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combiz / scFlow

Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.
https://combiz.github.io/scFlow/
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Dockerfile fails to build due to code/documentation mismatches in R CMD check #186

Closed RHReynolds closed 2 years ago

RHReynolds commented 2 years ago

Describe the bug When attempting to build the dockerfile image from github, the build fails due to the R CMD check failing.

To Reproduce Steps to reproduce the behavior:

  1. In bash: docker build https://github.com/combiz/scFlow.git#0.7.1 --tag combiz/scflowtest:0.7.1 (I'd suggest doing this in a screen or via nohup, as the build takes a while)

  2. See error: see below and lines 18101-18126 in attached log file

    ❯ checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'plot_reduced_dim':
plot_reduced_dim
Code: function(sce, feature_dim = "Cluster", reduced_dim = "UMAP",
               highlight_feature = NA, label_clusters = FALSE, size =
               getOption("scflow_reddimplot_pointsize", default =
               0.1), alpha = getOption("scflow_reddimplot_alpha",
               default = 0.2))
Docs: function(sce, feature_dim = "Cluster", reduced_dim = "UMAP",
               highlight_feature = NA, label_clusters = FALSE, size =
               0.1, alpha = 0.2)
Mismatches in argument default values:
  Name: 'size' Code: getOption("scflow_reddimplot_pointsize", default = 0.1) Docs: 0.1
  Name: 'alpha' Code: getOption("scflow_reddimplot_alpha", default = 0.2) Docs: 0.2

Codoc mismatches from documentation object 'plot_reduced_dim_gene':
plot_reduced_dim_gene
Code: function(sce, reduced_dim = "UMAP", gene = "PLP1", size =
               getOption("scflow_reddimplot_pointsize", default =
               0.1), alpha = getOption("scflow_reddimplot_alpha",
               default = 0.2), palette = c("grey80", "#440154FF"))
Docs: function(sce, reduced_dim = "UMAP", gene = "PLP1", size = 0.1,
               alpha = 0.2, palette = c("grey80", "#440154FF"))
Mismatches in argument default values:
  Name: 'size' Code: getOption("scflow_reddimplot_pointsize", default = 0.1) Docs: 0.1
  Name: 'alpha' Code: getOption("scflow_reddimplot_alpha", default = 0.2) Docs: 0.2

Expected behavior Would expect the dockerfile to successfully build the image.

Proposed solution Looking at the .R files for plot_reduced_dim and plot_reduced_dim_gene, I think the discrepancy arises because the default options differ between these and the .html files in ./docs/reference. I think it may be a simple case of re-building the package documentation with pkgdown::build_reference(). I would have done this in a pull request, but it requires that scFlow is installed -- and I am unable to install it on our current server due to dependency issues (hence why I was attempting to build the docker image).

System

Log file

01_docker_build_scflow.log

NathanSkene commented 2 years ago

Hi Regina,

I believe this is deliberate. The dockerfile should only build if all checks pass.

From: Regina Hertfelder Reynolds @.> Sent: 05 November 2021 09:20 To: combiz/scFlow @.> Cc: Subscribed @.***> Subject: [combiz/scFlow] Dockerfile fails to build due to code/documentation mismatches in R CMD check (Issue #186)

This email from @.*** originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders listhttps://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address.

Describe the bug When attempting to build the dockerfile image from github, the build fails due to the R CMD check failing.

To Reproduce Steps to reproduce the behavior:

  1. In bash: docker build https://github.com/combiz/scFlow.git#0.7.1 --tag combiz/scflowtest:0.7.1 (I'd suggest doing this in a screen or via nohup, as the build takes a while)
  2. See error: see below and lines 18101-18126 in attached log file

❯ checking for code/documentation mismatches ... WARNING

Codoc mismatches from documentation object 'plot_reduced_dim':

plot_reduced_dim

Code: function(sce, feature_dim = "Cluster", reduced_dim = "UMAP",

               highlight_feature = NA, label_clusters = FALSE, size =

               getOption("scflow_reddimplot_pointsize", default =

               0.1), alpha = getOption("scflow_reddimplot_alpha",

               default = 0.2))

