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New biodb package : framework for developing database connectors. #2068

Closed pkrog closed 3 years ago

pkrog commented 3 years ago

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bioc-issue-bot commented 3 years ago

Hi @pkrog

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: biodb
Title: biodb, a library and a development framework for connecting to chemical and biological databases
Version: 0.99.0
Authors@R: c(person("Pierrick", "Roger", email = "pierrick.roger@cea.fr", role = c("aut", "cre")),
   person("Alexis", "Delabrière", email = "delabriere@imsb.biol.ethz.ch", role = "ctb"))
Description: The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.
biocViews: Software, Infrastructure, DataImport
Depends:
    R (>= 4.0)
License: AGPL-3
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Suggests:
    BiocStyle,
    roxygen2,
    devtools,
    testthat (>= 2.0.0),
    knitr,
    rmarkdown,
    covr,
    xml2,
    git2r
Imports:
    R6,
    methods,
    chk,
    lgr,
    progress,
    lifecycle,
    XML,
    stringr,
    plyr,
    yaml,
    jsonlite,
    RCurl,
    Rcpp,
    rappdirs,
    stats,
    openssl,
    RSQLite,
    withr
LinkingTo:
    Rcpp,
    testthat
NeedsCompilation: yes
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Collate:
    'BiodbObject.R'
    'Biodb.R'
    'BiodbChildObject.R'
    'BiodbConnBase.R'
    'BiodbConn.R'
    'BiodbCompounddbConn.R'
    'BiodbObserver.R'
    'BiodbConfig.R'
    'BiodbConnObserver.R'
    'BiodbEntry.R'
    'BiodbCsvEntry.R'
    'BiodbDbInfo.R'
    'BiodbDbsInfo.R'
    'BiodbDownloadable.R'
    'BiodbEditable.R'
    'BiodbEntryField.R'
    'BiodbEntryFields.R'
    'BiodbFactory.R'
    'BiodbXmlEntry.R'
    'BiodbHtmlEntry.R'
    'BiodbJsonEntry.R'
    'BiodbListEntry.R'
    'BiodbMassdbConn.R'
    'BiodbPersitentCache.R'
    'BiodbRequestScheduler.R'
    'BiodbRemotedbConn.R'
    'BiodbUrl.R'
    'BiodbRequest.R'
    'BiodbRequestSchedulerRule.R'
    'BiodbTxtEntry.R'
    'BiodbSdfEntry.R'
    'BiodbSqlExpr.R'
    'BiodbSqlBinaryOp.R'
    'BiodbSqlField.R'
    'BiodbSqlList.R'
    'BiodbSqlLogicalOp.R'
    'BiodbSqlQuery.R'
    'BiodbSqlValue.R'
    'BiodbWritable.R'
    'CsvFileConn.R'
    'CompCsvFileConn.R'
    'CompCsvFileEntry.R'
    'SqliteConn.R'
    'CompSqliteConn.R'
    'CompSqliteEntry.R'
    'ExtGenerator.R'
    'ExtFileGenerator.R'
    'ExtConnClass.R'
    'ExtCpp.R'
    'ExtDefinitions.R'
    'ExtDescriptionFile.R'
    'ExtEntryClass.R'
    'ExtGitignore.R'
    'ExtLicense.R'
    'ExtMakefile.R'
    'ExtPackage.R'
    'ExtPackageFile.R'
    'ExtRbuildignore.R'
    'ExtReadme.R'
    'ExtTests.R'
    'ExtTravisFile.R'
    'ExtVignette.R'
    'FileTemplate.R'
    'MassCsvFileConn.R'
    'MassCsvFileEntry.R'
    'MassSqliteConn.R'
    'MassSqliteEntry.R'
    'Progress.R'
    'Range.R'
    'RcppExports.R'
    'catch-routine-registration.R'
    'fcts_biodb.R'
    'fcts_ext.R'
    'fcts_mass.R'
    'fcts_misc.R'
    'generic_tests.R'
    'http_consts.R'
    'package.R'
    'spec-dist.R'
    'test_framework.R'
bioc-issue-bot commented 3 years ago

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

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

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bioc-issue-bot commented 3 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 build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/biodb to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 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 build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/biodb to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

pkrog commented 3 years ago

Sorry, but I do not understand the build report, it is empty. It seems the code of my package was never found: "Git clone Failed", while the DESCRIPTION file was found by the bot.

lshep commented 3 years ago

Sorry for the inconvenience -- this is on our end. When the issue is resolved I will manually force an initial build for you

pkrog commented 3 years ago

OK, thanks.

bioc-issue-bot commented 3 years ago

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

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/biodb to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2916f849a0b4f27606aa4cf2b7481fab77cfeddf

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/biodb to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2dc0238636b29dd446c1d1a74c3e5ff384b5f143

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/biodb to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 852943fd8e54f96609ff99daa65b1762108d10bb

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/biodb to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

pkrog commented 3 years ago

@lshep , could you help me on this warning (appears on Windows build):

Found the following significant warnings:
  Rd warning: Previous alias or file overwritten by alias: biodb
See 'C:/Users/pkgbuild/packagebuilder/workers/jobs/2068/852943fd8e54f96609ff99daa65b1762108d10bb/biodb.Rcheck/00install.out' for details.
bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: cc5b226d77c23093365be227774644b958579494

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/biodb to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 99ae5e8d3b1f9bad80370a98e37c5f3098ee795b

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/biodb to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 88cc9db43fbde177fdfa1843b182f395f00752a2

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/biodb to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

pkrog commented 3 years ago

@lshep , could you help me on this warning (appears on Windows build):

Found the following significant warnings:
  Rd warning: Previous alias or file overwritten by alias: biodb
See 'C:/Users/pkgbuild/packagebuilder/workers/jobs/2068/852943fd8e54f96609ff99daa65b1762108d10bb/biodb.Rcheck/00install.out' for details.

I think I've found the issue, I'll give it a try.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 56d9dfd0576332ea67112bd7ed3997c78f42c0ef

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/biodb to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/biodb to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep commented 3 years ago

Thank you for the submission. Please see the following review:

Build report

general

description

README

inst

vignette

Warning message:
vignette 'intro' found more than once,
using the one found in '/home/shepherd/R-Libraries/4.1-Bioc3.13/biodb/doc'

It happened to open the right one but depending on a users system and the order of the packages loaded it may not.

R/man

Please address the above concerns and when ready do a version bump to trigger a new build report. Please comment back here addressing the above issues and that you are ready for a re-review. Cheers

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 91041860ac4e92b4914e162a771f4be1e100b575

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/biodb to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 54ec6ae6a49c843e2fa4b07c9991f95eaf43763a

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/biodb to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 70fbedddcad901acaa41f425009d6e7db32c4933

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/biodb to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

pkrog commented 3 years ago

I've answered your remarks as much as I was able:

lshep commented 3 years ago

Thank you. The changes are acceptable and I will move forward accepting the package. Cheers,

bioc-issue-bot commented 3 years ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

pkrog commented 3 years ago

Thanks.

vjcitn commented 3 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

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lshep commented 3 years ago

@pkrog Hello. It slipped my notice when I was reviewing but it looks like the default cache is placed in a users home directory. Could you please use tools::R_user_dir("my.biodb.cache", which="cache") as the default caching locations.

pkrog commented 3 years ago

Thanks @lshep , I have also received an email from Lori Shepherd, I will answer that.