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crisprseekplus #107

Closed nephantes closed 8 years ago

nephantes commented 8 years ago

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

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bioc-issue-bot commented 8 years ago

Hi @nephantes

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: crisprseekplus
Type: Package
Title: crisprseekplus
Version: 0.99.0
Date: 2016-07-25
Author: Sophie Wigmore <Sophie.Wigmore@umassmed.edu>,
    Alper Kucukural <alper.kucukural@umassmed.edu>,
    Lihua Julie Zhu <julie.zhu@umassmed.edu>,
    Michael Brodsky <Michael.Brodsky@umassmed.edu>,
    Manuel Garber <Manuel.Garber@umassmed.edu>
Maintainer: Alper Kucukural <alper.kucukural@umassmed.edu>
Description: Bioinformatics platform containing interface 
    to work with offTargetAnalysis and compare2Sequences in 
    the CRISPRseek package, and GUIDEseqAnalysis.
Depends:
    R (>= 3.3.0),
    shiny,
    shinyjs,
    CRISPRseek
License: GPL-3 + file LICENSE
LazyData: true
Imports:BSgenome.Hsapiens.UCSC.hg19,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    org.Hs.eg.db,
    DT,
    utils,
    GUIDEseq,
    GenomicRanges,
    GenomicFeatures,
    hash
RoxygenNote: 5.0.1
Suggests: testthat,
    rmarkdown,
    knitr,
    R.rsp
VignetteBuilder: knitr,  R.rsp
URL: https://github.com/UMMS-Biocore/crisprseekplus
BugReports: https://github.com/UMMS-Biocore/crisprseekplus/issues/new
biocViews:
    GeneRegulation,
    SequenceMatching,
    Software
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: "abnormal". 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/crisprseekplus_buildreport_20160908111344.html

nephantes commented 8 years ago

What is wrong I couldn't find out? Since, bioc-issue-bot could read Description file without any problem. However, in the report, it couldn't see anything in the repository. Could you please help to fix the problem?

vobencha commented 8 years ago

Lori investigated and found that you only have a devel branch in your git repo. The single package builder (SPB) is looking for a master branch. The specific url that is causing the SPB to fail is 'https://raw.githubusercontent.com/UMMS-Biocore/crisprseekplus/master/DESCRIPTION'

Please change this to a master branch and all should be ok.

nephantes commented 8 years ago

Changed it master. How can I trigger the builder? I added a web hook but not sure if that’s working or not. Thanks,

Alper Kucukural, PhD Assistant Professor, Program in Molecular Medicine Bioinformatics Core University of Massachusetts Medical School 368 Plantation St.Room AS4.2067 Worcester, MA 01605-2324 Phone: 774-312-4493tel:774-312-4493 E-mail: Alper.Kucukural@umassmed.edumailto:Alper.Kucukural@umassmed.edu

On Sep 12, 2016, at 12:17 PM, vobencha notifications@github.com<mailto:notifications@github.com> wrote:

Lori investigated and found that you only have a devel branch in your git repo. The single package builder (SPB) is looking for a master branch. The specific url that is causing the SPB to fail is 'https://raw.githubusercontent.com/UMMS-Biocore/crisprseekplus/master/DESCRIPTION'

Please change this to a master branch and all should be ok.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/Contributions/issues/107#issuecomment-246401609, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AEpOPBhGBM8LUg9sKnpcdBGHpUZiX5HKks5qpXsqgaJpZM4J4FXP.

vobencha commented 8 years ago

A new build is triggered each time you bump the version in DESCRIPTION. Change the version to 0.99.1 and it should rebuild.

bioc-issue-bot commented 8 years ago

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

12dcd4d version updated

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/crisprseekplus_buildreport_20160912200027.html

bioc-issue-bot commented 8 years ago

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

61cd762 trueFalse function fixed c18eff4 Merge pull request #27 from nephantes/master true...

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/crisprseekplus_buildreport_20160912203739.html

bioc-issue-bot commented 8 years ago

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

7ce731b remove test 09043fb Merge pull request #28 from nephantes/master true... 3be375c Merge pull request #29 from nephantes/master remo... 2a3e779 Merge pull request #30 from UMMS-Biocore/master M...

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/crisprseekplus_buildreport_20160912211121.html

bioc-issue-bot commented 8 years ago

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

67a1406 vignette fix 47ec857 Merge pull request #31 from nephantes/master vign...

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/crisprseekplus_buildreport_20160912215319.html

vobencha commented 8 years ago

Please fix these issues flagged in the single package builder output. Once they are addressed I'll do a full review.

Undefined global functions or variables: Celegans Dmelanogaster Hsapiens Mmusculus Rnorvegicus TxDb.Celegans.UCSC.ce6.ensGene TxDb.Dmelanogaster.UCSC.dm3.ensGene TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene TxDb.Rnorvegicus.UCSC.rn5.refGene a biocLite fluidRow org.Ce.egSYMBOL org.Dm.egSYMBOL org.Mm.egSYMBOL org.Rn.egSYMBOL renderPrint strong

Valerie

vobencha commented 8 years ago

Are you planning to submit a new version?

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:

c167342 Update DESCRIPTION

nephantes commented 8 years ago

Here we are installing BSgenome.Hsapiens.UCSC.hg19 or TxDb.Mmusculus.UCSC.mm10.knownGene or others, when they are needed. So, we don't want to install those at the beginning since there are many. The REQUIRED counts are 0 in my case.

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/crisprseekplus_buildreport_20160927135828.html

bioc-issue-bot commented 8 years ago

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

13557a1 Merge branch 'master' of https://github.com/UMMS-B... 3f5f4f4 Merge branch 'develop' of https://github.com/UMMS-... 7fee71b Deposition error fix a92d0ff Merge pull request #33 from nephantes/master Mast...

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/crisprseekplus_buildreport_20160927160819.html

vobencha commented 8 years ago

1) Fix this:

2) Move these to 'depends': Imports:BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db,

3) Add the org.*, BSgenome and TxDb for fly, rat, mouse and worm to 'depends'.

Bump the version and we'll see where we're at with the warnings. Valerie

vobencha commented 8 years ago

Alternatively you could put the org.*, TxDb and BSgenome packages in imports. In the code, assign them to a variable to avoid the 'no visible binding for global variable' warning:

txdb <- "TxDb.Hsapiens.UCSC.hg19.knownGene"
orgdb <- "org.Hs.eg.db"

etc. Valerie

bioc-issue-bot commented 8 years ago

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

4d00d07 warnings removed ed1d86a Merge pull request #34 from nephantes/master warn...

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/crisprseekplus_buildreport_20161007140710.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:

aa73444 version increased 101c271 Merge pull request #36 from nephantes/master vers...

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/crisprseekplus_buildreport_20161007144349.html

vobencha commented 8 years ago

Thanks for making the changes. I'm marking as accepted and you should get an email in the next week with svn credentials and next steps. Valerie