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SBGNview #1085

Closed chemokine closed 5 years ago

chemokine commented 5 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]'

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For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 years ago

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

6343215 Added Readme. Shorter functions

bioc-issue-bot commented 5 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.

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bioc-issue-bot commented 5 years ago

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

cd2257c Removed function: sbgn.interactions

bioc-issue-bot commented 5 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 build report for more details.

chemokine commented 5 years ago

Dear Dr. Morgan @mtmorgan, Thank you for the suggestions. We have updated the package:

  1. Removed unnecessary files : DESCRIPTION~ and vignettes/*html
  2. SBGNview now supports SummarizedExperiment objects. We also constructed SummarizedExperiment objects for test datasets.
  3. Removed the "source()" codes. They were used for quick test. The package can be installed and used.

We are planning to use AGPLv3 licence, but it introduced a WARNING. Can we proceed with this licence? Please give us suggestions if you have time to review the package. Thank you!

Xiaoxi

Kayla-Morrell commented 5 years ago

Hello @chemokine,

In order to use a non-standard license, you need to include a file named LICENSE in your package which contains the full terms of the license. Then you need to use "file LICENSE" (without the double quotes) in the "License:" field of the DESCRIPTION file.

Best, Kayla

chemokine commented 5 years ago

Thank you very much Kayla, I’ll include the file.

Xiaoxi

On Wed, May 1, 2019 at 12:54 PM Kayla-Morrell notifications@github.com wrote:

Hello @chemokine https://github.com/chemokine,

In order to use a non-standard license, you need to include a file named LICENSE in your package which contains the full terms of the license. Then you need to use "file LICENSE" (without the double quotes) in the "License:" field of the DESCRIPTION file.

Best, Kayla

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1085#issuecomment-488340586, or mute the thread https://github.com/notifications/unsubscribe-auth/AA5ZCUNZD2AQSYAKKBNP7A3PTHDLJANCNFSM4HEWX4LQ .

bioc-issue-bot commented 5 years ago

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

c50d1b0 Added licence

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

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chemokine commented 5 years ago

Dear Kayla @Kayla-Morrell @mtmorgan , I have updated the licence and included a LICENCE file. Please let us know of any suggestions how to improve the package. Thank you!

Xiaoxi

chemokine commented 5 years ago

Dear Kayla @Kayla-Morrell, I am browsing the reviews of other packages and found that it might be better if I submit a data package for SBGNview (Currently SBGNview downloads data from another GitHub repository). Should I open a new issue with the data package and then submit SBGNview there as "additional package?". Or can I submit the data package here as "additional package"? I feel that the first approach is better since SBGNview will depend on the data package. Please let me know. Thank you!

Best, Xiaoxi

Kayla-Morrell commented 5 years ago

@chemokine - Feel free to just submit the data package on this issue with "additional package". This way should work out just fine.

Thanks, Kayla

chemokine commented 5 years ago

Thank you @Kayla-Morrell, Here is the data package I would like to submit: Should I change the code (of how SBGNview loads data) after this data package is accepted? Currently SBGNview downloads data from Github http links. As I understand, SBGNview won't build if its code try to use the data package before the data package is accepted. Thank you!

Best, Xiaoxi

bioc-issue-bot commented 5 years ago

Dear @chemokine ,

I could not find a DESCRIPTION file in the default branch of the GitHub repository at https://github.com/datapplab/SBGNview.data . This repository should contain an R package.

Kayla-Morrell commented 5 years ago

Hello @chemokine,

You can change the code now if you'd like. With the use of the 'Additional Package:' tag the builder will look for the current state of the data package when building. This means it doesn't have to be accepted before being used.

My advice is to work on cleaning up the data package (for example the latest comment is that there is no DESCRIPTION file in the data package) so a build report can be produced. Continue to make changes to the software package until there is a relative clean build of the data package. Then make the necessary changes to the software package. Once both packages are relatively clean then I will do the formal review of both packages. If you need help during the process feel free to comment here and I'll help the best I can.

