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ChIPexoQualExample #79

Closed welch16 closed 7 years ago

welch16 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 @welch16

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: ChIPexoQualExample
Type: Package
Title: Example data for the ChIPexoQual package, which implements a quality
    control pipeline for ChIP-exo data
Version: 0.99.0
Depends:
    R (>= 3.3)
Date: 2016-07-18
Author: Rene Welch, Dongjun Chung, Sunduz Keles
Maintainer: Rene Welch <welch@stat.wisc.edu>
Description: Data for the ChIPexoQual package, consisting of (3) chromosome 1
    aligned reads from a ChIP-exo experiment for FoxA1 in mouse liver cell lines
    aligned to the mm9 genome.
License: GPL (>= 2)
URL: http://www.github.com/keleslab/ChIPexoQual
LazyLoad: yes
biocViews: ExperimentData, ChIPexo, Genome
NeedsCompilation: no
RoxygenNote: 5.0.1
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/ChIPexoQualExample_buildreport_20160808153015.html

bioc-issue-bot commented 8 years ago

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

35efb01 removed data file exampleExoData to avoid circular...

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/ChIPexoQualExample_buildreport_20160808162745.html

bioc-issue-bot commented 8 years ago

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

4f47a25 changed version and added knitr build 5dd9ecb changed versions in vignettes

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/ChIPexoQualExample_buildreport_20160808164852.html

welch16 commented 8 years ago

Hi @LiNk-NY , I hope everything is going great. I only submitted an Experiment package. In the submission guidelines it said that I need to pass the 'moderator' step, is the moderator step you being assigned to review the package or should I need to wait for and fixed your comments to submit the actual package ? Thanks in advance, Rene

welch16 commented 8 years ago

AdditionalPackage: https://github.com/welch16/ChIPexoQual

bioc-issue-bot commented 8 years ago

Hi @welch16,

Starting build on additional package https://github.com/welch16/ChIPexoQual.

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: ChIPexoQual
Type: Package
Title: ChIPexoQual
Version: 0.99.0
Date: 2016-07-18
Author: Rene Welch, Dongjun Chung, Sunduz Keles
Maintainer: Rene Welch <welch@stat.wisc.edu>
Description: Package with a quality control pipeline for ChIP-exo/nexus data.
URL: https:github.com/keleslab/ChIPexoQual
License: GPL (>=2)
Depends:
R (>= 3.3.0),
GenomicAlignments (>= 1.0.1)
Imports: 
methods,
GenomeInfoDb,
stats,
parallel,
GenomicRanges (>= 1.14.4),
ggplot2 (>= 1.0),
data.table (>= 1.9.7),
Rsamtools (>= 1.16.1),
IRanges (>= 1.6),
S4Vectors (>= 0.10),
biovizBase (>= 1.20),
broom (>= 0.4),
RColorBrewer (>= 1.1),
dplyr (>= 0.5),
scales (>= 0.4.0),
viridis (>= 0.3),
hexbin (>= 1.27),
Suggests:
ChIPexoQualExample (>= 1.00),
knitr (>= 1.10),
BiocStyle,
rmarkdown,
gridExtra (>= 2.2),
testthat
VignetteBuilder: knitr
biocViews: 
ChIPexo,
Sequencing,
Transcription,
Visualization,
QualityControl
RoxygenNote: 5.0.1
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/ChIPexoQual_buildreport_20160810135936.html

bioc-issue-bot commented 8 years ago

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

1786985 changed data.table version in DESCRIPTION

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/ChIPexoQual_buildreport_20160810142941.html

LiNk-NY commented 8 years ago

Hi @welch16, The moderator step includes verifying package submission and appropriately labeling the issue. You should also submit the software package along with the data package so that they are both reviewed. update: Seems like you already have submitted the software package via the AdditionalPackage tag.

welch16 commented 8 years ago

Hi @LiNk-NY ,

Thanks for the explanation and the review. Then, should I trigger another build on ChIPexoQual, since the report showed an error since ChIPexoQualExample wasn't available?

LiNk-NY commented 8 years ago

Hi @welch16, Sorry, I just saw that you added the additional package.

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:

881a8e8 triggering another build 4d1d9f7 Merge branch 'master' of github.com:welch16/ChIPex...

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/ChIPexoQual_buildreport_20160829125109.html

LiNk-NY commented 8 years ago

Once the first package builds and passes the build process it should become available for your software package ChIPexoQual. I'm not sure why you're getting this error. I will check.

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/ChIPexoQualExample_buildreport_20160830112212.html

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/ChIPexoQual_buildreport_20160831094956.html

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/ChIPexoQual_buildreport_20160831144434.html

lshep commented 8 years ago

Please note there will be an ERROR concerning package dependencies.

In ChIPexoQual you have specified ChIPexoQualExample (>= 1.00) in Suggests of the DESCRIPTION file.

ChIPexoQualExample the current version is Version: 0.99.2

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/ChIPexoQual_buildreport_20160831151915.html

bioc-issue-bot commented 8 years ago

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

c7fac6a corrected ChIPexoQualExample version to agree with...

