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gdrplatform release [fifth package: gDRcore] #3003

Closed bczech closed 1 year ago

bczech commented 1 year ago

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bioc-issue-bot commented 1 year ago

Hi @bczech

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:

Type: Package
Package: gDRcore
Title: Processing functions and interface to process and analyze drug
    dose-response data
Version: 0.99.0
Date: 2023-03-20
Authors@R: c(
    person("Support", "gDR", , "gdr-support-d@gene.com", role = "cre",
 comment = c(ORCID = "0009-0006-9310-1135")),
    person("Bartosz", "Czech", , "bartosz.czech@contractors.roche.com", role = "aut"),
    person("Arkadiusz", "Gladki", role = "aut"),
    person("Marc", "Hafner", role = "aut"),
    person("Pawel", "Piatkowski", role = "aut"),
    person("Natalia", "Potocka", role = "aut"),
    person("Dariusz", "Scigocki", role = "aut"),
    person("Sergiu", "Mocanu", role = "aut"),
    person("Allison", "Vuong", role = "aut")
  )
Description: This package contains core functions to process and analyze drug response data. The package provides tools for normalizing, averaging,
  and calculation of gDR metrics data. All core functions are wrapped into the pipeline function allowing analyzing the data in a straightforward way.
License: file LICENSE
Imports:
    BumpyMatrix,
    BiocParallel,
    checkmate,
    futile.logger,
    gDRutils (>= 0.99.0),
    methods,
    MultiAssayExperiment,
    purrr,
    plyr,
    reshape2,
    stringr,
    S4Vectors,
    SummarizedExperiment,
    tibble,
    zoo
Suggests:
    gDRstyle (>= 0.99.0),
    gDRimport (>= 0.99.0),
    gDRtestData (>= 0.99.0),
    IRanges,
    knitr,
    pkgbuild,
    qs,
    testthat,
    yaml
VignetteBuilder: 
    knitr
biocViews: Software, ShinyApps
ByteCompile: TRUE
DeploySubPath: gDRcore
Encoding: UTF-8
LazyLoad: yes
NeedsCompilation: yes
RoxygenNote: 7.2.3
SwitchrLibrary: gDRcore
vjcitn commented 1 year ago

i updated all sources, still

* checking dependencies in R code ... WARNING
'loadNamespace' or 'requireNamespace' call not declared from: ‘gDRinternalData’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'gDRcore-Ex.R' failed
The error most likely occurred in:

> ### Name: convert_mae_to_raw_data
> ### Title: Transform mae into raw data
> ### Aliases: convert_mae_to_raw_data
> 
> ### ** Examples
> 
> mae <- get_synthetic_data("finalMAE_small.RDS")
Error in get_synthetic_data("finalMAE_small.RDS") :
could not find function "get_synthetic_data"
commit 5ff49eab65e766cb03fcceaa21dc95d795d9fe3a (HEAD -> master, origin/master, origin/HEAD)
Merge: 7abac1a 7d59f92
Author: gladkia <41166437+gladkia@users.noreply.github.com>
Date:   Sat Apr 15 16:51:56 2023 +0200

    Merge pull request #68 from gdrplatform/GDR-1919_2

    Gdr 1919 2

commit 7d59f92e6cb30d61563df122b68bcf50072107a4
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date:   Sat Apr 15 15:45:16 2023 +0200

    bugfix: move .clear_rownames to prepare_input step
gladkia commented 1 year ago

Hi @vjcitn, Thanks! Fixed.

Please assure that you have the latest gDRtestData (https://github.com/gdrplatform/gDRtestData/commit/4a32e86749ca455d8c5fa98a8aeb5f46c8822e5b; v 0.99.4; current master) and gDRimport (https://github.com/gdrplatform/gDRimport/commit/61afe11980ae59d8fb0bf86d25d1ebd5bb5b8236); v 0.99.4; current main).

bioc-issue-bot commented 1 year ago

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bioc-issue-bot commented 1 year 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, skipped". 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/gDRcore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

vjcitn commented 1 year ago

7d59f92 still has

* checking examples ... ERROR
Running examples in 'gDRcore-Ex.R' failed
The error most likely occurred in:

> ### Name: convert_mae_to_raw_data
> ### Title: Transform mae into raw data
> ### Aliases: convert_mae_to_raw_data
> 
> ### ** Examples
> 
> mae <- get_synthetic_data("finalMAE_small.RDS")
Error in get_synthetic_data("finalMAE_small.RDS") : 
vjcitn commented 1 year ago

could not find function "get_synthetic_data"

vjcitn commented 1 year ago

hold on a minute.

vjcitn commented 1 year ago
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  10/12 mismatches (average diff: 214421)
  [2]   55913 -  61367 ==   -5454
  [3]   61367 - 159394 ==  -98027
  [4]   14426 - 455904 == -441478
  [5]  159394 -  54833 ==  104561
  [6]   34391 - 146833 == -112442
  [7]  455904 -  55913 ==  399991
  [8]  455901 -  14426 ==  441475
  [9]   54833 -  34391 ==   20442
  [10]  41199 - 455901 == -414702
  ...

