RITANdata

[MTZimmermann]

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• Repository: https://github.com/MTZimmer/RITANdata

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[bioc-issue-bot]

Hi @MTZimmer

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: RITANdata
Type: Package
Title: This package contains the annotation and network data sets
Version: 0.99.0
Date: 2016-07-28
Author: Michael Zimmermann
Maintainer: Michael Zimmermann <zimmermann.michael@mayo.edu>
Description: Data such as is contained in these two R data files in this
    package are required for the RITAN package. Users may use their own 
    or additional resources in conjunction with RITANdata.
    See the RITAN vignettes for more information.
Depends: R (>= 3.3)
License: file LICENSE
RoxygenNote: 5.0.1
LazyData: TRUE
biocViews: Network, NetworkInference, GeneSetEnrichment
NeedsCompilation: no
Packaged: 2017-02-01 02:26:00 UTC; m107607

[bioc-issue-bot]

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.

[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: "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/RITANdata_buildreport_20170303180621.html

[bioc-issue-bot]

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

bddca87 version bump to trigger BioConductor build

[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: "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/RITANdata_buildreport_20170305204050.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/RITANdata_buildreport_20170310142421.html

[bioc-issue-bot]

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

71439da biocViews updated biocViews to be "Annotation Dat...

[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/RITANdata_buildreport_20170310150713.html

[bioc-issue-bot]

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

fcc0156 biocViews Bioc requires additional Views 9058954 version bump

[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/RITANdata_buildreport_20170310151244.html

[bioc-issue-bot]

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

53ca28b update biocViews update biocViews a4dc0aa version bump

[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/RITANdata_buildreport_20170310152246.html

[bioc-issue-bot]

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

10c023b update biocViews

[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, 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/RITANdata_buildreport_20170310153137.html

[bioc-issue-bot]

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

9b910b6 update R version dependence

[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". 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/RITANdata_buildreport_20170310153650.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.

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

Please see the following build report for more details:

http://bioconductor.org/spb_reports/RITANdata_buildreport_20170313094806.html

[MTZimmermann]

AdditionalPackage: https://github.com/MTZimmer/RITAN

[bioc-issue-bot]

Hi @MTZimmer,

Starting build on additional package https://github.com/MTZimmer/RITAN.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your additional package repository will NOT trigger a new build.

The DESCRIPTION file of this additional package is:

Package: RITAN
Type: Package
Title: Rapid Integration of Term Annotation and Network resources
Version: 0.99.0
Author: Michael Zimmermann
Maintainer: Michael Zimmermann <zimmermann.michael@mayo.edu>
Description: Tools for comprehensive gene set enrichment and extraction of
multi-resource high confidence subnetworks.
LazyData: TRUE
Depends: R (>= 3.3), ProNet
Imports: grid, gridExtra, reshape2, gplots, ggplot2, plotrix,
    RColorBrewer, STRINGdb, MCL, linkcomm, hash, png, sqldf,
    igraph, RITANdata
VignetteBuilder: knitr
Collate: 'lib_enrichment.R' 'lib_network.R'
    'interconnectivity_functions.R'
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown
License: file LICENSE
RemoteType: local
RemoteUrl: /data2/bsi/staff_analysis/m107607/VRG_Poland/RITAN/RITAN
RemoteSha: 1.0
biocViews: QualityControl, Network, NetworkEnrichment,
    NetworkInference, GeneSetEnrichment, FunctionalGenomics
NeedsCompilation: no
Packaged: 2017-02-01 04:53:01 UTC; m107607

[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, TIMEOUT, 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/RITAN_buildreport_20170315113508.html

[bioc-issue-bot]

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

9f66280 speeding up vignettes cached data and updates to ... 8c32dc4 version bump to trigger bioC build

[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/RITAN_buildreport_20170330132212.html

[bioc-issue-bot]

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

fcc6cc9 version bump to trigger bioC build

[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, 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/RITANdata_buildreport_20170330132922.html

[bioc-issue-bot]

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

597bdc4 update imports to include knitr for vignettes

[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/RITAN_buildreport_20170330133635.html

[bioc-issue-bot]

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

8e08eab docs 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.

