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Package Pirat
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- Repository: https://github.com/prostarproteomics/Pirat
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Hi @samWieczorek
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: Pirat
Type: Package
Title: Precursor or Peptide Imputation under Random Truncation
Description: Pirat enables the imputation of missing values (either MNARs or
MCARs) in bottom-up LC-MS/MS proteomics data using a penalized maximum
likelihood strategy. It does not require any parameter tuning, it models
the instrument censorship from the data available, it accounts for sibling
peptides correlations and it can leverage complementary transcriptomics
measurements.
Version: 0.99.0
Authors@R:
c(person(given = "Lucas",
family = "Etourneau",
email = "[email protected]",
role = c("aut")),
person(given = "Laura",
family = "Fancello",
email = " [email protected]",
role = c("aut")),
person(given = "Samuel",
family = "Wieczorek",
email = "[email protected]",
role = c("cre", "aut")),
person(given = "Nelle",
family = "Varoquaux",
email = " [email protected]",
role = c("aut")),
person(given = "Thomas",
family = "Burger",
email = "[email protected]",
role = c("aut")))
License: GPL-2
Encoding: UTF-8
biocViews: Proteomics, MassSpectrometry, Preprocessing, Software
RoxygenNote: 7.3.1
BiocViews: Proteomics, MassSpectrometry
Depends:
R (>= 4.4.0)
Imports:
reticulate, progress, ggplot2, MASS, invgamma, grDevices, stats,
graphics, rstudioapi, SummarizedExperiment
Suggests: knitr
VignetteBuilder: knitr
URL: http://www.prostar-proteomics.org/
BugReports: https://github.com/prostarproteomics/Pirat/issues
Thanks for this contribution. Please see https://bioconductor.org/packages/3.19/bioc/html/basilisk.html for the preferred approach to declaring and using python dependencies. I see that you have LBFGS optimization in python source code, and a second python file that uses it via import python.LBFGS. It would be good to indicate why a scipy optimizer won't do here. You can use reticulate within basilisk to get your sources using source_python. This would enable you to remove the miniconda installation and the manipulation of RETICULATE_PYTHON from your package. Happy to discuss further.
hi
thank you for getting back to me because I hadn't seen your first message and I've just read it. I'll see how I can modify Pirat to simplify installation. Indeed, if I could do without installing miniconda and avoid having to handle RETICULATE_PYTHON, I'd prefer that. I'll keep you posted on this concern.
I was just about to write to you because I have a question about using the set.seed function, which generates a warning when I execute the BiocCheck::BiocCheck('new-package'=TRUE) function.
I use the set.seed function to be able to reproduce exactly the results obtained which are published in an article. It's important for me to be able to continue using it. Is there a solution for keeping it and remaining compliant with Bioconductor?
Thank you for your help
A set seed can be used in examples and vignettes just make sure it is done outside any internal package code. it should be set visibly, before a function is called.
Following your advice, I modified the Pirat code and now use the basilisk package. It's much simpler. All I have to do now is fix the problem with the set.seed() function
Please let us know when it is addressed and we will re-evaluate moving this forward in the process.
Hi, I have fixed this warning with the set.seed() function. Please let me know if i have to do anything else ?
Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: ERROR before build products produced.
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/Pirat to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Please fix the ERROR in the build report before the package will move into review.
I have posted a question on the Bioc mailing list but have no answer yet. Here is the question:
As you adviced me, I use the package basilisk
I have followed the instructions of the basilisk package to build mine. Expecially, there are two files named ‘configure’ and ‘configure.win’ which are necessary to install any package which import basilisk.
However, I still have the following build error : ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual' on the Linux OS.
In my local Guithub repository, thoses files have 777 has permissions. And I do not know how to fix this issue.
Do you have any idea ?
It looks like when it was cloned onto git.bioconductor.org it lost execute permissions. I pushed up a change from a local checkout to add execute back and manually kicked off a build. Lets see what the next report says.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): Pirat_0.99.1.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/Pirat to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 58bdb6f28301dd551f1438e58556f00f842ee0e5
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): Pirat_0.99.2.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/Pirat to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: f4d4ee0a9739c2d53f5131f5cbe12a982111e5b8
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): Pirat_0.99.3.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/Pirat to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: dc6a7a98d0488aeb8dc6a0a67b7ad34d4e5daae9
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): Pirat_0.99.4.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/Pirat to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 4b35be30d2e4ab4ff9934d210c09afb146df0349
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): Pirat_0.99.5.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/Pirat to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 51b76d0c2f2237001029a6902a1e32e0270808a5
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): Pirat_0.99.6.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/Pirat to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 0b7c96cf6d5d3e23ca69ae807a3490a94cde51fa
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): Pirat_0.99.7.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/Pirat to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 7e3fd9eac2498cfafcc88f219b7ce5894aec9905
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): Pirat_0.99.4.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/Pirat to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 11be7befe78a5d64d3880109a4b92106d2eac698