  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  Error: Test failures
  Execution halted
stvjc@stvjc-XPS-13-9300:~/SUBMISSIONS/APR1/gDRcore/FOO/gDRcore$ git remote -v
origin  git@git.bioconductor.org:packages/gDRcore (fetch)
origin  git@git.bioconductor.org:packages/gDRcore (push)
stvjc@stvjc-XPS-13-9300:~/SUBMISSIONS/APR1/gDRcore/FOO/gDRcore$ git log |head -5
commit e573ad8640674d0fca7cc24d3cbfb831c978e718
Merge: 4df322e e279b9f
Author: gladkia <41166437+gladkia@users.noreply.github.com>
Date:   Mon Apr 17 14:37:07 2023 +0200

give me an email when you think the git.bioconductor.org package images are synchronized and should pass check, regardless of what the single-package builder results are. stvjc@channing.harvard.edu

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 9553d53c3f8fbdfcfbc523c6828b97a9aa900b8c

bioc-issue-bot commented 1 year 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, skipped". 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/gDRcore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

gladkia commented 1 year ago
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  10/12 mismatches (average diff: 214421)
  [2]   55913 -  61367 ==   -5454
  [3]   61367 - 159394 ==  -98027
  [4]   14426 - 455904 == -441478
  [5]  159394 -  54833 ==  104561
  [6]   34391 - 146833 == -112442
  [7]  455904 -  55913 ==  399991
  [8]  455901 -  14426 ==  441475
  [9]   54833 -  34391 ==   20442
  [10]  41199 - 455901 == -414702
  ...

  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  Error: Test failures
  Execution halted
stvjc@stvjc-XPS-13-9300:~/SUBMISSIONS/APR1/gDRcore/FOO/gDRcore$ git remote -v
origin    git@git.bioconductor.org:packages/gDRcore (fetch)
origin    git@git.bioconductor.org:packages/gDRcore (push)
stvjc@stvjc-XPS-13-9300:~/SUBMISSIONS/APR1/gDRcore/FOO/gDRcore$ git log |head -5
commit e573ad8640674d0fca7cc24d3cbfb831c978e718
Merge: 4df322e e279b9f
Author: gladkia <41166437+gladkia@users.noreply.github.com>
Date:   Mon Apr 17 14:37:07 2023 +0200

give me an email when you think the git.bioconductor.org package images are synchronized and should pass check, regardless of what the single-package builder results are. stvjc@channing.harvard.edu

@vjcitn, fixed (and an email sent as well).

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0eb96482fa6d4a091bcc838b62d4b7d3d9074a99

bioc-issue-bot commented 1 year 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, skipped". 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/gDRcore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d0b229f953c1a3102a38d70379ae8f89df90fc32

bioc-issue-bot commented 1 year 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, skipped". 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/gDRcore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

vjcitn commented 1 year ago
* checking dependencies in R code ... WARNING
'loadNamespace' or 'requireNamespace' call not declared from: ‘gDRinternalData’

a concern?

gladkia commented 1 year ago

I think not. gDRcore supports two scenarios for fetching the annotations for drugs and cell lines. In the first scenario (internal use) the annotations are fetched gDRinternalData. In the second scenario (public use) the annotations are fetched from the (publicly available) gDRtestData. Please find the key code chunks in the link1 and link2.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f250a8f902d138a5b211ea83238ed5b063c25cab

bioc-issue-bot commented 1 year 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, skipped". 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/gDRcore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: e06f3c97978b68085a75f6e9bc0c4f4afab382ad

bioc-issue-bot commented 1 year 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, skipped". 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/gDRcore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 1edf140657800906daa83160aa9511e25feb2f52

bioc-issue-bot commented 1 year 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, skipped". 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/gDRcore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 93006b3e10903d42aa4321813cea6e34296f8300

bioc-issue-bot commented 1 year 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, skipped". 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/gDRcore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 52f9edad98a1e509acbe36f2af3b790165cf6366

bioc-issue-bot commented 1 year 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/gDRcore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 510fb2bbfe50de120d7d17243e288ddb093be37a

bioc-issue-bot commented 1 year ago

Dear Package contributor,

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

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

gladkia commented 1 year ago

Hi @vjcitn,

Thanks for your current support! FYI, we've just fixed all the warnings and errors in gDRcore. The review should be much simpler now (hopefully). Thanks in advance.

bioc-issue-bot commented 1 year ago

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