MACPET

[IoannisVardaxis]

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

• Repository: https://github.com/IoannisVardaxis/MACPET

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[bioc-issue-bot]

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

62db6f7 Version update

[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 build report for more details.

[nturaga]

@IoannisVardaxis Why do you have a sysdata.rda file in your R/ directory within your package?

[IoannisVardaxis]

@nturaga Because this is a list of data.frames and each data.frame contains coordinates of black listed regions based on the genome used. I use sysdata to remove input data which overlaps with those coordinates.

[nturaga]

Hi,

You have warnings because of the way you are referencing your man pages. (https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Cross_002dreferences).

I think the links are wrong, you want \code{\link[Rbowtie:Rbowtie]{bowtie}}

[bioc-issue-bot]

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

20ab45f Version and packages update fcef21e Updates for the references to other packages, as w... 2228404 Article reference update.

[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 build report for more details.

[bioc-issue-bot]

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

48dc7eb Changing Biostrings::narrow to IRanges::narrow fe26e09 Updating 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: "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 build report for more details.

[IoannisVardaxis]

Hi, I did as you suggested but I get the same warnings again.

[nturaga]

Hi @IoannisVardaxis

Your package looks fine and is ready to be accepted. But the warnings are caused because you reference the wrong files.

\item{object}{An object of \code{\link[InteractionSet:GInteractions]{GInteractions}} class.}

is supposed to be

\item{object}{An object of \code{\link[InteractionSet:GInteractions-class]{GInteractions}} class.}

Take a look the GInteractions-class.Rd file in the InteractionSet package. That's the best way to reference these classes.

I will accept your package as soon as you fix this.

[bioc-issue-bot]

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

d8dd0a0 Version update and packages versions update 6fc3445 Changes to the Ginteractions class reference afb430b Small change to the Stage_3_PeakFinderSubFunctions...

[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 build report for more details.

[IoannisVardaxis]

I made the changes but I still get error on windows. I will try to fix it in one of the following days.

Note I made a small modification to the Stage_3_PeakFinderSubFunctions such that it returns four more parameters which I am going to need on a later update after the package is accepted. So i also needed to update vignette and the data for documenting those four parameters. But the changes are not big.

[nturaga]

@IoannisVardaxis Thanks. Once you are done fixing them, let me know.

[bioc-issue-bot]

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

3d42e46 Tring to fix the windows errors

[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 build report for more details.

[bioc-issue-bot]

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

b02ae72 Trying to fix the windows error for the Rbowtie

[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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

[IoannisVardaxis]

@nturaga now everything seems to be ok! Thank you for your help!

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be sent to the maintainer email address in the next several days.

Thank you for contributing to Bioconductor!

[mtmorgan]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/IoannisVardaxis.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using biocLite(\"MACPET\"). The package 'landing page' will be created at

https://bioconductor.org/packages/MACPET

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.