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aracne.networks #21

Closed federicogiorgi closed 8 years ago

federicogiorgi commented 8 years ago

Dear all,

I would like to submit a Bioconductor package called aracne.networks. This package contains gene regulatory networks extracted from the biggest cancer dataset ever created (TCGA). These networks are used extensively in pipelines to infer protein activity, already implemented in the viper package, and have been the scaffold for several network-based analyses published over the years from the Califano Lab at Columbia University.

Repository: https://github.com/federicogiorgi/aracne.networks Confirm the following by editing each check box to '[x]'

I understand that by submitting my package to Bioconductor,

I am familiar with the essential aspects of Bioconductor software management, including:

bioc-issue-bot commented 8 years ago

Hi @federicogiorgi

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: aracne.networks
Type: Package
Title: ARACNe-inferred gene networks from TCGA tumor datasets
Version: 0.99.0
Author: Federico M. Giorgi
Maintainer: Federico M. Giorgi <federico.giorgi@gmail.com>
Suggests: viper
Description: This package contains ARACNe-inferred networks from TCGA tumor datasets and functions to import new ones and export them into plain-text format
License: LGPL-3
LazyData: TRUE
biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData
NeedsCompilation: no
Packaged: 2016-06-09 03:25:05 UTC; malvarez
bioc-issue-bot commented 8 years ago

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 commented 8 years ago

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/aracne.networks_buildreport_20160613134152.html

bioc-issue-bot commented 8 years ago

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 commented 8 years ago

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

43e8528 commit

bioc-issue-bot commented 8 years ago

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/aracne.networks_buildreport_20160613174219.html

bioc-issue-bot commented 8 years ago

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 commented 8 years ago

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

f7c14fe commit

bioc-issue-bot commented 8 years ago

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/aracne.networks_buildreport_20160614111444.html

federicogiorgi commented 8 years ago

Dear all,

not sure how to proceed now. The only warning I get concerns the size of the package:

  • checking installed package size ... NOTE installed size is 191.3Mb
  • checking data for ASCII and uncompressed saves ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data
lshep commented 8 years ago

Hello,

You can ignore these WARNINGS for now as this will be an ExperimentalData package. We will review your package further and get back to you shortly.

Lori

On Tue, Jun 14, 2016 at 11:14 PM, federicogiorgi notifications@github.com wrote:

Dear all,

not sure how to proceed now. The only warning I get concerns the size of the package:

-

checking installed package size ... NOTE installed size is 191.3Mb

checking data for ASCII and uncompressed saves ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/21#issuecomment-226077539, or mute the thread https://github.com/notifications/unsubscribe/AR22HKkXYvCAQru9OImXAUbLmL7JxyKaks5qL24GgaJpZM4IzZkp .

federicogiorgi commented 8 years ago

Thank you so much! Looking forward to hearing from you.

Federico On Jun 15, 2016 10:22 AM, "lshep" notifications@github.com wrote:

Hello,

You can ignore these WARNINGS for now as this will be an ExperimentalData package. We will review your package further and get back to you shortly.

Lori

On Tue, Jun 14, 2016 at 11:14 PM, federicogiorgi <notifications@github.com

wrote:

Dear all,

not sure how to proceed now. The only warning I get concerns the size of the package:

checking installed package size ... NOTE

installed size is 191.3Mb

checking data for ASCII and uncompressed saves ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub < https://github.com/Bioconductor/Contributions/issues/21#issuecomment-226077539 , or mute the thread < https://github.com/notifications/unsubscribe/AR22HKkXYvCAQru9OImXAUbLmL7JxyKaks5qL24GgaJpZM4IzZkp

.

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lshep commented 8 years ago

Hi Federico,

Please see the comments below.

  1. Add an example in aracne.networks-package.Rd
  2. Remove static package version/date information in the aracne.networks-package.Rd : duplicated from DESCRIPTION file
  3. Please add depends >= R 3.3
  4. It seems like the "regulon" class is the class definition and format used in the viper package. We do not want duplicated classes across packages as it can create confusion for the user, duplicate help page entries, and duplicate code. Also when the user loads the data they now have a regulon object to deal with. Any getters/setters/methods viper has defined on the regulon class won't be available unless viper is on the search path; by adding viper to 'depends' these functions do become available and the user can manipulate the object as expected. Please remove the class from your package, move viper to a depends field in DESCRIPTION, and import in the NAMESPACE.
  5. Please enhance the value section for the datasets. "regulon" is not a well-known class and should be better defined as far as object's elements, dimensions, etc. And/or assuming the above is implemented, reference the viper help page \link[viper]{regulon-class}.
  6. It is suggested that you might add in a little detail describing the ARACNe algorithm rather than just including a reference.
  7. It is also suggested that you might enhance the example included in the vignette to show a small workflow to demonstrate how the output from write.regulon() is utlized and truely useful.
  8. Please remove the following files from vignettes/ aracne.networks-concordance.tex aracne.networks.log aracne.networks.pdf aracne.networks.synctex.gz aracne.networks.tex
  9. The vignette indicates the data were downloaded on April 15, 2016. This information should also be included in the man pages. Is there a version associated with the data or just a download date?

Look forward to hearing from you. Cheers, Lori

bioc-issue-bot commented 8 years ago

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

2e5ef62 Implemented suggestions by Lori

bioc-issue-bot commented 8 years ago

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, 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/aracne.networks_buildreport_20160617194753.html

bioc-issue-bot commented 8 years ago

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

6adc518 Attempt to fix bibliography latex problem in Windo...

bioc-issue-bot commented 8 years ago

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/aracne.networks_buildreport_20160617215428.html

bioc-issue-bot commented 8 years ago

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

93d01fa Added a 'regulator' argument in the docs for funct...

bioc-issue-bot commented 8 years ago

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/aracne.networks_buildreport_20160620123307.html

lshep commented 8 years ago

Hi Federico,

Thank you for making those changes. The package looks okay now and will be accepted. You should get svn instructions via email in the next couple of days. Thank you for your time and effort

Lori

federicogiorgi commented 8 years ago

Dear Lori,

no thank YOU for your time and effort :-) I really appreciate your help.

Federico

federicogiorgi commented 8 years ago

Dear Lori,

can you please send me the instructions on how to proceed with SVN? No rush, at your earliest convenience :-)

Federico

On 20 June 2016 at 19:04, Martin Morgan notifications@github.com wrote:

Closed #21 https://github.com/Bioconductor/Contributions/issues/21.

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mtmorgan commented 8 years ago

On 06/23/2016 04:04 PM, federicogiorgi wrote:

Dear Lori,

can you please send me the instructions on how to proceed with SVN? No rush, at your earliest convenience :-)

The instructions will arrive shortly, today or tomorrow. Martin

Federico

On 20 June 2016 at 19:04, Martin Morgan notifications@github.com wrote:

Closed #21 https://github.com/Bioconductor/Contributions/issues/21.

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federicogiorgi commented 8 years ago

Dear Martin,

sorry to bug you again about the aracne.networks package, but you said you would send the instructions within one or two days :-)

Thanks and sorry again!

Federico

On 23 June 2016 at 17:06, Martin Morgan notifications@github.com wrote:

On 06/23/2016 04:04 PM, federicogiorgi wrote:

Dear Lori,

can you please send me the instructions on how to proceed with SVN? No rush, at your earliest convenience :-)

The instructions will arrive shortly, today or tomorrow. Martin

Federico

On 20 June 2016 at 19:04, Martin Morgan notifications@github.com wrote:

Closed #21 https://github.com/Bioconductor/Contributions/issues/21.

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