CVE

[andreasmock]

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[lshep]

Some new additional comments:

GENERAL: From the new section in the vignette, it is my understanding that this application only works with output from the Oncotator Annotation Tool. This should be specified in the packages descriptions and made more clear. It is okay to have specialized tools but it should be stated.

DESCRIPTION/NAMESPACE: It appears your shiny app requires RColorBrewer, gplots, plyr, and ggplot2 in order to display correctly. These packages should be listed in Depends of the DESCRIPTION file and removed from Imports. They can also be removed in the NAMESPACE imports.

DESCRIPTION: where is impute used? This should be removed if not used.

MAN:
openCVE.Rd: add a \value section indicating that the shiny app is launched.

WGCNAmelanoma_extension.Rd: you included all the individual data files in WGCNAmelanoma_extension.RData object. Could you also include a WGCNAmelanoma_extension.Rd file indicating these objects can be loaded by loading that data file.

VIGNETTE: WGCNA_from_TCGA_RNAseq.Rmd It is unclear to me what this documentation describes. Is this how you created the extension data you use in the package or does a user have to go through all these steps in order to use the shiny app? None of the code in this vigentte is evaluated, why? We generally like code evaluated when generating the vignette. I can't run through the example in this vignette because the RNAseq object you utilize right away is not included with the package data and it is not clear how that is created.

Thank you Lori

[bioc-issue-bot]

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]

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]

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]

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

7f49ca8 version change

[bioc-issue-bot]

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

689bd5b version change

[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 following build report for more details:

http://bioconductor.org/spb_reports/CVE_buildreport_20160714181812.html

[bioc-issue-bot]

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

a1dcb77 change of tests 2049e78 version change

[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 following build report for more details:

http://bioconductor.org/spb_reports/CVE_buildreport_20160715031014.html

[bioc-issue-bot]

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

d742b9a changing NAMESPACE

[bioc-issue-bot]

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]

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

027c0ed version change

[bioc-issue-bot]

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

e79dc46 version change

[bioc-issue-bot]

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

5a9974d version change

[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 following build report for more details:

http://bioconductor.org/spb_reports/CVE_buildreport_20160719085025.html

[andreasmock]

Dear Lori, @lshep,

thanks, this is most helpful!

1) I have added the description of the input file to the DESCRIPTION file.

2) I have updated the DESCRIPTION/NAMESPACE. It turns out, that CVE and its extension need all packages in “depends” to execute properly.

3) MAN: a \value section was added to openCVE.Rd

4) VIGNETTE: WGCNA_from_TCGA_RNAseq.Rmd I understand that having vignettes that are not executable is not common in Bioconductor packages. This vignette was only thought to be a source of additional information for those interested in using WGCNA for RNAseq data. It is not the focus of the package and the manuscript and is not needed to use the Shiny app. We even thought about of excluding this tutorial, in order not to confuse the user of the package. We did not supply the RNAseq object because (i) it is the exact RNAseq2 level 3 data from the TCGA data portal for cutaneous melanoma and I was not sure about the policy to redistribute TCGA data and (ii) it is with approx. 30 MB quite large.

Best regards, Andreas

[lshep]

Thank you for your updates. Your package is looking good. Just a few other comments.

R CODE: If you run the application with the extension data
openCVE(oncotator_example, sample_names='case study', extension='WGCNAmelanoma')

When you click on Melanoma WGCNA tab a Warning message comes up. If this is possible to fix please fix it, if not please explain why (if it is a problem with a different program). This warning is repeated any time you click on that tab or change any of the widgets on that page. Example warning: Warning in rect(9, 5, 10, 5.7, add = TRUE, xpd = TRUE, col = "grey", border = "grey") : "add" is not a graphical parameter Warning in rect(8.75, 2, 10.25, 8, add = TRUE) : "add" is not a graphical parameter

NAMESPACE:
This is my fault from my last comment, please add the packages in depends of the DESCRIPTION file to the NAMESPACE as import()

DESCRIPTION:
Please update the R version requirement from 3.2.1 to 3.3

MAN:
Please add a WGCNAmelanoma_extension.Rd to indicate what is loaded with data(WGCNAmelanoma_extension). The individual man files for the objects are great! but there should be a man page for the this too to indicate where all those objects are come from.

VIGNETTE: CVE_tutorial.Rmd: Please add a table of contents

WGCNA_from_TCGA_RNAseq.Rmd: Thank you for clarifying in your last comment. Two suggestions: a. At the very least could you please clarify at the beginning of the vignette that it is a proof of principal example and can't be run as listed. I think it is good to still include this to show how someone would create the data. b. Consider exploring the Bioconductor experimental data packages for example data that can be freely loaded and used. You can search the packages here. I'm not sure if it is appropriate for your application but some available software packages are "pasilla" and "pasillaBamSubset" that have RNASeq data. Including this vignette as a runable example would be a great help to the bioconductor community, showing how to use existing data/data objects with your application.

Thank you Lori

[bioc-issue-bot]

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

6eb6391 changes as suggested by Ishep

[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 following build report for more details:

http://bioconductor.org/spb_reports/CVE_buildreport_20160722052307.html

[andreasmock]

Dear Lori, @Ishep,

thanks again, I am very grateful for your help.

I have

• fixed the Warning message in the Melanoma WGCNA tab
• updated the NAMESPACE
• changed the R version requirement
• added a WGCNAmelanoma_extension.Rd documentation

Regarding the vignette WGCNA_from_TCGA_RNAseq

• Indeed, a great amount of work was put into a recent experimental data package summarising all TCGA data (RTCGA package). Unfortunately, the TCGA Data Portal is no longer operational and the data was moved to Genomic Data Commons. Hence, major changes are needed to account for this change in data structure.
• As a consequence I abstained from using the RTCGA data, but I am very happy to update my vignette once the changes have been undertaken.
• As suggested by you, I have clarified at the beginning of the vignette, that it can’t be run as listed at the moment and only serves as a proof of principal example.

Best wishes, Andreas

[lshep]

Thank you for making those changes. Please add import(RColorBrewer) to the NAMESPACE. Once this is done and the new build completes, I will recommend your package be accepted. You should get svn instructions via email in the next couple of days. Thank you for all your time and effort.
Lori

[bioc-issue-bot]

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

3037928 add RColorBrewer to 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 following build report for more details:

http://bioconductor.org/spb_reports/CVE_buildreport_20160722080144.html

[andreasmock]

I added import(RColorBrewer), Thank you gain for your great help and valuable suggestions! Andreas

[modarzi]

Hi, I install R version 3.4.4 and try to install "WGCNA_from_TCGA_RNAseq" package but in my RStudio console receive this warning:

Warning message: package ‘WGCNA_from_TCGA_RNAseq’ is not available (for R version 3.4.4)

I appreciate if you share your comment with me. Best Regards, Mohammad

[mtmorgan]

@modarzi ask support questions on https://support.bioconductor.org. Provide enough detail for your question to be reproduced. 'WGCNA_from_TCGA_RNAseq' does not seem like a package name.