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

Please see the following build report for more details:

http://bioconductor.org/spb_reports/RITANdata_buildreport_20170331000607.html

[bioc-issue-bot]

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

d648e53 docs and NAMESPACE 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 following build report for more details:

http://bioconductor.org/spb_reports/RITAN_buildreport_20170331002133.html

[bioc-issue-bot]

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

8862b99 added import exception to avoid function masking ...

[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 following build report for more details:

http://bioconductor.org/spb_reports/RITAN_buildreport_20170331092032.html

[hpages]

Hi Michael,

Thanks for your submission.

1. Please also submit the RITAN software package (in this same issue). There is not much point for us to add RITANdata to Bioconductor if it's not accompanied by the RITAN package.

2. R CMD build RITANdata is not building the HTML vignette because of 2 problems: a) You already have a prebuilt HTML version of the vignette in the inst/doc/ folder. It needs to be removed. b) You also need to add the following line

      VignetteBuilder: knitr

   to the DESCRIPTION file of the package.

   With these changes R CMD build RITANdata will build the HTML vignette and include it in the resulting source package tarball. This is the standard mechanism for producing a source tarball that contains an HTML vignette that is guaranteed to be in sync with the Rmd vignette.

3. Please remove the last line of the DESCRIPTION file:

   Packaged: 2017-02-01 02:26:00 UTC

   This line will be automatically added to the source package tarball when we run R CMD build on the package (and it will reflect the real packaging time).

4. The vignette doesn't say anything about the cached_coding_genes data set. Is this intended? Also the man page for this data set says:

   gene symbols for protein coding genes - cached for use in vignettes -

   but I can't figure out where it's used in the vignette.

5. The man pages for the data sets should explain how these data sets were generated e.g. where the data is coming from, how it was curated, etc... Ideally, and for the sake of reproducibility, the code used to generate them should be made available.

Regards, H.

[bioc-issue-bot]

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

126f3ca version bump

[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 following build report for more details:

http://bioconductor.org/spb_reports/RITANdata_buildreport_20170407105343.html

[MTZimmermann]

Dear @hpages ,

I believe I have made all changes that you itemized last week. The most recent versions of both RITANdata and RITAN have passed the buildreport without errors or warnings. Please let me know if you find any additional items that need adjustment, or if you have any further questions.

Sincerely,

[hpages]

Thanks Michael,

Packages (software and data) look good and I'm marking them as accepted. There are a few minor issues (see below). However, because we are very short of time for the release, I'm only listing them here as an FYI in the hope that you'll be able to address them at some point.

Thanks for you contribution to the project, H.

6. You need to import the following packages: graphics, stats, utils.

7. Calling readSIF(), readGMT(), or writeGMT() with no argument currently displays a message explaining how to use the function but they should raise an error instead (and the current message should be the message displayed by the error).

8. The readSIF(), readGMT(), and writeGMT() functions need to have real examples in their man pages.

9. There are several problems with the man pages of the vac1. and vac2. data sets:

   • The *.Rd files should contain \docType{data}
   • The \description sections should not contain code showing how to use the data set. Instead they should describe the data set. The code they contain should be moved to an \examples section.
   • Since you are using LazyData: TRUE in the DESCRIPTION file, you don't need to load the data sets with data() before you can use them. You can use them immediately.

[MTZimmermann]

Dear Hpages and BioC Moderators,

With the BioC version 3.5 builds, RITAN builds now return an immediate error that RITANdata cannot be found. Were both packages accepted? If so, is there an additional step needed to enable access to packages new to the most recent release?

Please let me know if there's any additional information I can provide.

Also, due to family events, I won't be able to immediately, but I willupdate RITAN with the additional points out have outlined above.

Sincerely,

[mtmorgan]

RITANdata has been added to the experiment data repository in both release (as version 1.0.0) and devel (version 1.1.0). Sorry for the delay; the first builds with these packages available will report on Sunday afternoon.