(inactive) PhosMap - Githubissues

ecnuzdd commented 6 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/ecnuzdd/PhosMap

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

[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

I am familiar with the essential aspects of Bioconductor software management, including:

[x] The 'devel' branch for new packages and features.
[x] The stable 'release' branch, made available every six months, for bug fixes.
[x] Bioconductor version control using Git (optionally via GitHub).

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

bioc-issue-bot commented 6 years ago

Hi @ecnuzdd

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: PhosMap
Type: Package
Title: A Modular Analysis Package for Phosphoproteomic Data
Version: 1.1.1
Author: Dongdong Zhan
Maintainer: Dongdong Zhan <ecnuzdd@163.com>
Description: Functions summary:
    1. Extracting the confidence probability of phosphorylation sites at peptide level from identification results searched by Mascot.
    2. Generating the quality control file of phosphorylation sites based on score of sites from Mascot.
    3. Pre-processing phosphoproteomic data.
    4. Kinase substrate enrichment analysis.
    5. Motif enrichment analysis.
    6. Data visualization
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Date: 2018-11-07
Imports: graphics, stats, utils
Suggests: stringr, ggseqlogo, rmotifx, pheatmap, samr, limma, RankProd, ksea, e1071, ClueR, tourr

mtmorgan commented 6 years ago

This package does not have a vignette, and does not re-use standard Bioconductor classes and methods for interoperability, and is therefore not suitable for Bioconductor.

ecnuzdd commented 5 years ago

Hi, I have updated PhosMap, please help me reopen the issue to make it work.

bioc-issue-bot commented 5 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

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 5 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

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 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: "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 build report for more details.

mtmorgan commented 5 years ago

Your package can depend only on CRAN or Bioconductor packages.

bioc-issue-bot commented 5 years ago

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

4b64afa update

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: "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 build report for more details.

ecnuzdd commented 5 years ago

Does Bioconducor not support non-CRAN or non-Bioconductor packages? The rmotifx and ksea packages are not located on CRAN and Bioconductor. In DESCRIPTION file, I wrote that: Additional_repositories: https://github.com/omarwagih/rmotifx/,https://github.com/evocellnet/ksea/

mtmorgan commented 5 years ago

Packages must be on CRAN or Bioconductor, since these have at least minimal quality control and certainty of availability.

ecnuzdd commented 5 years ago

In proteome, kinase-substrate enrichment analysis (KSEA) and Motif enrichment analysis (rmotifx) are two general methods. For this case, how do I use the two packages? In DESCRIPTION file, if I modified them to "Suggests" labels, does it work? it is successful while executing 'R CMD build'.

mtmorgan commented 5 years ago

It's successful from R CMD build because you have the packages installed. The build system will not install them, and they cannot be in the Depends:, Imports:, or Suggests: fields. If these packages are central to the functionality of your own package, then it means that your package cannot be accepted to Bioconductor.

ecnuzdd commented 5 years ago

Thanks for your help. They are not core functionality but a part of my package. I will update my package by separating their functions of external packages.

bioc-issue-bot commented 5 years ago

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

6525fb1 Update DESCRIPTION

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: "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 build report for more details.

bioc-issue-bot commented 5 years ago

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

36237f3 Update DESCRIPTION

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: "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 build report for more details.

bioc-issue-bot commented 5 years ago

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

0f23d8d update_20181217_0201

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: "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 build report for more details.

bioc-issue-bot commented 5 years ago

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

ca32580 Update DESCRIPTION

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: "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 build report for more details.

bioc-issue-bot commented 5 years ago

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

f6772ee Update DESCRIPTION

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: "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 build report for more details.

ecnuzdd commented 5 years ago

Hi, reviewer, I have updated my package and passed "R CMD check" and "R CMD build" in local development machine (Windows). There were no ERRORS and WARNINGs happening. I don't konw why it happend that "Quitting from lines 254-323 (introduction_of_PhosMap.Rmd) Error: processing vignette 'introduction_of_PhosMap.Rmd' failed with diagnostics: numbers of columns of arguments do not match Execution halted". I have also executed these cmd located in lines 254-323 by pefroming a single steps, it looks anything is OK. Please help me find out why and the I will figure out it.

bioc-issue-bot commented 5 years ago

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

c59c831 Update introduction_of_PhosMap.Rmd d57d907 Update DESCRIPTION

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: "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 build report for more details.

bioc-issue-bot commented 5 years ago

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

cc1ac2b comment ksea

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: "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 build report for more details.

bioc-issue-bot commented 5 years ago

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

52c96b3 MEA_pheatmap

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, 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:

1514940 update11 c19d229 update

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: "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 build report for more details.

mtmorgan commented 5 years ago

I tried to build your package but apparently you have commited an invalid version of the file data/BRAFi.rda

PhosMap master$ bioc-devel
> load("data/BRAFi.rda")
Error in load("data/BRAFi.rda") :
  bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file 'BRAFi.rda' has magic number 'versi'
  Use of save versions prior to 2 is deprecated

ecnuzdd commented 5 years ago

Thanks for your operations. In this version, I have commented lines 254-323 in "introduction_of_PhosMap.Rmd", so you can see the error. I'm trying to solve it and then submit a new version. Currently, I don't find a correct method. I also have another question, does Bioconductor allow for embedded library files over 100 MB?

mtmorgan commented 5 years ago

'embedded library file'? If you mean compiled (e.g., C) code, then that is not the correct solution.

Please do not comment out lines that do not work, as this makes it difficult to know which lines do not work!!!

ecnuzdd commented 5 years ago

The 'embedded library file' means that references files used for analysis, sucha as protein fasta file from NCBI, the collected kinase-substrate regulation relations and constructed background file for motif enrichment analysis. The existence of files are to help users start perform analysis rapidly and expediently, reduce time cost of file collection and background construction. All these files are put into 'inst/extdata' directory for use.

mtmorgan commented 5 years ago

Large data files should not be included in the package. If they are easily available from online sources then I suggest writing a small helper function that uses BiocFileCache to retrieve the files (the first time) and read them from a local cache (first and subsequent times). If the data require curation (by you) before being useful, then they should be added to ExperimentHub.

mtmorgan commented 5 years ago

Will you be updating your package, or shall we mark this as 'inactive'?

bioc-issue-bot commented 5 years ago

This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.

Thank you for interest in Bioconductor.

mtmorgan commented 5 years ago

Please increment the version number (to 0.99.14) to trigger a build. Please follow this issues (https://github.com/Bioconductor/Contributions/issues/935) for further updates

ecnuzdd commented 5 years ago

Thanks for your quick reply.

I will update version number in description to trigger a build.

Best regards! Dongdong Zhan The Institute of Biomedical Sciences East China Normal University 500 Dongchuan Road Shanghai 200241, China On 5/9/2019 18:17，Martin Morgannotifications@github.com wrote：

Please increment the version number (to 0.99.14) to trigger a build. Please follow this issues (#935) for further updates

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

bioc-issue-bot commented 5 years ago

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

2e11be7 update version number

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, 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:

c781ec0 Update DESCRIPTION

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, 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:

05300a8 Update DESCRIPTION

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: "TIMEOUT". 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:

5ec9dd4 Update DESCRIPTION

bioc-issue-bot commented 5 years ago

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

5ec9dd4 Update DESCRIPTION

Bioconductor / Contributions

(inactive) PhosMap #935