Closed shbrief closed 1 year ago
Hi @shbrief
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: AnVILWorkflow
Title: Run workflows implemented in Terra/AnVIL workspace
Version: 0.99.0
Date: 2022-10-7
Authors@R:
person(given = "Sehyun",
family = "Oh",
role = c("aut", "cre"),
email = "Sehyun.Oh@sph.cuny.edu",
comment = c(ORCID = "0000-0002-9490-3061"))
Description: The AnVIL is a cloud computing resource developed in part
by the National Human Genome Research Institute. The main cloud-based
genomics platform deported by the AnVIL project is Terra. The
AnVILWorkflow package allows remote access to Terra implemented workflows,
enabling end-user to utilize Terra/ AnVIL provided resources - such as
data, workflows, and flexible/scalble computing resources - through the
conventional R functions.
Depends:
R (>= 4.1),
Imports:
AnVIL,
httr,
utils,
methods
Suggests:
knitr
License: Artistic-2.0
biocViews:
Infrastructure,
Software
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.1
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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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Hi @Kayla-Morrell ,
I updated my email address to the one used for the bioc-devel mailing list.
But I'm unsure how to resolve the other error (* ERROR: At least 80% of man pages documenting exported objects must have runnable examples.
), because more than 80% of functions in this package are a wrapper around API calls. Is there any suggestion on this case? Thanks!
Sehyun
Hello @shbrief
There do need to be examples in the man pages for exported objects. Would utilizing something like the following work?
if (AnVIL::gcould_exists()) {
## run example code
}
You could also look into donttest{}
as a last resort (we prefer runnable, testable code over using donttest{}
/dontrun{}
). If you must use one of these options we prefer donttest{}
because it requires valid R code.
Best, Kayla
Hi @Kayla-Morrell I fixed all the errors. Could you look at whether it's ready for the next step in review? Thanks!
@shbrief - You need to push a version bump to the git version of the package to kick of a new build report. Without a clean build report I can't continue with my portion of the review. Please see here for how to get this set up.
Best, Kayla
I have some permission issues accessing upstream. I'll push the new version as soon as I figure this out. Thanks!
Received a valid push on git.bioconductor.org; starting a build for commit id: e11d4ec0906fbda7a3f63f72ae872dae899f282d
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Received a valid push on git.bioconductor.org; starting a build for commit id: 67e7114c571fe8be813dc8043a5dc2c05257e9b0
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Received a valid push on git.bioconductor.org; starting a build for commit id: 3aa378e4294cd2c67d3e1723c98fe90775756ca5
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Received a valid push on git.bioconductor.org; starting a build for commit id: 68388ecb5530e52908e1e6d34345f71f196cf600
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Received a valid push on git.bioconductor.org; starting a build for commit id: 86a5490ddcd47ee26a34623660d7920480c6a27d
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Received a valid push on git.bioconductor.org; starting a build for commit id: 266815847e551e0b3f694ade03d362f2eb159c85
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Received a valid push on git.bioconductor.org; starting a build for commit id: 57c2b52b484866f9bfaf9a71bdff024f102d6e3d
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Received a valid push on git.bioconductor.org; starting a build for commit id: 70ff82745ec288f0b9c878933bfebf52cbcc8bff
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Received a valid push on git.bioconductor.org; starting a build for commit id: b0938924f0fdb1ef6b41f54670a77b0a4c561cf0
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This is the automated single package builder at bioconductor.org.
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Received a valid push on git.bioconductor.org; starting a build for commit id: 19e6ecc959f653d3706eaec724f8286148bb1331
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Hi @Kayla-Morrell I cleared all the errors/warnings. Please let me know what else needs to be done. Thanks!
@shbrief - When trying to build the package locally I get the following error:
* creating vignettes ... ERROR
--- re-building ‘salmon.Rmd’ using rmarkdown
Loading required package: dplyr
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Quitting from lines 193-195 (salmon.Rmd)
Error: processing vignette 'salmon.Rmd' failed with diagnostics:
'gcloud auth print-access-token' failed:
ERROR: (gcloud.auth.print-access-token) Your current active account [shbrief@gmail.com] does not have any valid credentials
Please run:
$ gcloud auth login
to obtain new credentials.
