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(inactive) bioAnno #1404

Closed guokai8 closed 3 years ago

guokai8 commented 4 years ago

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

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bioc-issue-bot commented 4 years ago

Hi @guokai8

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: bioAnno
Type: Package
Title: Build Annotation From Online Database
Version: 0.99.0
Author: Kai Guo
Maintainer: guokai8 <guokai8@gmail.com>
Description: This package provide function for building annotation package 
  by using information from KEGG, NCBI, Ensembl and return OrgDb 
  object such as org.Hs.eg.db.
License: GPL-2
Encoding: UTF-8
LazyData: true
Depends:
    R (>= 3.6.0)
Imports:
      AnnotationForge,
      AnnotationHub,
      AnnotationDbi,
      RSQLite,
      KEGGREST,
      biomaRt,
      data.table,
      dplyr,
      jsonlite,
      R.utils,
      utils,
      stats,
      magrittr
Suggests:
    GO.db,
    knitr,
    testthat,
    rmarkdown
VignetteBuilder: knitr
biocViews: Software, Annotation, Clustering, GO, KEGG,Pathways, Reactome
RoxygenNote: 7.0.2

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bioc-issue-bot commented 4 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 4 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 4 years ago

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

0076762 Update DESCRIPTION

bioc-issue-bot commented 4 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 4 years ago

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

2d672c1 Update DESCRIPTION

guokai8 commented 4 years ago

Hi @hpages, The Error is out of memory since it require to download big files from online resources. How can I fix it. Can I just add not test in the example page. Kai

bioc-issue-bot commented 4 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 4 years ago

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

304a22b Update DESCRIPTION

bioc-issue-bot commented 4 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 4 years ago

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

42b3e1a Update DESCRIPTION

bioc-issue-bot commented 4 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 4 years ago

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

b11ca9f Update DESCRIPTION

bioc-issue-bot commented 4 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 4 years ago

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

a2f80ec Update DESCRIPTION

bioc-issue-bot commented 4 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 4 years ago

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

d1a984b Update DESCRIPTION

bioc-issue-bot commented 4 years ago

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

0d78313 Update DESCRIPTION

bioc-issue-bot commented 4 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 4 years ago

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

f360e7e Update DESCRIPTION

bioc-issue-bot commented 4 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 4 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 4 years ago

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

917f13d Update DESCRIPTION

bioc-issue-bot commented 4 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 4 years ago

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

2d9b294 Update DESCRIPTION

bioc-issue-bot commented 4 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 4 years ago

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

f6180b3 Update DESCRIPTION

bioc-issue-bot commented 4 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 4 years ago

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

99d4e07 Update DESCRIPTION

bioc-issue-bot commented 4 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.

guokai8 commented 4 years ago

Hi @bioc-issue-bot @hpages , I just wonder do you find time to review my package since it already one month now. Kai

hpages commented 4 years ago

Hi Kai,

Sorry for the delay. Unfortunately the HTML vignette in bioAnno (created by R CMD build bioAnno) is cluttered with about 80 occurrences of the following warning:

## Warning in result_fetch(res@ptr, n = n): SQL statements must be issued with
## dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().

which makes it almost impossible to follow.

Please address. Thanks!

H.

bioc-issue-bot commented 4 years ago

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

b187b5b Update DESCRIPTION

bioc-issue-bot commented 4 years ago

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

484e4a6 Update DESCRIPTION

guokai8 commented 4 years ago

Hi @bioc-issue-bot @hpages , The warnings happened due by the AnnotationForge package. I add suppressWarnings in the code. Please let me know if it works now. Kai

bioc-issue-bot commented 4 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 4 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.

hpages commented 4 years ago

The vignette looks a little bit better thanks.

There are many problems with the bioAnno package.

I'll start with the documentation. It has many English mistakes and also mistakes like this one in the vignette:

BiocManager::install("VennDetail")

where this is supposed to be the command for installing the bioAnno package. Or this one in the man page for fromAnnHub():

## build annoataion package for yeast
fromAnnHub(species = "celegans", install = FALSE)

Please re-read and check carefully all your documentation (man pages and vignette) and make sure it is clear, accurate, and concise. It needs a lot of improvement.

Also it is not good design that your functions install and/or remove packages in a somewhat obscure manner. They should focus on making annotations. If these annotations end up in a package, then print a clear error message at the end of your function explaining where that package can be found and how to install it. The user will decide if they want to install it or not. But they should be able to take a look at it before they do so.

Thanks, H.

bioc-issue-bot commented 4 years ago

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

fd785fb Add files via upload

bioc-issue-bot commented 4 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.

guokai8 commented 4 years ago

Hi @hpages @bioc-issue-bot ,

1. I'll start with the documentation. It has many English mistakes and also mistakes like this one in the vignette:

BiocManager::install("VennDetail")

where this is supposed to be the command for installing the bioAnno package. Response: Sorry for the error. I replace with the new version

2. Or this one in the man page for fromAnnHub():

build annotation package for yeast

   fromAnnHub(species = "celegans", install = FALSE)

Response: fixed the typo in man page

3. Please re-read and check carefully all your documentation (man pages and vignette) and make sure it is clear, accurate, and concise. It needs a lot of improvement.

Response: I revised the vignette and man pages. Thanks for your suggestions. I am not good at writing man pages and vignette.

4. Also it is not good design that your functions install and/or remove packages in a somewhat obscure manner. They should focus on making annotations. If these annotations end up in a package, then print a clear error message at the end of your function explaining where that package can be found and how to install it. The user will decide if they want to install it or not. But they should be able to take a look at it before they do so.

Response: I add function to display the whole path of the package and how to install it if the user choose not to install it. And I also add the function getTable to help the user to extract annotation tables if the user just want have annotation table instead of installing the whole package.

guokai8 commented 4 years ago

Hi @hpages @bioc-issue-bot ,

1. I'll start with the documentation. It has many English mistakes and also mistakes like this one in the vignette:

BiocManager::install("VennDetail")

where this is supposed to be the command for installing the bioAnno package. Response: Sorry for the error. I replace with the new version

2. Or this one in the man page for fromAnnHub():

build annotation package for yeast

   fromAnnHub(species = "celegans", install = FALSE)

Response: fixed the typo in man page

3. Please re-read and check carefully all your documentation (man pages and vignette) and make sure it is clear, accurate, and concise. It needs a lot of improvement.

Response: I revised the vignette and man pages. Thanks for your suggestions. I am not good at write man pages and vignette.

4. Also it is not good design that your functions install and/or remove packages in a somewhat obscure manner. They should focus on making annotations. If these annotations end up in a package, then print a clear error message at the end of your function explaining where that package can be found and how to install it. The user will decide if they want to install it or not. But they should be able to take a look at it before they do so.

Response: I add function to display the whole path of the package and how to install it if the user choose not to install it. And I also add the function getTable to help the user to extract annotation tables if the user just want have annotation table instead of installing the whole package.

bioc-issue-bot commented 4 years ago

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

d0c5877 Update DESCRIPTION

bioc-issue-bot commented 4 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 4 years ago

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

bbf9f63 Update DESCRIPTION

bioc-issue-bot commented 4 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 4 years ago

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

901d2b5 Update DESCRIPTION

bioc-issue-bot commented 4 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 4 years ago

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

a19bc64 Update DESCRIPTION

bioc-issue-bot commented 4 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.