Docs: function(sce, feature_dim = "Cluster", reduced_dim = "UMAP",

               highlight_feature = NA, label_clusters = FALSE, size =

               0.1, alpha = 0.2)

Mismatches in argument default values:

  Name: 'size' Code: getOption("scflow_reddimplot_pointsize", default = 0.1) Docs: 0.1

  Name: 'alpha' Code: getOption("scflow_reddimplot_alpha", default = 0.2) Docs: 0.2

Codoc mismatches from documentation object 'plot_reduced_dim_gene':

plot_reduced_dim_gene

Code: function(sce, reduced_dim = "UMAP", gene = "PLP1", size =

               getOption("scflow_reddimplot_pointsize", default =

               0.1), alpha = getOption("scflow_reddimplot_alpha",

               default = 0.2), palette = c("grey80", "#440154FF"))

Docs: function(sce, reduced_dim = "UMAP", gene = "PLP1", size = 0.1,

               alpha = 0.2, palette = c("grey80", "#440154FF"))

Mismatches in argument default values:

  Name: 'size' Code: getOption("scflow_reddimplot_pointsize", default = 0.1) Docs: 0.1

  Name: 'alpha' Code: getOption("scflow_reddimplot_alpha", default = 0.2) Docs: 0.2

Expected behavior Would expect the dockerfile to successfully build the image.

Proposed solution Looking at the .R files for plot_reduced_dim and plot_reduced_dim_gene, I think the discrepancy arises because the default options differ between these and the .html files in ./docs/reference. I think it may be a simple case of re-building the package documentation with pkgdown::build_reference(). I would have done this in a pull request, but it requires that scFlow is installed -- and I am unable to install it on our current server due to dependency issues (hence why I was attempting to build the docker image).

System

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RHReynolds commented 2 years ago

Hi Nathan,

Thanks for the quick response! I appreciate that this is a deliberate (and good) check to have in place. I was just wondering if it would be possible to update the package reference documentation such that the build did not fail? As I mentioned, I would do this myself, but due to dependency issues on our server, my hands are tied and I cannot install scFlow in order to resolve the issue.

All the best, Regina

NathanSkene commented 2 years ago

Absolutely, sorry, just misinterpreted on my phone, Combiz can advise why it's failing

From: Regina Hertfelder Reynolds @.> Sent: 05 November 2021 09:50 To: combiz/scFlow @.> Cc: Skene, Nathan G @.>; Comment @.> Subject: Re: [combiz/scFlow] Dockerfile fails to build due to code/documentation mismatches in R CMD check (Issue #186)

This email from @.*** originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders listhttps://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address.

Hi Nathan,

Thanks for the quick response! I appreciate that this is a deliberate (and good) check to have in place. I was just wondering if it would be possible to update the package reference documentation such that the build did not fail? As I mentioned, I would do this myself, but due to dependency issues on our server, my hands are tied and I cannot install scFlow in order to resolve the issue.

All the best, Regina

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/combiz/scFlow/issues/186#issuecomment-961758560, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AH5ZPEYEECS5VXMCNYJ4VRTUKOSHZANCNFSM5HNMLRXQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

RHReynolds commented 2 years ago

No worries, Nathan!

Just to say, I think this may only be an issue with the 0.7.1 release. Trying to build directly from the master branch with the command: docker build https://github.com/combiz/scFlow.git#master --tag combiz/scflowtest:latest. I'll let you know if the issue persists.

Al-Murphy commented 2 years ago

Hi Regina,

Perhaps I am missing something here but there is no need for you to build the docker image yourself, all scFlow version's docker images can be pulled from almurphy/scfdev, see the tags for the versions. The latest version 0.7.1 built fine for us and is available at the previous link. Let me know if there is a reason you are trying to build the docker image yourself however.

Thanks, Alan.

RHReynolds commented 2 years ago

Hi Alan,

My mistake. I looked for the docker image in combiz's dockerhub profile. I hadn't appreciated it was in yours. But now that I know that it is, will just pull from there. Thanks very much!! :)

Best, Regina

Al-Murphy commented 2 years ago

No problem at all, glad that sorted things!