GmicR

[Rvirgenslane]

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[bioc-issue-bot]

Hi @Rvirgenslane

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: GmicR
Type: Package
Title: Combines WGCNA and xCell readouts with bayesian network
        learrning to generate a Gene-Module Immune-Cell network (GMIC)
Version: 0.2.0
Author: Richard Virgen-Slane
Maintainer: The package maintainer <RVS.BioTools@gmail.com>
Description: This package uses bayesian network learning to detect relationships between 
    Gene Modules detected by WGCNA and immune cell signatures defined by xCell.
    It is a hypothesis generating tool.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Imports: GOstats, WGCNA, ape, bnlearn, org.Hs.eg.db, org.Mm.eg.db,
        shiny, AnnotationDbi, Category, DT, gRbase, GSEABase, gRain
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
biocViews: Software, SystemsBiology, GraphAndNetwork, Network,
        NetworkInference, GUI, ImmunoOncology, GeneExpression,
        QualityControl, Bayesian, Clustering
NeedsCompilation: no
Packaged: 2019-07-25 20:30:21 UTC; richardvirgen-slane

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[Rvirgenslane]

Checking new package version number...

• ERROR: New package version starting with 0.99.* (e.g., 0.99.0, 0.99.1, ...); got '0.2.0'.

I changed the current version to 0.99.3

Namespace dependency not required: data.table

I removed this

Checking DESCRIPTION/NAMESPACE consistency...

• WARNING: Import data.table, grDevices, graphics, stats, utils in DESCRIPTION as well as NAMESPACE.

I added these to the DESCRIPTION

[bioc-issue-bot]

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

b6209ac Add files via upload Version 0.99.4 fixing DESCRI...

[bioc-issue-bot]

Dear Package contributor,

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[bioc-issue-bot]

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

25625b0 Add files via upload Version 0.99.5 more fixes

[bioc-issue-bot]

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

fe30f85 Add files via upload Version: 0.99.6 more fixes

[bioc-issue-bot]

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

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

5dc92e3 Add files via upload Version: 0.99.7 More fixes

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

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

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

223c73c Add files via upload Version: 0.99.8

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

6b53701 Update DESCRIPTION Bump to Version: 0.99.9 as per...

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[dvantwisk]

Can you perform a version bump so that we can remove the "version bump required" tag.

[bioc-issue-bot]

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

49f36be Update DESCRIPTION Version: 0.99.10

[bioc-issue-bot]

Dear Package contributor,

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

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[bioc-issue-bot]

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

73ca6ed Add files via upload Version: 0.99.11

[bioc-issue-bot]

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[bioc-issue-bot]

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

fe2dca1 Update DESCRIPTION Version bump

[bioc-issue-bot]

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[bioc-issue-bot]

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

72e404d Added support for GO enrichment with conditioning ...

[bioc-issue-bot]

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.

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[bioc-issue-bot]

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

e32290c Updating manual Version bump: 00.99.14

[bioc-issue-bot]

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

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[bioc-issue-bot]

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

d3751e4 version 00.99.15

[bioc-issue-bot]

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

7614f8a Update DESCRIPTION version bump to fix error

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[Rvirgenslane]

How goes the review process?

[Rvirgenslane]

How goes the review process? Is there anything I can do to help?

Richard

On Wed, Jul 31, 2019 at 9:09 AM Daniel Van Twisk notifications@github.com wrote:

Can you perform a version bump so that we can remove the "version bump required" tag.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1192?email_source=notifications&email_token=AMWYHJ5XGWHQEHXQEG2744TQCG2M3A5CNFSM4IG6I6Q2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3HYKKA#issuecomment-516916520, or mute the thread https://github.com/notifications/unsubscribe-auth/AMWYHJ2RBXBV4FAWEOQBVCTQCG2M3ANCNFSM4IG6I6QQ .

[dvantwisk]

Apologies for the wait! I should have it in today.

[Rvirgenslane]

Great! Thanks for the update.

[dvantwisk]

Here is a review of your package. The code is very well done and most of my issues stand with the documentation. [REQUIRED] tags describe changes that must be addressed or changed. [CONSIDER] tags describe changes that are advisable but not necessary. Please message me back when you are done making changes.

• [ ] [REQUIRED] roxygen notes mention "boolean" values. In R these are called logical and should be changed accordingly. In general, it's best to explicitly state what type of data is used by a certain results or a parameter.

vignettes

• [ ] [REQUIRED] Remove the Stangled file GmicR_vignette.R. It shouldn't be needed in the repo.

vignettes/GmicR_vignette.Rmd

• [ ] [REQUIRED] L41-43: BiocManager::install() can and should be used to download R packages that are on CRAN. Also, the line doesn't seem necessary to the user as the package should install the packages that are in the Depends and Imports section of your DESCRIPTION file. This also goes for the extra packages that you have listed in L31-33. All that needs to be shown to the user about installing the package should be:

  if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
  BiocManager::install('GmicR')

  -[ ] [REQUIRED] L130,183,196, 271, 278: We generally want to see using facing code run on the build machines, so the eval=FALSEs should be removed. There are some cases when they are okay, such as when the code would open up something interactive. Do all these code chunks open shiny interfaces? If so, then they can stay.

[bioc-issue-bot]

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

a18bb59 Response to review of package. Push to Version 0....

[bioc-issue-bot]

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

61889c8 One more change to vignette to address reviewer co...

