ChIPexoQualExample #79

welch16 · 2016-08-08T19:10:24Z

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Repository: https://github.com/welch16/ChIPexoQualExample

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bioc-issue-bot · 2016-08-08T19:10:26Z

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 · 2016-08-08T19:22:40Z

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 · 2016-08-08T19:28:56Z

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 · 2016-08-08T20:21:24Z

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

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

bioc-issue-bot · 2016-08-08T20:26:23Z

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 · 2016-08-08T20:41:43Z

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

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

bioc-issue-bot · 2016-08-08T20:47:33Z

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 · 2016-08-09T17:38:52Z

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 · 2016-08-10T17:42:24Z

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

bioc-issue-bot · 2016-08-10T17:42:29Z

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 · 2016-08-10T17:58:13Z

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 · 2016-08-10T18:14:10Z

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

1786985 changed data.table version in DESCRIPTION

bioc-issue-bot · 2016-08-10T18:28:18Z

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 · 2016-08-18T16:45:08Z

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 · 2016-08-29T16:35:32Z

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 · 2016-08-29T16:40:22Z

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

bioc-issue-bot · 2016-08-29T16:42:56Z

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 · 2016-08-29T16:44:54Z

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 · 2016-08-29T16:49:32Z

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 · 2016-08-29T19:38:08Z

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 · 2016-08-30T15:20:35Z

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 · 2016-11-21T17:35:34Z

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_20161121123542.html

bioc-issue-bot · 2016-11-28T22:46:19Z

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 · 2016-11-28T22:49:44Z

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

182175b updated version
22f22fa Merge branch 'master' of github.com:Welch16/ChIPex...

bioc-issue-bot · 2016-11-28T23:02:26Z

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_20161128180247.html

LiNk-NY · 2016-11-29T18:14:41Z

Hi René, @welch16
Are you missing an import RSQLite directive in the DESCRIPTION?

Thanks,
Marcel

 Error in library.dynam(lib, package, package.lib) : 
    shared object 'RSQLite.so' not found

welch16 · 2016-11-29T18:22:22Z

Hi Marcel, @LiNk-NY

I am not sure about it, as BiocCheck is working correctly in the systems that I am using. Also, this commit was only to downgrade the versions of S4Vectors and BiovizBase in the DESCRIPTION file. Could it be an issue with BiocCheck ?

Thanks, Rene

bioc-issue-bot · 2016-11-30T20:59:49Z

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 · 2016-11-30T22:00:39Z

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 · 2016-12-01T03:42:53Z

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 · 2016-12-01T03:46:57Z

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.

LiNk-NY · 2016-12-06T20:40:48Z

Hi René, @welch16
I don't get an error when building locally or when checking using BiocCheck. Did you bump the version to trigger another build with your latest updates?
Thanks,
Marcel

welch16 · 2016-12-06T21:08:00Z

Hi Marcel, @LiNk-NY ,

I didn't got an error either, that is way I thought it has something to do with the building process. I haven't triggered another build, as I was just creating a static documentation for the package with pkgdown and I don't think that is supposed to raise any issues. Should I trigger a new build here ?

Best, Rene

LiNk-NY · 2016-12-06T22:25:04Z

Hi René, @welch16

Yes, you should trigger a new build. Any changes you make should warrant an update of the version number.

Regards,
Marcel

Also, it should be okay to use R-devel and include this in the DESCRIPTION file.

bioc-issue-bot · 2016-12-08T00:11:19Z

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

4b7954c added parameters to keep numeric order in paramDis...

bioc-issue-bot · 2016-12-08T00:31:22Z

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, 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_20161207193202.html

welch16 · 2016-12-09T18:29:30Z

Hi Marcel @LiNk-NY ,

I triggered a new build and it seems there is an error in the MAC build check, it seems pdflatex is not available in that machine, as the following message appears:

LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without hyperrefs or index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm ... looks like a package
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  pdflatex is not available
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  pdflatex is not available
Error in running tools::texi2pdf()

Thanks in advance, Rene

LiNk-NY · 2016-12-14T20:11:16Z

Hi René, @welch16
We are looking into this texi2dvi error.
Unfortunately, we need to have a clean build report for the software package to build.

I will look at it manually.

Regards,
Marcel

bioc-issue-bot · 2016-12-20T19:57:49Z

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_20161220145748.html

bioc-issue-bot · 2016-12-28T22:07:15Z

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.

LiNk-NY · 2016-12-30T18:26:57Z

Hi René @welch16,
Thanks for submitting to Bioconductor. Your packages have been approved.
Regards,
Marcel

LiNk-NY · 2016-12-30T18:31:03Z

Additional comments to keep in mind:

From goodpractice::gp("ChIPexoQual"):

use '<-' for assignment instead of '='. '<-' is the
    standard, and R users and developers are used it and it is easier
    to read your code for them if you use '<-'.

    R/base_summaryPlots.R:173:19
    R/base_summaryPlots.R:404:14
    R/base_summaryPlots.R:471:31

Also, please consider adding unit tests.

bioc-issue-bot added the 1. awaiting moderation label Aug 8, 2016

bioc-issue-bot added 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place and removed 1. awaiting moderation labels Aug 8, 2016

bioc-issue-bot assigned LiNk-NY Aug 8, 2016

bioc-issue-bot added the ERROR label Aug 8, 2016

bioc-issue-bot added OK and removed ERROR labels Aug 8, 2016

bioc-issue-bot added the ERROR label Aug 10, 2016

bioc-issue-bot removed the ERROR label Aug 29, 2016

bioc-issue-bot removed the ERROR label Nov 21, 2016

bioc-issue-bot added the ERROR label Nov 28, 2016

SiminaB mentioned this issue Dec 14, 2016

swfdr #213

Closed

bioc-issue-bot removed the ERROR label Dec 20, 2016

LiNk-NY added 3a. accepted will be ingested into Bioconductor daily builder for distribution and removed 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place labels Dec 30, 2016

mtmorgan closed this as completed Jan 5, 2017

bioc-issue-bot mentioned this issue Oct 22, 2017

esATAC #529

Closed

8 tasks

bioc-issue-bot mentioned this issue Mar 27, 2019

celda #1041

Closed

8 tasks

ChIPexoQualExample #79

ChIPexoQualExample #79

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