(inactive) Epicopy

[sean-cho]

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• Repository: https://github.com/sean-cho/Epicopy

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[bioc-issue-bot]

Hi @sean-cho

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: Epicopy
Type: Package
Title: Get CNV information from 450K array
Version: 0.99.0
Date: 2015-02-25
Authors@R: c(
    person('Sean, Soonweng', 'Cho', email = 'sean.cho@jhmi.edu', role = c('aut','cre')),
    person('Hyunseok', 'Kim', email = 'hkim190@jhmi.edu', role = c('aut')),
    person('Leslie', 'Cope', email = 'lcope1@jhmi.edu', role = c('aut')))
Description: Get CNV information from 450K array
License: Artistic License 2.0
Depends:
    Biobase,
    BiocGenerics
Imports:
    RColorBrewer,
    gplots,
    Hmisc,
    minfi,
    GenomicRanges,
    IRanges,
    DNAcopy,
    GenomeInfoDb,
    ParDNAcopy,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    modeest,
    org.Hs.eg.db
Suggests:
    Gviz,
    knitr,
    rmarkdown,
    EpicopyData
biocViews:
    DNAMethylation, CopyNumberVariation, MethylationArray
VignetteBuilder: knitr
RoxygenNote: 5.0.1

[sean-cho]

AdditionalPackage: https://github.com/sean-cho/EpicopyData

[bioc-issue-bot]

Can't build unless issue is open and '2. review in progress' label is present, or issue is closed and 'TESTING' label is present.

[bioc-issue-bot]

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]

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/Epicopy_buildreport_20160628185900.html

[mtmorgan]

Looks like you submitted the packages in reverse order -- should have started with the package that does not depend on the other. We'll sort this out manually, but probably not until tomorrow morning.

[mtmorgan]

Actually, can you be sure to add a web hoook to EpicopyData and then try to increment the version of EpicopyData to 0.99.1?

[sean-cho]

Hi Martin, I pushed 0.99.1 to test the webhook. How should I reverse the order on the two packages? Thanks!

[mtmorgan]

OK, can you try posting a comment like the one above,

AdditionalPackage: https://github.com/sean-cho/EpicopyData

[dtenenba]

Actually just post a comment like that in the current issue (#39)

[sean-cho]

AdditionalPackage: https://github.com/sean-cho/EpicopyData

[bioc-issue-bot]

Hi @sean-cho,

Starting build on additional package https://github.com/sean-cho/EpicopyData.

IMPORTANT: Please read the instructions for setting up a
push hook on your repository, or further changes to your
additional package repository will NOT trigger a new build.

The DESCRIPTION file of this additional package is:

Package: EpicopyData
Type: Package
Title: Epicopy datasets
Version: 0.99.1
Date: 2015-11-02
Authors@R: c(
person('Sean, Soonweng', 'Cho', email = 'sean.cho@jhmi.edu', role = c('aut','cre')),
person('Hyunseok', 'Kim', email = 'hkim190@jhmi.edu', role = c('aut')),
person('Leslie', 'Cope', email = 'lcope1@jhmi.edu', role = c('aut')))
Maintainer: Sean Cho <sean.cho@jhmi.edu>
Description: Package holding test data and normal data for Epicopy.
License: GPL3
Suggests: 
Epicopy
Imports: 
minfi
biocViews:
DNAMethylation, CopyNumberVariation, MethylationArray

[bioc-issue-bot]

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/EpicopyData_buildreport_20160629155134.html

[mtmorgan]

OK, next issue -- I see that you're using git lfs. The single package builder is not equipped to use lfs, but the right solution is to enable it. Again this will take some work on our end, please be patient.

[mtmorgan]

Can you try to version bump EpicopyData again? git lfs should be enabled across build systems.

[bioc-issue-bot]

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

4efc422 v 0.99.2 - LFS push.

[sean-cho]

Just bumped. Thanks for helping me figure this out.

[bioc-issue-bot]

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/EpicopyData_buildreport_20160705184933.html

[mtmorgan]

One last version bump on the data package, removing Epicopy from the Suggests: field

[bioc-issue-bot]

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

03b0ec4 V 0.99.3: Remove Epicopy from suggested packages.

[bioc-issue-bot]

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/EpicopyData_buildreport_20160708121616.html

[mtmorgan]

OK, the next steps are up to you -- address the issues in the build report, then bump & commit.

• The correct notation for the GPL version three is GPL-3. The LICENSE file claims Artistic-2, and this isn't appropriate -- choose one or the other (or some other license); neither GPL-3 nor Artistic-2 require a LICENSE file.
• Provide a man page for all.normals
• re-compress the allNormals.rda file -- the saving is substantial
• subscribe to the bioc-devel mailing list, or if already subscribed align your email address on the mailing list and in the DESCRIPTION file.
• ExperimentData packages do not require a vignette, but one can be helpful in describing the data presented in a more extended version than on the man page.

[mtmorgan]

If you need help, please let me know. Otherwise, I'll close the issue in a couple of days.

[sean-cho]

Hi Martin,

Thanks for the feedback and for offering to help. I've made most of the changes you suggested.

I'm trying to understand re-compressing the allNormals.rda. It was saved as a default .gz compressed file. I re-compressed as .bz, but I save a small amount (~17MB). Is this in line with your suggestion, or is there another specific re-compression process you were referring to?

Thanks,
Sean

[mtmorgan]

I followed the suggestion in the build report and did

R CMD build --resave-data EpicopyData

and then extracted the relevant file

tar zxvf EpicopyData_0.99.1.tar.gz EpicopyData/data/allNormals.rda

and then EpicopyData/data/allNormals.rda is 400Mb rather than the original.

[bioc-issue-bot]

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, 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/Epicopy_buildreport_20160802192656.html

[bioc-issue-bot]

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

c85590d 0.99.4: Fix getLRR example.

[bioc-issue-bot]

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, 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/Epicopy_buildreport_20160802224622.html

[bioc-issue-bot]

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

da7088e 0.99.5: Various fixes.

[bioc-issue-bot]

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/Epicopy_buildreport_20160803182733.html

[bioc-issue-bot]

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

9ac2dee 0.99.6: Dependencies.

[bioc-issue-bot]

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/Epicopy_buildreport_20160814111418.html

[sean-cho]

Hi Martin,

Epicopy is not building because it is looking for EpicopyData -- do you know if I have to bump EpicopyData again?

Thanks,
Sean

[bioc-issue-bot]

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/EpicopyData_buildreport_20160818163221.html

[bioc-issue-bot]

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, 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/Epicopy_buildreport_20160818175623.html

[mtmorgan]

Hi -- I triggered a manual build of the EpicopyData and then Epicopy packages. It looks like your package is still far from ready to review. I suggest that you remove the github webhook, close this issue, continue developing your package on your own system, and when it is ready for review create a new issue.

[bioc-issue-bot]

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, 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/Epicopy_buildreport_20160818184603.html

[mtmorgan]

OK I closed the issue; not a big deal, just start another when your package is building without warnings / errors under the 'devel' version of Bioconductor.

[sean-cho]

Thanks Martin.