hello,

We had some trouble with the initial build and check of your package. It appears that the code at some point is trying to connect to a local server. May we suggest enclosing the part of the example that runs the server in \donttest{}, so that the user can see and run it but the builder does not. Also it doesn't appear that you have any unit tests for your package. It is highly recommended that you add some unit tests for the overall functionality of the code. An example would be adding unit test that pings the server and fails gracefully (e.g., time out after a suitable short time, a few seconds). I look forward to working with you further on reviewing your package.

Cheers, Lori

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:

eabaf20 Change version

andreasmock commented 8 years ago

Dear Lori,

thank you very much for your quick review of the package. As recommended, I have enclosed the examples in \donttest{} and added a unit test that pings the local server for the Shiny app and checks the right format of the input file.

Best regards, Andreas

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/CVE_buildreport_20160622161740.html

bioc-issue-bot commented 8 years ago

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

9433951 change version 208f211 modify test function 3d3ca50 modify metadata

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/CVE_buildreport_20160622172227.html

bioc-issue-bot commented 8 years ago

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

a82464d New version with ascii encoding

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, WARNINGS, 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/CVE_buildreport_20160626154722.html

bioc-issue-bot commented 8 years ago

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

80da1a2 Fixing vignette 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: "skipped, WARNINGS, 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/CVE_buildreport_20160626160252.html

bioc-issue-bot commented 8 years ago

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

bbd52f8 Vignette encoding

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, WARNINGS, 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/CVE_buildreport_20160627113143.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

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

751af90 version change

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, WARNINGS, 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/CVE_buildreport_20160627114314.html

bioc-issue-bot commented 8 years ago

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

f152e28 debugging of testing

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:

989eda5 version change

bioc-issue-bot commented 8 years ago

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

0d51f20 vignette builds

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, WARNINGS, 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/CVE_buildreport_20160627123043.html

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, WARNINGS, 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/CVE_buildreport_20160627123426.html

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, WARNINGS, 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/CVE_buildreport_20160627123540.html

bioc-issue-bot commented 8 years ago

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

211dcee Changing style to BiocStyle

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/CVE_buildreport_20160627124820.html

bioc-issue-bot commented 8 years ago

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

9db0772 Changing style to BiocStyle eec34fd Merge branch 'master' of github.com:andreasmock/CV...

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, WARNINGS, 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/CVE_buildreport_20160627130037.html

andreasmock commented 8 years ago

Dear Lori, @lshep

I have resolved all required issues except for having runnable examples. This is due to using \donttest{} in the openCVE function that calls the local server for the Shiny app. How do I proceed?

Best, Andreas

lshep commented 8 years ago

I will review your package and reply with any comments or concerns soon.

lshep commented 8 years ago

Hello,

Thank you for submitting your package to Bioconductor. Please see the following comments/suggestions/questions and respond accordingly:

GENERAL It appears that there is a large amount of Data provided with the current application. Please remove the Data in the package and submit as an ExperimentalData package. The package then can be linked to the current package ( https://github.com/Bioconductor/Contributions#submitting-related-packages ) The related package would then be listed in the appropriate field of the description and namespace. Unless there is a reason not to? This will help clarify what are the main functions and applications vs what is specific to data provided.
This should work for a users' provided data and it seemed unclear at what generic data could be. A more generic example would be helpful.

GENERAL There seem to be random .DS_Store files in a number of different directorys (Data/, inst/ , etc.). Is there a purpose for this file or can it be removed?

DESCRIPTION In the description file there are some problems with depends, imports, suggests.

  1. Please remove BiocStyle and rmarkdown from imports and leave in suggests.
  2. The suggests field should contain the packages used in the the inst/doc ,vignettes, and test but not in code. Please move the following to suggests: pingr, limma, phytools,
  3. It was unclear where GO.db, GO.stats, GSEABase, impute, and prepocessCore are used. I see that some of them are used in the vignette. Please move the ones that were used in the vignette to suggests and remove any that are not used. Please also add the library call to the code section of the vignette that utilizes these rather than just referencing the package in the text.

