cnAnalysis450k - Githubissues

mknoll commented 7 years ago

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

Repository: https://github.com/mknoll/cnAnalysis450k

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bioc-issue-bot commented 7 years ago

Hi @mknoll

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: cnAnalysis450k
Type: Package
Title: Copy Number Analysis for 450k Illumina Methylation Arrays
Version: 0.98.0
Date: 2016-12-03
Author: Maximilian Knoll
Maintainer: Maximilian Knoll <m.knoll@dkfz.de>
Description: Segmentation and aggregation of (normalized) 450k Illumina methylation copy number data.
License: GPL-3
RoxygenNote: 5.0.1
Imports:  AnnotationDbi,
    changepoint,
    conumee,
    CopyNumber450kData,
    fastmatch,
    foreach,
    doParallel,
    parallel,
    GenomicFeatures,
    GenomicRanges,
    graphics,
    Homo.sapiens,
    IRanges,
    minfi,
    org.Hs.eg.db,
    pheatmap,
    plyr,
    S4Vectors,
    stats,
    TxDb.Hsapiens.UCSC.hg19.knownGene
Suggests: knitr,
    rmarkdown,
    testthat
VignetteBuilder: knitr
biocViews: Software,
    AssayDomain,
    CopyNumberVariation

bioc-issue-bot commented 7 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 7 years ago

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bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 years ago

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

625cf44 Version increment

bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 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 7 years ago

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

3717ecb Version increment

bioc-issue-bot commented 7 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.

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bioc-issue-bot commented 7 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 7 years ago

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

6046756 colData problem

bioc-issue-bot commented 7 years ago

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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bioc-issue-bot commented 7 years ago

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

a36ec0a colData slot added

bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 years ago

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

00bfd3e missing Slot colData

bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 years ago

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

d3b6b50 colData adaption in Vignettes

bioc-issue-bot commented 7 years ago

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

fd03841 Included BiocGenerics in NAMESPACE and DESCRIPTION

bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 years ago

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

582a3ca minor fixes for BiocCheck

bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 years ago

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

cfa6bec Removed check warnings

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bioc-issue-bot commented 7 years ago

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

c88fa78 Trying to fix to pdflatex not found error on MacOS...

bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 years ago

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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.

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lshep commented 7 years ago

Hi. Please ignore the pdflatex ERROR I believe this is an ERROR on our system.

hpages commented 7 years ago

Hi Max,

Thanks for submitting the cnAnalysis450k package. I see 2 important issues at the moment:

1) All the man pages need to have examples illustrating the use of the functions. Right now, the examples contain this single line:

print("Please refer to the 'completeWorkflow' vignette!")

2) Also please don't use the RGcontrolSetEx data set from the CopyNumber450kData package in your vignette. This data set is currently broken in devel:

library(CopyNumber450kData)
RGcontrolSetEx
# class: RGChannelSet 
# Error in nrow(x@elementMetadata) : 
#   no slot of name "elementMetadata" for this object of class "RGChannelSet"
validObject(RGcontrolSetEx)
# Error in slot(from, what) : 
#   no slot of name "colData" for this object of class "RGChannelSet"

This issue actually shows up on the daily build report for CopyNumber450kData

But most importantly the package seems abandoned (we've been trying to contact its maintainers for months without success) so we will likely deprecate it soon. If you really want to use that data set in your vignette, you might want to try to contact the maintainers yourself, maybe you'll have more luck. If they're not interested in continuing the maintenance of CopyNumber450kData maybe you can discuss the possibility that they transfer ownership to you.

I'll have more feedback for you but these 2 important issues would need to be addressed first.

Thanks, H.

bioc-issue-bot commented 7 years ago

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Your package has been built on Linux, Mac, and Windows.

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bioc-issue-bot commented 7 years ago

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

c0e51ab Add EPIC support / parallelization

bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 years ago

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

509dee4 Fixed diverse bugs

bioc-issue-bot commented 7 years ago

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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

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mknoll commented 7 years ago

Thanks for the feedback.

1) The CopyNumber450kData package is now removed; datasets for illustions now come from the minfiData and minfiDataEPIC packages.

2) Runnable examples are added for each function.

Best Max

bioc-issue-bot commented 7 years ago

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

863b180 conumee CNV.load somehow broken - workaround added... 89915de conumee CNV.load somehow broken - workaround added... f1842bf Had to adapte the CNV.fit function from the conume... d2e7fa4 Had to adapte the CNV.fit function from the conume... 8db239d runConumee adapted to changed conumee functions

bioc-issue-bot commented 7 years ago

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

b4e5e67 Adapted vignettes

bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 years ago

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

eb58000 fixed methylset / df error in runConumee c628612 runConumme id bug fixed

bioc-issue-bot commented 7 years ago

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

cd9df14 Timout error for conumee examples - smaller exampl...

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

efa7919 createConumeeMatrix.segment bug fixed

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

fc75b68 WARNING

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bioc-issue-bot commented 7 years ago

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

93b2f97 identifyCutoffs: assure, that changepoint determin...

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bioc-issue-bot commented 7 years ago

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

cd67598 typo

Bioconductor / Contributions

cnAnalysis450k #208