[bioc-issue-bot]

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, 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]

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, 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]

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

1375f98 Push to version 0.99.19 Correcting Vignette

[bioc-issue-bot]

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]

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

505717e More updates version 0.99.20

[bioc-issue-bot]

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]

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

7b1219a Additional update to vignette Version 0.99.21

[bioc-issue-bot]

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.

[Rvirgenslane]

Thank you dvantwisk for this review!

Here is a review of your package. The code is very well done and most of my issues stand with the documentation. [REQUIRED] tags describe changes that must be addressed or changed. [CONSIDER] tags describe changes that are advisable but not necessary. Please message me back when you are done making changes.

• [ ] [REQUIRED] roxygen notes mention "boolean" values. In R these are called logical and should be changed accordingly. In general, it's best to explicitly state what type of data is used by a certain results or a parameter.

I have changed all the "boolean" value references to "logical".

vignettes

• [ ] [REQUIRED] Remove the Stangled file GmicR_vignette.R. It shouldn't be needed in the repo.

File removed.

vignettes/GmicR_vignette.Rmd

• [ ] [REQUIRED] L41-43: BiocManager::install() can and should be used to download R packages that are on CRAN. Also, the line doesn't seem necessary to the user as the package should install the packages that are in the Depends and Imports section of your DESCRIPTION file. This also goes for the extra packages that you have listed in L31-33. All that needs to be shown to the user about installing the package should be:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install('GmicR')

I removed the lines referencing installation of cran packages and added:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install('GmicR')

-[ ] [REQUIRED] L130,183,196, 271, 278: We generally want to see using facing code run on the build machines, so the eval=FALSEs should be removed. There are some cases when they are okay, such as when the code would open up something interactive. Do all these code chunks open shiny interfaces? If so, then they can stay.

I removed all "eval=FALSE' arguments. This lead to errors during the vignette build tests. To solve this issue, I add the argument "results=FALSE" to L128.

Thank you again for you review. Please let me know if you have any other concerns.

On Mon, Sep 23, 2019 at 3:16 PM Daniel Van Twisk notifications@github.com wrote:

Here is a review of your package. The code is very well done and most of my issues stand with the documentation. [REQUIRED] tags describe changes that must be addressed or changed. [CONSIDER] tags describe changes that are advisable but not necessary. Please message me back when you are done making changes.

• [REQUIRED] roxygen notes mention "boolean" values. In R these are called logical and should be changed accordingly. In general, it's best to explicitly state what type of data is used by a certain results or a parameter.

vignettes

• [REQUIRED] Remove the Stangled file GmicR_vignette.R. It shouldn't be needed in the repo.

vignettes/GmicR_vignette.Rmd

• [REQUIRED] L41-43: BiocManager::install() can and should be used to download R packages that are on CRAN. Also, the line doesn't seem necessary to the user as the package should install the packages that are in the Depends and Imports section of your DESCRIPTION file. This also goes for the extra packages that you have listed in L31-33. All that needs to be shown to the user about installing the package should be:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install('GmicR')

-[ ] [REQUIRED] L130,183,196, 271, 278: We generally want to see using facing code run on the build machines, so the eval=FALSEs should be removed. There are some cases when they are okay, such as when the code would open up something interactive. Do all these code chunks open shiny interfaces? If so, then they can stay.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1192?email_source=notifications&email_token=AMWYHJYWELMZDMCU7QCETTTQLE55HA5CNFSM4IG6I6Q2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7MN7MY#issuecomment-534306739, or mute the thread https://github.com/notifications/unsubscribe-auth/AMWYHJ3VXRWBKSH4PUPGHD3QLE55HANCNFSM4IG6I6QQ .

[Rvirgenslane]

Sorry about the formatting issue. Here is a better version:

Thank you dvantwisk for this review!

Here is a review of your package. The code is very well done and most of my issues stand with the documentation. [REQUIRED] tags describe changes that must be addressed or changed. [CONSIDER] tags describe changes that are advisable but not necessary. Please message me back when you are done making changes.

• [ ] [REQUIRED] roxygen notes mention "boolean" values. In R these are called logical and should be changed accordingly. In general, it's best to explicitly state what type of data is used by a certain results or a parameter.

I have changed all the "boolean" value references to "logical".

vignettes

• [ ] [REQUIRED] Remove the Stangled file GmicR_vignette.R. It shouldn't be needed in the repo.

File removed.

vignettes/GmicR_vignette.Rmd

• [ ] [REQUIRED] L41-43: BiocManager::install() can and should be used to download R packages that are on CRAN. Also, the line doesn't seem necessary to the user as the package should install the packages that are in the Depends and Imports section of your DESCRIPTION file. This also goes for the extra packages that you have listed in L31-33. All that needs to be shown to the user about installing the package should be:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install('GmicR')

I removed the lines referencing installation of cran packages and added:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install('GmicR')

-[ ] [REQUIRED] L130,183,196, 271, 278: We generally want to see using facing code run on the build machines, so the eval=FALSEs should be removed. There are some cases when they are okay, such as when the code would open up something interactive. Do all these code chunks open shiny interfaces? If so, then they can stay.

I removed all "eval=FALSE' arguments. This lead to errors during the vignette build tests. To solve this issue, I add the argument "results=FALSE" to L128.

Thank you again for you review. Please let me know if you have any other concerns.

[Rvirgenslane]

Hi dvantwisk,

Have you had time to see my updates?

[Rvirgenslane]

Hi dvantwisk,

Is there anything else that you require from me?