Best, Kayla

chemokine commented 5 years ago

Thank you @Kayla-Morrell, I'm working on the data package. AdditionalPackage: https://github.com/datapplab/SBGNview.data

bioc-issue-bot commented 5 years ago

Hi @chemokine,

Starting build on additional package https://github.com/datapplab/SBGNview.data.

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: SBGNview.data
Title: Pathway information and ID mapping data for SBGNview package
Description: 
This package contains data needed to run SBGNview on pre-collected SBGN-ML files and example gene expression datasets. 
It contains 1. information of pathways collected: pathway IDs, names etc. and 
2. ID mapping from common gene, protein and compound ID types to pathway glyph IDs.
3. Two gene expression datasets
Version: 0.99.1
Authors: 
Xiaoxi Dong, Weijun Luo
Author:
Xiaoxi Dong, Weijun Luo
Maintainer: Xiaoxi Dong <dfdongxiaoxi@gmail.com>
Depends: R (>= 2.10)
Imports: 
RdMacros: 
License: EPL
Collate: data.R
Suggests:
VignetteBuilder: knitr
RoxygenNote: 6.1.1
bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 years ago

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

f3a9167 0.99.2

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 years ago

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

a177ccb Untrack .Rproj file

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 years ago

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

28daace Readme file with demo example; Added more examples... d0408a9 Added example to vignette: download and use ID map...

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

chemokine commented 5 years ago

Hi @Kayla-Morrell, I ran BiocCheck on the data package but received WARNING, because several files are larger than 5Mb (~40Mb for the largest one). These data are not mandatory for running SBGNview (they are helpful for some specific input pathway files). Can I still use the http download without a data package? I included an example in vignette about how to download and use these data. Thank you. I have cleaned the main package SBGNview. Can you do a formal review when you have time? Thanks!

Regards, Xiaoxi

Kayla-Morrell commented 5 years ago

Hello @chemokine - Having a data package this large is not ideal and we prefer not to have users download the data from http (incase there are connectivity issues or the data gets moved). There are a few suggestions I can make to help with this.

First thing is to be sure you are only including data specific to a particular analysis or experiment. If you don't use it in the vignette or examples than it shouldn't be included. Second suggestion would be to see if there is data already available in Bioconductor (whether in AnnotationHub or ExperimentHub) so you wouldn't have to include the data in your package. Please see the vignette about accessing data from ExperimentHub. The final suggestion would be to submit the data as an ExperimentHub package instead. This will create a web resource for your data. Please see the vignette about creating an ExperimentHub package.

Let me know what your thoughts are, I'd be happy to help.

Best, Kayla

bioc-issue-bot commented 5 years ago

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

f2ed965 Removed data >5Mb

chemokine commented 5 years ago

Thanks Kayla @Kayla-Morrell The data larger than 5Mb are not used in vignette or examples. I'll remove them and continue working on the data package AdditionalPackage: https://github.com/datapplab/SBGNview.data

bioc-issue-bot commented 5 years ago

Dear @chemokine ,

You (or someone) has already posted that repository to our tracker.

See https://github.com/Bioconductor/Contributions/issues/1085

You cannot post the same repository more than once.

If you would like this repository to be linked to issue number: 1085, Please contact a Bioconductor Core Member.

bioc-issue-bot commented 5 years ago

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

d1a82e8 0.99.5 test if SBGNview.data is relinked as additi...

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 years ago

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

e2596ce Keeping only the data used in examples/vignettes

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 years ago

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

163d48a User samller SBGNview.data package

bioc-issue-bot commented 5 years ago

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

e4082ee Added vignette

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 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.

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bioc-issue-bot commented 5 years ago

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

5c4ff41 Added knitr; correct RNASeqData

bioc-issue-bot commented 5 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 build report for more details.

bioc-issue-bot commented 5 years ago

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

d5c2a31 Depend on R 3.6

bioc-issue-bot commented 5 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.

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bioc-issue-bot commented 5 years ago

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

2fc58d0 test SBGNview.data

bioc-issue-bot commented 5 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.