NAMESPACE Please import the functions, classes, or packages that are being used with import(), importFrom(), importClassFrom(), etc.
In general you should not need to access these packages with the (::) . The (::) should be removed in the code and add the needed calls to the namespace. Everything that is listed in the import section of the description file should have some entry in the namespace.

INST/DOC This seems to have the same information/documentation as the vignettes. Please remove since duplicated.

VIGNETTE CVE_tutorial It would be helpful to have a clarification on what is being displayed in the Shiny app. A description of the widgets and tabs that are produced and what it is showing? What widgets are user interactive? A more generic implementation of how the user could implement their data would also be helpful WGCNA_from_TCGA_RNAseq As mentioned earlier please also include the library call in the code of section 4 to the GOstats

Thank you for your efforts and I look forward to an updated submission and comments.

Lori

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:

3ef5560 changes suggested by Ishep 71ddc7b version - changes suggested by Ishep Merge branch...

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

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/CVE_buildreport_20160701123502.html

bioc-issue-bot commented 8 years ago

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

dba7403 typos in NAMESPACE b747abd Merge branch 'master' of github.com:andreasmock/CV...

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:

fab3404 version change

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/CVE_buildreport_20160701124200.html

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/CVE_buildreport_20160701124506.html

bioc-issue-bot commented 8 years ago

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

847c872 change NAMESPACE

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/CVE_buildreport_20160701125604.html

bioc-issue-bot commented 8 years ago

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

a351ff0 NAMESPACE change

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/CVE_buildreport_20160701130746.html

andreasmock commented 8 years ago

Dear Lori, @lshep

thank you very much for your quick review and your valuable suggestions. Please find my comments to your remarks in the following:

GENERAL It appears that there is a large amount of Data provided with the current application. Please remove the Data in the package and submit as an ExperimentalData package. The package then can be linked to the current package ( https://github.com/Bioconductor/Contributions#submitting-related-packages ) The related package would then be listed in the appropriate field of the description and namespace. Unless there is a reason not to? This will help clarify what are the main functions and applications vs what is specific to data provided.

This should work for a users' provided data and it seemed unclear at what generic data could be. A more generic example would be helpful.

_There seem to be random .DSStore files in a number of different directorys (Data/, inst/ , etc.). Is there a purpose for this file or can it be removed?

_DESCRIPTION In the description file there are some problems with depends, imports, suggests.

  1. Please remove BiocStyle and rmarkdown from imports and leave in suggests.
  2. The suggests field should contain the packages used in the the inst/doc ,vignettes, and test but not in code. Please move the following to suggests: pingr, limma, phytools,
  3. It was unclear where GO.db, GO.stats, GSEABase, impute, and prepocessCore are used. I see that some of them are used in the vignette. Please move the ones that were used in the vignette to suggests and remove any that are not used. Please also add the library call to the code section of the vignette that utilizes these rather than just referencing the package in the text._
    • Thank you for the helpful remarks, I changed the description file accordingly.

NAMESPACE Please import the functions, classes, or packages that are being used with import(), importFrom(), importClassFrom(), etc. In general you should not need to access these packages with the (::) . The (::) should be removed in the code and add the needed calls to the namespace. Everything that is listed in the import section of the description file should have some entry in the namespace.

INST/DOC This seems to have the same information/documentation as the vignettes. Please remove since duplicated.

_VIGNETTE CVEtutorial It would be helpful to have a clarification on what is being displayed in the Shiny app. A description of the widgets and tabs that are produced and what it is showing? What widgets are user interactive? A more generic implementation of how the user could implement their data would also be helpful

_WGCNA_from_TCGARNAseq As mentioned earlier please also include the library call in the code of section 4 to the GOstats

Best wishes, Andreas

andreasmock commented 7 years ago

Dear Lori, @lshep did you already encounter additional issues with the package I can address? Best regards, Andreas