IntEREst

[gacatag]

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• Repository: https://github.com/gacatag/IntEREst

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[gacatag]

Dear Valerie ( @vobencha ), Hi again! In the newest version bump IntEREst 0.99.17 I added an isPaired parameter that by setting it as FALSE the analysis would be adaptable to single read (not paired!) sequencing .bam files. It would read and analyze the single/unpaired read .bam file correctly.

Cheers!

[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/IntEREst_buildreport_20170213101857.html

[vobencha]

Thanks for your patience. I'll take a look at this tomorrow. Valerie

[bioc-issue-bot]

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

dab7c86 Correct and improve vignette document

[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/IntEREst_buildreport_20170222080835.html

[vobencha]

Hi,

Thank you for working on the package. It's looking much better.

I'm not clear on what your intentions are with the MDS.Chr22.U12Genes data package. Currently the software package is self contained and does not use it. The data package has 15 bam files which is excessive for an experimental data package. I would recommend you proceed with the software package and not the experimental data package.

Valerie

[bioc-issue-bot]

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

6abe666 Remove MDS.Chr22.U12Genes dependency + add data ge...

[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/IntEREst_buildreport_20170223102246.html

[bioc-issue-bot]

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

1339e80 Version bump.

[gacatag]

Hi Valerie ( @vobencha ). Thank you for your response. I removed the MDS.Chr22.U12Genes dependency (suggestion) and also updated the vignette document accordingly; instead of the large data package, I included all the scripts needed to generate the test data mdsChr22Obj in /inst/scripts/. I included the scripts in case a user wished to generate the test data mdsChr22Obj manually using the interest() and the readInterestResults() functions, or if a user wanted to see how the test data was generated.

The reason that I was initially planing to include the data package MDS.Chr22.U12Genes is that, although I already had included the test data mdsChr22Obj in the package, that could be used as a demo to test plotting and other DOWNSTREAM analysis, I also wanted to include the source .bam files as an attached package (suggsted by IntEREst) to show a demo on running the intron-retention estimation functions, i.e. interest() and interest.sequential() which lead to building mdsChr22Obj. As I mentioned, based on your comment, in the latest version bump I added the scripts that one can use to make the test data mdsChr22Obj to the package and I also provided the path to the readme.txt file and the scripts in the vignette.

Cheers,

Ali

[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/IntEREst_buildreport_20170223110446.html

[vobencha]

Thanks for making the changes. The package looks good and I'm approving it. The RMySQL on the mac is expected and won't be fixed anytime soon since the binaries aren't available from CRAN.

Valerie

[vobencha]

You'll get an email in the next few days with svn credentials and instructions for working on the package in svn.

Valerie

[gacatag]

Great! Thank you for your comments.

Cheers! Ali