For service account, please activate it first:
$ gcloud auth activate-service-account ACCOUNT
exit status: 1
--- failed re-building ‘salmon.Rmd’
SUMMARY: processing the following file failed:
‘salmon.Rmd’
Error: Vignette re-building failed.
Execution halted
Received a valid push on git.bioconductor.org; starting a build for commit id: b8dca5aa420585cf96c5ebf8b54f866ce086a90b
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.
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Received a valid push on git.bioconductor.org; starting a build for commit id: b60bd46eeda59679952f3894595dbf5dc830a956
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.
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Received a valid push on git.bioconductor.org; starting a build for commit id: 370c085fd6999d69c1cb74adefec590f51d3d148
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.
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Hi @Kayla-Morrell, I think it should work now.
Will it be possible to include this package in the BioC 3.16 release? @vjcitn @lshep
Hi Sehyun -- it may be possible. But I am looking at the vignette as produced on my machine. A key point is
knitr::knit_exit(fully=FALSE)
So most of the vignette is not produced. Is this what you want?
Oh sorry, I was experimenting with something and accidentally pushed it. I'll fix it now.
Received a valid push on git.bioconductor.org; starting a build for commit id: 1185537aeb116d1c6a1fe9ab8820aa9fae437959
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/AnVILWorkflow
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@vjcitn Fixed. Let me know if you find any other issues. Thanks!
@Kayla-Morrell is the assigned reviewer and will still have to review and accept
@shbrief - I still need to do a full initial review of this package (besides just a clean build report) which takes time and reviews are not the only thing that I currently work on. This is an especially busy time with the release so please be patient. I will try to get to the review by the end of the day but I do not foresee it being a part of the 3.16 release since the deadline was Wednesday.
Best, Kayla
@Kayla-Morrell Do you know when you would have time to review this package? I haven't heard anything for a while and just want to make sure I didn't miss any communication. Thanks! - Sehyun
@shbrief - Sorry for the delay, with the release and being out sick last week I'm a bit behind. I will work on getting a review posted early this week.
@shbrief - I still cannot build the package locally in order to do a review. This is the error I get when trying to run R CMD build:
* creating vignettes ... ERROR
--- re-building ‘salmon.Rmd’ using rmarkdown
Loading required package: dplyr
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Warning in rm(resp) : object 'resp' not found
Warning in rm(resp) : object 'resp' not found
Quitting from lines 219-221 (salmon.Rmd)
Error: processing vignette 'salmon.Rmd' failed with diagnostics:
'gcloud auth print-access-token' failed:
ERROR: (gcloud.auth.print-access-token) Your current active account [shbrief@gmail.com] does not have any valid credentials
Please run:
$ gcloud auth login
to obtain new credentials.
For service account, please activate it first:
$ gcloud auth activate-service-account ACCOUNT
exit status: 1
--- failed re-building ‘salmon.Rmd’
SUMMARY: processing the following file failed:
‘salmon.Rmd’
Error: Vignette re-building failed.
Execution halted
It seems like the gcloud enviroment of your local machine is misconfigured - the package is building on the build system and because the build system does not have gcloud installed so no code chunks will be evaluated. Is there a reason you try to build this locally? Could you use the build system instead? Also, just to confirm the configuration issue, could you tell me the output for the following code in your local machine? Thanks!
AnVIL::gcloud_account()
AnVIL::gcloud_project()
@shbrief - Part of the review process is for the reviewer to be able to build and check the package locally. The build system may not have gcloud installed but my local system does and this may be the case for other users. This was my initial result of the code you posted:
> gcloud_exists()
[1] TRUE
> gcloud_account()
[1] "shbrief@gmail.com"
My cloud environment must have been overwritten from an early attempt at building your package. I reset my cloud environment to my account and project and was still unable to build the package. The new error is:
* creating vignettes ... ERROR
--- re-building ‘salmon.Rmd’ using rmarkdown
Loading required package: dplyr
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Warning in rm(resp) : object 'resp' not found
Warning in rm(resp) : object 'resp' not found
Quitting from lines 219-221 (salmon.Rmd)
Error: processing vignette 'salmon.Rmd' failed with diagnostics:
Workspace doesn't exit or you don't have access to it.
--- failed re-building ‘salmon.Rmd’
SUMMARY: processing the following file failed:
‘salmon.Rmd’
Error: Vignette re-building failed.
Execution halted
Best, Kayla
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