samexplorer RNA-seq depth analysis

shaileshtripathi commented 7 years ago

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bioc-issue-bot commented 7 years ago

Hi @shaileshtripathi

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: samExploreR
Type: Package
Title: samExploreR package: high-performance read summarisation to
        count vectors with avaliability of sequencing depth reduction
        simulation
Version: 1.0.0
Depends: ggplot2,pBrackets,colorspace
Author: Alexey Stupnikov, Shailesh Tripathi and Frank Emmert-Streib with contributions from Wei Shi and Yang Liao
Maintainer: Alexey Stupnikov,Shailesh Tripathi <email@mail>
Description: This R package is designed for subsampling procedure to
        simulate sequencing experiments with reduced sequencing depth.
        This package can be used to anlayze data generated from all
        major sequencing platforms such
        as Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and
        LifeTech Ion PGM/Proton sequencers. It supports multiple
        operating systems incluidng Linux, Mac OS X, FreeBSD and
        Solaris.
        Was developed with usage of Rsubread 1.16.1
URL:
License: GPL-3
LazyLoad: yes
Suggests: BiocStyle,RUnit,BiocGenerics,Matrix
biocViews: Sequencing, SequenceMatching, RNASeq, ChIPSeq, DNASeq,
        WholeGenome, GeneTarget, Alignment, GeneExpression,
        GeneticVariability, GeneRegulation, Preprocessing,
        GenomeAnnotation, Software
Packaged: 2015-07-28 13:59:18 UTC; stripathi
NeedsCompilation: yes

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.

mtmorgan commented 7 years ago

Hi -- It looks like this package contains extensive code from (R)subread. Instead of including this code, please re-factor your package so that it Imports: Rsubread and uses functionality available through Rsubread's public API. Please also take some time to format your code, e.g., using the prettyR package, so that it is more readable.

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:

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bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 years ago

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shaileshtripathi commented 7 years ago

My package is building fine on Mac and Linux servers. I found one problem on windows server that it is not able to find "Rnterface.h" header file, it is giving following error, Rinterface.h: No such file or directory. How can I solve this problem.

Also one more check error which is "REQUIRED: Maintainer should subscribe to the bioc-devel mailing" I have already subscribed to the mailing list but not approved yet.

shaileshtripathi commented 7 years ago

Hi @mtmorgan My package is building fine on Mac and Linux servers. I found one problem on windows server that it is not able to find "Rnterface.h" header file, it is giving following error, Rinterface.h: No such file or directory. How can I solve this problem.

Also one more check error which is "REQUIRED: Maintainer should subscribe to the bioc-devel mailing" I have already subscribed to the mailing list but not approved yet.

bioc-issue-bot commented 7 years ago

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mtmorgan commented 7 years ago

@shaileshtripathi from Rinterfaces.h

/* This header file is to provide hooks for alternative front-ends,
   e.g. GUIs such as GNOME and Cocoa.  It is only used on Unix-alikes.

so the header is not present on Windows. Also, please note my comment from 15 days ago about the appropriate way to use Rsubread -- via the existing package R API, rather than by including its source code again.

shaileshtripathi commented 7 years ago

@mtmorgan Hi Martin

I am aware that I should have imported the Rsubread API, but when I want to use that API I realized that they don't provide enough flexibility so that we could import functions and to analyze RNA-seq data, so we made necessary modifications inside existing functions in Rsubread and keep them for the package. We would develop our own set of API for this analysis and update that in couple of months. But for a while we want to keep the current code in the package.

Bioconductor / Contributions

samexplorer RNA-seq depth analysis #62