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MONSTER #110

Closed dschlauch closed 7 years ago

dschlauch commented 8 years ago

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

Confirm the following by editing each check box to '[x]'

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

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

bioc-issue-bot commented 8 years ago

Hi @dschlauch

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: MONSTER
Type: Package
Title: Modeling Network State Transitions from Expression and Regulatory data
    (MONSTER)
Version: 0.99.0
Date: 2016-04-04
Author: Dan Schlauch
Maintainer: Dan Schlauch <dschlauch@fas.harvard.edu>
Description: Indentifies transcription factor drivers of state change from
    expression data
biocViews: StatisticalMethod, GraphAndNetwork, Microarray, GeneRegulation, NetworkInference, GeneExpression, Transcription, Network
Imports: reshape2, 
    ggplot2, ggdendro, grid,
    MASS,
    igraph,
    assertthat,
    testthat
License: GPL-2
RoxygenNote: 5.0.1
Suggests: knitr,
    rmarkdown,
    testthat,
    Biobase
VignetteBuilder: rmarkdown
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/MONSTER_buildreport_20160915022801.html

lshep commented 8 years ago

Any package utilized should be listed in the DESCRIPTION file as a Depends, Imports, Suggests, or Enhances and if applicable imported (or specific functions importFrom) in the NAMESPACE.

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:

baf1350 increment version

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/MONSTER_buildreport_20160919121019.html

bioc-issue-bot commented 8 years ago

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

35ae6f0 updated vignetteBuilder

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/MONSTER_buildreport_20160919151545.html

bioc-issue-bot commented 8 years ago

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

a5cf005 adding import penalized to namespace

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/MONSTER_buildreport_20160919153637.html

bioc-issue-bot commented 8 years ago

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

9df3486 removed ggrepel, added penalized predict 139a43d increment version

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/MONSTER_buildreport_20160919154800.html

lshep commented 8 years ago

Thank you for your submission to Bioconductor.

Please address the following WARNING/NOTE issues from the buildreport: MONSTER

DESCRIPTION: remove testthat from Imports and leave in Suggests. add Methods to Imports

DESCRIPTION/NAMESPACE: Please consider adding the imports and imports from suggested in the package build report to remove the "no visible global function definition" notes: Add:

  importFrom("methods", "new")
  importFrom("stats", "as.dendrogram", "as.dist", "coefficients", "cor",
             "cov", "dist", "hclust", "lm", "order.dendrogram", "pnorm",
             "princomp", "sd")
  import(pandaR)
  importFrom("tidyr", "spread")
  importFrom("reshape2", "melt")

We would appreciate if you could also correct the package build report notes on "no visible binding for global variable". See ?globalVariables

MAN: add a documentation entry for yeast

fix checking Rd \usage sections ... WARNING (see the build report)

DATA: For the uncompressed saves Run R CMD build --resave-data MONSTER This will create a tarball that has the data files compressed as small as possible. Untar this file and copy the data files in it over the ones in your git working copy, then recommit those.

Once these are address we will further review your package for acceptance. I look forward to reviewing your updates.

bioc-issue-bot commented 8 years ago

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

0c56778 addressed warnings, added monsterRes.rda

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, 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/MONSTER_buildreport_20160926171903.html

bioc-issue-bot commented 8 years ago

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

450bc00 added tidyr to imports, incremented version 5897d9c incremented version

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, 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/MONSTER_buildreport_20160926173147.html

bioc-issue-bot commented 8 years ago

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

9baaf64 fixed data loading

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, 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/MONSTER_buildreport_20160926175315.html

bioc-issue-bot commented 8 years ago

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

eb69f64 updated examples to fix loading error 49b5420 increment version

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, 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/MONSTER_buildreport_20160926180930.html

bioc-issue-bot commented 8 years ago

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

a303f47 re-adding export monsterNI 7d5a1c5 increment version

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, 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/MONSTER_buildreport_20160926182340.html

bioc-issue-bot commented 8 years ago

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

fcd2279 importing functions

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, 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/MONSTER_buildreport_20160926212651.html

bioc-issue-bot commented 8 years ago

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

bad6025 fixing methods import

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/MONSTER_buildreport_20160926215609.html

bioc-issue-bot commented 8 years ago

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

71a4d72 cleaned up igraph import 8cfc50f fixed argument mismatches, sped up examples 3f9765b sped up examples, version increment

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: "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/MONSTER_buildreport_20160926223451.html

bioc-issue-bot commented 8 years ago

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

fff0007 added V, E to igraph imports 62c36fa version increment

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: "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/MONSTER_buildreport_20160926224559.html

bioc-issue-bot commented 8 years ago

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

3f8c830 added V<-, E<- to igraph imports 140a1b1 version increment

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/MONSTER_buildreport_20160926225834.html

bioc-issue-bot commented 8 years ago

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

2355cc3 removed requires 3b32823 cleanup up bereFull 02b3394 version increment

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/MONSTER_buildreport_20160926231100.html

bioc-issue-bot commented 8 years ago

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

cdc0712 detect cores addition

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/MONSTER_buildreport_20160926231745.html

bioc-issue-bot commented 8 years ago

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

0a1058f importing parallel 63a98cb version increment

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/MONSTER_buildreport_20160926232126.html

bioc-issue-bot commented 8 years ago

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

9702047 importing doParallel 82d39ac version increment

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/MONSTER_buildreport_20160926232458.html

bioc-issue-bot commented 8 years ago

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

21cc9fc added foreach 5c4a945 version increment

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/MONSTER_buildreport_20160926234948.html

bioc-issue-bot commented 8 years ago

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

56f860c updated R dependency to 3.3 7526678 expanded monster-package fd5e2d6 version increment

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.

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/MONSTER_buildreport_20160927000737.html

bioc-issue-bot commented 8 years ago

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

a308f41 dropping empty ref section e5d3ae6 completified Description field

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.

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/MONSTER_buildreport_20160927001951.html

bioc-issue-bot commented 8 years ago

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

9ff52c1 globalVariables

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.

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/MONSTER_buildreport_20160927115712.html