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, 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/ChIPexoQual_buildreport_20160831154221.html

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, 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/ChIPexoQual_buildreport_20160902075758.html

welch16 commented 8 years ago

Hi @LiNk-NY ,

I saw the review, how can I see the report of the MAC build ? Also, the warning in the linux build occurs due to the size of an example run that I used in the vignette. Should I I generate that run in the vignette?

LiNk-NY commented 8 years ago

Hi @welch16, It seems like the package is failing on Windows and Mac OS X. Were you able to see the report for the Mac build?

If you're going to include data in ChIPexoQual, please be aware that your package cannot be greater than 4 Mb in size after R CMD build. You would have to reduce the size of the example data in ChIPexoQual.

welch16 commented 8 years ago

Hi @LiNk-NY ,

Thanks for all your help. I saw that there was an error and it must be related to a test, but wasn't able to see the specific report in the file : /Users/pkgbuild/packagebuilder/workers/jobs/ChIPexoQual/c7fac6a/ChIPexoQual.Rcheck/00check.log

How can I see that file ?

LiNk-NY commented 8 years ago

Hi @welch16, The 00check.log contains largely the same information posted in the check output. I will see if this is easily accessible. By the way, you can see the line numbers in the files for the tests that are failing.

Update: I have looked at the log and it contains the same information as printed in the check results.

bioc-issue-bot commented 8 years ago

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

0a9f827 added an example, with dontrun instead of fake one 981e95f Changed exampleExoData with the 3 replicates for e...

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, 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/ChIPexoQual_buildreport_20160921222917.html

welch16 commented 8 years ago

Hi @LiNk-NY ,

I reviewed the report above for version 0.99.4 , and it seems I don't have any warnings or notes from running R CMD check. However, in the summary table at the top I still have a warning label. Is that alright?

Also, I reviewed the test in MAC build and find very weird that I have an error in that test but not in others that are similar. Is there a way to have more details in that run ?

Thanks for the patience

LiNk-NY commented 8 years ago

Hi @welch16, You have a couple of errors with your build. First, you're not using appropriate biocViews for the package. See: https://www.bioconductor.org/developers/how-to/biocViews/

Second, there is an error in the vignette. 

 ERROR
Quitting from lines 77-88 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
'mc.cores' > 1 is not supported on Windows
Execution halted

Third, you are getting an error from the unit tests for morelia.

Regards, Marcel

bioc-issue-bot commented 8 years ago

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

5386d09 Changed uses of mcmapply and mclapply for their co... b01572c changed expect_identical to expect_equal to correc...

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/ChIPexoQual_buildreport_20161007200433.html

bioc-issue-bot commented 8 years ago

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

41352f5 Added @return field to the exoExample documentatio...

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/ChIPexoQual_buildreport_20161007212432.html

LiNk-NY commented 8 years ago

Hi @welch16, Thank you for submitting to Bioconductor! I took a quick look at your data package.

ChIPexoQual

Grammar

welch16 commented 8 years ago

Hi @LiNk-NY ,

Thanks for your response,

I don't follow the first point completely. For example, I have this function named .MA_DF, I started with a period as this function is internal and that way roxygen2 will ignore the documentation comments that I added. Should I have added another name as .MADF or .MA_DataFrame ?

LiNk-NY commented 8 years ago

Hi @welch16,

Our convention is to use camelCase on exported functions.

But why do these functions need to be internal methods or generics in the first place?

Aren't they just helper functions? You should be able to apply them in the appropriate context within a function. It doesn't seem like the way to go to me.. Regards, Marcel

LiNk-NY commented 8 years ago

Hi @welch16, It doesn't seem to me like there are many classes that you're dispatching these internal methods on. There would be some value if you had a specific method per signature but it doesn't seem the case.

bioc-issue-bot commented 8 years ago

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

805cb92 - Changed name of functions to camelCase. - The g...

welch16 commented 8 years ago

Hi @LiNk-NY ,

I am really sorry if I made your work harder, I updated the package with the fixes you mentioned above. I am not sure why the build hasn't proceed into the bioc system. For the next time, should I wait a bit before making a new build or should I work this changes as you mention them ?

Thanks for your patience

lshep commented 8 years ago

Sorry. We were making updates to the builder around the same time as your commit. I will get a new build on for you.

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/ChIPexoQual_buildreport_20161018123304.html

LiNk-NY commented 8 years ago

Thanks @lshep!

@welch16, thank you for making the changes. For the functions such as MADataFrame, do they need to be exported? Do you think an end-user of your package would need it? Perhaps, this is an intermediate step and could be best written if you use a naming convention such as .MADataFrame to avoid exporting the function and to use it as a helper.

Thank you for your attention.

Regards, Marcel

welch16 commented 8 years ago

@LiNk-NY, Originally I thought they wont be necessary. But as these function generate the data used for the qc plots that the package generates, I thought they may be used to perform more complex analysis.

Please let me know your thoughts,