Closed mooredf22 closed 2 years ago
Hi @mooredf22
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: protlocassigndoc
Title: Documentation for protlocassign package for constrained proportional assignment
Version: 0.99.0
Date: 2022-04-27
Authors@R:
person(given = "Peter",
family = "Lobel",
role = c("aut"),
email = "lobel@cabm.rutgers.edu")
person(given = "Dirk",
family = "Moore",
role = c("cre","aut"),
email = "dirkfmoore@gmail.com")
BiocType: Workflow
Description: This package constains documentation in the form of tutorials
(in vignette format) for the protlocassign package.
This package fits a constrained proportional assignment (cpa)
model to mass spectrometry data
to proportionally assign proteins to subcellular locations.
The package itself is here:
http://github.com/mooredf22/protlocassign
License: GPL-3
Encoding: UTF-8
LazyData: false
Depends:
R (>= 4.1.0),
lme4,
knitr
RoxygenNote: 7.1.2
biocViews: Proteomics, MassSpectrometry
VignetteBuilder: knitr
URL: http//github.com/mooredf22/protlocassigndoc
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This documentation package for the "protlocassign" package requires loading "protlocassign", which is the reason for the error. This package is currently under review (issue 2541) for Bioconductor and thus apparently cannot be directly loaded. Thus, it appears that we must wait for this other review to be completed before this one (protlocassigndoc) can move forward.
Looks like you should have used the related packages protocol. @lshep
I see, thanks. Could you point me to where I can find information about the "related packages protocol"? I have searched Bioconductor for that but have not found a description.
which is linked from 1.5 of the general guidelines
I re-submitted protlocassign (#2541) according to the guidelines and it ran without errors. It appears, though, that that issue and the current one need to be merged. Let me know if I need to do anything else to make that happen.
From the link posted above, it look like you need to add it to the protlocassign
issue by adding a comment containing
AdditionalPackage: https://github.com/mooredf22/protlocassigndoc
If we want to combined these issues and go the additional package route -- I will need to do some manual adjustments. @mooredf22 would you like to move this review to the other as an additional package?
Yes, for sure. Thanks for taking care of this. The DESCRIPTION file of protlocassign already references protlocassigndoc. Let me know if I need to do anything else on my end to make this happen.Sent from my iPhoneOn Oct 11, 2022, at 8:42 AM, lshep @.***> wrote: If we want to combined these issues and go the additional package route -- I will need to do some manual adjustments. @mooredf22 would you like to move this review to the other as an additional package?
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I manually updated the database to point this package to the 1541 issue. If you do a valid version bump and push to git.bioconductor.org for protlocassigndoc you should now see the build report results in issue 1541 now and you should be able to access the version of the package under review. @lgatto that will mean you should review both of these packages under the 1541 issue and not accept unless they are both ready.
I stand corrected. It didn't work to manually reassign it. Could you please use the AdditionalPackage: https://github.com/mooredf22/protlocassigndoc
in issue 1541 please to link the issues.
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This is a workflow package that is connected to the "protlocassign" package, Issue #2541. Since this workflow package consists of more extensive documentation than can fit in the protlocassign package, these two submissions should be considered together.