ChIPexoQualExample - Githubissues

welch16 commented 8 years ago

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

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

Confirm the following by editing each check box to '[x]'

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bioc-issue-bot commented 8 years ago

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

d0c1cae Added the ExoDataSubsampling function that returns... 0a81dcb added test to check if there is an error when 'sam...

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_20161026162025.html

bioc-issue-bot commented 8 years ago

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

e8898f9 changed R version to adapt to bioconductor's relea...

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_20161026202132.html

welch16 commented 8 years ago

Hi @LiNk-NY and @lshep,

I pushed a build today and it raised a warning due to the release of the new bioconductor version. To fix it, I installed the future R 3.4, and increased the required version in the package's DESCRIPTION, it seems that this is raising an error. Could you point me toward to the right way to proceed ?

Thanks in advance,

LiNk-NY commented 8 years ago

Hi @lshep, Is the SPB running BioC 3.4 or 3.5?

Thanks.

lshep commented 8 years ago

3.4. We are still in the process of moving over the SPB to 3.5. We hope to have it resolved soon. For now please ignore the warning with the version numbering.

LiNk-NY commented 8 years ago

Thanks @lshep!

@welch16, please lower the R version (to >= 3.3.1) so that it works with BioC 3.4 on the SPB. Also, bump the version for a new build.

Regards, Marcel

bioc-issue-bot commented 8 years ago

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

23d1903 increased version

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_20161031142933.html

welch16 commented 8 years ago

Hi @LiNk-NY ,

Before this issue with the release of Bioconductor 3.4 and the subsequent warnings and errors, we were discussing about exporting or not the functions that generate DataFrames for plots and such. Should I export those functions or not ?

Thanks for your help, Rene

LiNk-NY commented 8 years ago

Hi Rene @welch16, If you think this process is valuable to the user (i.e., the user takes data from your object to the DataFrame class often), then you should export these functions. Otherwise, you can handle this intermediate step and have your function output a familiar DataFrame class. Could it be included in the function that creates the ExoData object and the resulting DataFrame be specified via the arguments?

Considerations for `ChIPexoQual`

Output from MangoTheCat/goodpractice::gp

Please use the assignment operator (<-) for all object assignments.
Remove the date field from the DESCRIPTION
Add a BugReports field in the DESCRIPTION (link to github repository)
Do not import entire packages, try to selectively import the functions that you need in the NAMESPACE. You have done some of that already.

Considerations for `ChIPexoQualExample`

Do you have to use exportPattern in the NAMESPACE?

bioc-issue-bot commented 8 years ago

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

ebd5171 Fixing devtools warning where library function was... 4f2e693 removed data from extenal_data_store.txt and cor...

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/ChIPexoQualExample_buildreport_20161114143748.html

bioc-issue-bot commented 8 years ago

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

18af7e0 Changed assignment operator '=' for '<-'. Also now... 627f993 Added BugReports and removed Date fields f7905b3 Converted the intermediate step functions that gen...

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/ChIPexoQual_buildreport_20161115140039.html

welch16 commented 8 years ago

Hi @LiNk-NY , @lshep

The label above is a new one. Are you updating your system by any chance ?

Thanks for the help, Best, Rene

LiNk-NY commented 8 years ago

Hi Rene, @welch16 @lshep Lori is working on the build system and your package will likely require a manual rebuild. More updates from Lori soon.

Thanks, Marcel

lshep commented 8 years ago

The "abnormal" is an error on our end from updating the single package builder. Once the update is complete I will manually kick off a build of your package I will do a manual rebuild of both your data package and main package to ensure both get on the new build nodes so you may get a few build notices.

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/ChIPexoQualExample_buildreport_20161116093344.html

LiNk-NY commented 8 years ago

Thanks Lori!

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_20161116094715.html

welch16 commented 8 years ago

Hi @lshep ,

I hope you had a great weekend. When I checked the build report of the package I noticed the following error on the windows build.

Warning in dir.create(exdir, showWarnings = TRUE, recursive = TRUE) :
  'C:\Windows\TEMP\RtmpmA4sF0' already exists
Error in untar(pkgname, exdir = t) : 
  failed to create directory 'C:\Windows\TEMP\RtmpmA4sF0'
Calls: <Anonymous> -> BiocCheck -> .get_package_dir -> untar
Execution halted

It seems that this error is due to permissions or something. Is there anything I could do to fix it ?

Thanks for the help

lshep commented 8 years ago

I'm going to try to rerun the build manually to see if it might have just been a problem when we were updating the system. If it persists I'll investigate further.

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_20161121123542.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:

182175b updated version 22f22fa 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.

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 commented 8 years ago

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 commented 8 years ago

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 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

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

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

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 commented 8 years ago

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 commented 8 years ago

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 commented 8 years ago

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 commented 7 years ago

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

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

bioc-issue-bot commented 7 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, 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 commented 7 years ago

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 commented 7 years ago

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 commented 7 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_20161220145748.html

bioc-issue-bot commented 7 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.

LiNk-NY commented 7 years ago

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

LiNk-NY commented 7 years ago

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.

Bioconductor / Contributions

ChIPexoQualExample #79

Considerations for `ChIPexoQual`

Considerations for `ChIPexoQualExample`

Bioconductor / Contributions

ChIPexoQualExample #79

Considerations for ChIPexoQual

Considerations for ChIPexoQualExample

Considerations for `ChIPexoQual`

Considerations for `ChIPexoQualExample`