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chemokine commented 5 years ago

Hi Kayla @Kayla-Morrell, I have cleaned the data package: SBGNview.data to include the data used in vignette and examples and removed the large files not used. The remaining data files are small enough to make the package pass all checks. Also, I have updated the code in SBGNview package to use that data package. Please let me know any suggestions. Thanks.

Best regards, Xiaoxi

Kayla-Morrell commented 5 years ago

Hello @chemokine,

Thank you for making the necessary changes. Below is my initial review of 'SBGNview.data'. Please comment back here with updates that have been made and when the package is ready for a re-review.

DESCRIPTION

R

data

vignette

Best, Kayla

bioc-issue-bot commented 5 years ago

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

6174e7f Removed id.mapping files. Improved DESCRIPTION fil...

bioc-issue-bot commented 5 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 build report for more details.

chemokine commented 5 years ago

Hi Kayla @Kayla-Morrell, Thank you for the comments. I made the required changes. Please see the responses below for details. The only issue is: when I removed SummarizedExperiment from 'Depends', the R CMD check reported WARNING saying: "Failed with error: 'package 'DelayedArray' could not be loaded' Error loading dataset 'IFNg': Error in .requirePackage(package) : unable to find required package 'SummarizedExperiment'". Can I avoid this WARNING while excluding SummarizedExperiment from 'Depends'? The datasets are SummarizedExperiment objects. Thanks!

Regards, Xiaoxi

Hello @chemokine,

Thank you for making the necessary changes. Below is my initial review of 'SBGNview.data'. Please comment back here with updates that have been made and when the package is ready for a re-review.

DESCRIPTION

  • [ ] SUGGESTION: Improve the 'Description' of the package. The listing of what the package contains should be clearer and a complete sentence. Right now there is a period after the second item and no period after the third. I would remove the 'and' after the first point and replace it with a ',' then replace the '.' after the second point with a ','. That way you can end the sentence with '.' after the third point. This part is changed to the following: _This package contains:
    1. A microarray gene expression dataset from a human breast cancer study.
    2. A RNA-Seq gene expression dataset from a mouse study on IFNG knockout._
  • [ ] REQUIRED: Remove the 'Authors' tag. There should only be 'Author' and 'Maintainer' tags. Removed 'Authors' tag.
  • [ ] REQUIRED: If 'Imports:' is empty it should be removed. Removed 'Imports' tag.
  • [ ] REQUIRED: SummarizedExperiment does not need to be in the 'Depends', just the R version. Removed SummarizedExperiment from 'Depends'. But this introduced a WARNING message saying the data can't be loaded because "package SummarizedExperiment is not available" (the datasets "IFNg" and "cancer.ds" are SummarizedExperiment objects)
  • [ ] REQUIRED: 'RdMacros' should be removed. Removed 'RdMacros'.

R

  • [ ] REQUIRED: For 'mapping.table' where does this come from, this needs to be documented. 'mapping.table' is the variable name contained in data 'hsa_ENTREZID_pathwayCommons' etc. They are not strictly needed in the data package. So I removed them and only keeping two datasets: "IFNg" and "cancer.ds".

data

  • [ ] REQUIRED: The only two files that are documented in 'data.R' are 'IFNg.RData' and 'cancer.ds.RData'. There needs to be 'mapping.table' included in here because right now it's not available to the user. The other files should not be included unless they are used in the vignette or in examples. If they are used they need to be documented. not strictly needed in the data package. So I removed them and only keeping two datasets: "IFNg" and "cancer.ds". The un-documented data files are not strictly needed in this data package. I removed them. 'mapping.table' was the variable name of the un-documented data. Since the files are removed, I also removed 'mapping.table' from documentation.

vignette

  • [ ] REQUIRED: The vignette should be a description of the data, there should be no introduction to the functionality of SBGNview package (this is saved for that package). You should not load in the SBGNview package. Modified the vignette to add descriptions of the data and removed SBGNview function demo.

Best, Kayla