GISPA

[BhaktiDwivedi]

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• Repository: https://github.com/BhaktiDwivedi/GISPA

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[LiNk-NY]

Hi @BhaktiDwivedi, Please submit as soon as you can make the changes. Best regards, Marcel

[bioc-issue-bot]

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

e77b3fa revised version

[BhaktiDwivedi]

Hi @LiNk-NY, Please see the new version with changes. Below I have highlighted the responses

"you should really make use of the classes in GSEABase to represent gene sets." I have used GSEABase class in the code where it can be best used to represent gene sets or subset data by gene sets. As my package involves combining multiple data types by gene symbols, which can be duplicated depending on whether more than one variant or copy change or probe is reported in the input data-set, it's tricky to use the gene sets by each data type or data set separately. The results that are generated in this package are genes grouped by identified change points not necessarily by a phenotype or ontology or biological process or pathway. Although change point 1 profile is the most desirable, user with the help of the diagnostic plots can further access and evaluate the genes by change points that best represent the desired profile for their purposes. Please let me know if you still have concerns.

Data • Please document your datasets appropriately (see: http://r-pkgs.had.co.nz/data.html) • Combine your data documentation roxygen blocks into one document > data.R. o Made the changes

Code • Try to keep your code tidy. This means not having lines that are over 80 columns wide. o Fixed it

• Set default values in the function definition o Done

• Make arguments more descriptive and consistent (e.g., DM means data matrix and data frame in different functions) o Fixed it

• Some arguments are described as "vector" when you likely mean list (such as for f.sets) o Fixed it

• You should avoid using underscores (_) in arguments. o Fixed it

• There seems to be a lot of repetitive coding in stackedBarplot try to reduce this. o I tried, but given the output I need to generate by one-, two-, and three- feature analysis and the likert function {HH} library limitations I have to repeat them.

• Avoid empty else statements else { #nothing } o Fixed such statements

• return calls after stop() are unnecessary o Fixed it

• Do not use underscores _ in exported functions (gispa_method) o changed to '.', and Fixed it where-ever applies

• Separate plotting and calculation in the "gispa_method". The function does too much. o Fixed it. please see if this looks better.

[bioc-issue-bot]

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

ca3aa29 revised version

[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/GISPA_buildreport_20170214000136.html

[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/GISPA_buildreport_20170214000505.html

[bioc-issue-bot]

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

42b04d1 revised version

[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/GISPA_buildreport_20170214102744.html

[bioc-issue-bot]

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

e944c2e revised version

[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/GISPA_buildreport_20170214104346.html

[bioc-issue-bot]

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

bf6f5c9 revised version

[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/GISPA_buildreport_20170214105513.html

[LiNk-NY]

Hi Bhakti @BhaktiDwivedi, Thanks for making the changes. What is the difference between GISPA and gispaMethod? It seems to me like the names should be different if they are not doing the same thing. It may confuse your users.

The rest is looking better!

Regards, Marcel

[BhaktiDwivedi]

hi @LiNk-NY

Thank you so much. Yes, it's the function for the changepoint-based profile characterization model. I can change it to something other than gispaMethod. for example, 'cptModel'

Thank you.

[LiNk-NY]

That would be good! Thank you Bhakti!

[bioc-issue-bot]

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

9950e96 revised version 61f0385 revised version a634fbd revised version

[BhaktiDwivedi]

Done. Please see the submitted revised version. Thank you very much @LiNk-NY !

[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/GISPA_buildreport_20170223100621.html

[LiNk-NY]

Hi Bhakti @BhaktiDwivedi, You are having some errors with the package, namely due to the version number. The version number of you package should be 0.99.z where z is the number of times you have pushed changes to your package (you can also just make it 0.99.8 to keep it consistent with your commits). The package has not been published on Bioconductor and therefore it cannot be anything above a 1.0.0 version.

Best regards, Marcel

[BhaktiDwivedi]

Hi @LiNk-NY, Sure, I just changed the version to 0.99.8. I kept increasing to 1.0.# asI was getting the version bump required tag and to get a valid push. Hope this helps. Please let me know if there is anything else needed. Thank you. Bhakti

[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, 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/GISPA_buildreport_20170224134936.html

[BhaktiDwivedi]

Hi @LiNk-NY Is there anything else that I need to fix or resolve in the final version? Please let me know. Thank you. Regards, Bhakti

[LiNk-NY]

Hi Lori, @lshep Can you kick off another build? Thanks.

The HH CRAN package has been installed on Oaxaca.

Regards, Marcel

[LiNk-NY]

Hi Bhakti, @BhaktiDwivedi

Package development is a continual process. We hope that you consider adding unit tests to your package in order to make it more robust and less prone to bugs.

Please see the GitHub repository: MangoTheCat/goodpractice for more tips on improving your package's robustness. After installation (BiocInstaller::biocLite("MangoTheCat/goodpractice")), you can run goodpractice::gp(".") within your package's directory to get additional recommendations for your package.

Once your package builds on Oaxaca, it will be ready to be accepted. Thank you for submitting to Bioconductor!

Best regards, Marcel

[BhaktiDwivedi]

Hi @LiNk-NY , Thank you. I will take a look at the unit tests. I thought the reason I am getting a build error on Oaxaca is because of library {HH} prerequisites not being installed on the build system. Am i missing something here? Regards, Bhakti

[LiNk-NY]

Yes, that's right. We have installed it on Oaxaca and it should be ready to go. We are just making sure that your package fully checks out on Oaxaca. Thanks. Marcel

[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 following build report for more details:

http://bioconductor.org/spb_reports/GISPA_buildreport_20170228065335.html

[LiNk-NY]

The package is building as expected! Thanks again.

[BhaktiDwivedi]

Thank you @LiNk-NY !! This is good news!

Please let me know when I will be able to obtain the URL.

Also, as I make updates and improvement in the package, I hope I am able to commit those changes on Bioconductor release version.

Thank you.

Regards, Bhakti

[LiNk-NY]

Hi Bhakti, @BhaktiDwivedi When the package is added to the devel build system, the following URL should work: https://bioconductor.org/packages/GISPA

You will be contacted with SVN credentials for making further changes your package.

Best regards, Marcel