samWieczorek commented 4 months ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Repository: https://github.com/prostarproteomics/Pirat

Confirm the following by editing each check box to '[x]'

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bioc-issue-bot commented 4 months ago

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 = "lucas.etourneau@univ-grenoble-alpes.fr", 
role = c("aut")),
    person(given = "Laura", 
family = "Fancello", 
email = " laura.fancello@cea.fr", 
role = c("aut")),
    person(given = "Samuel", 
family = "Wieczorek",
email = "samuel.wieczorek@cea.fr",
role = c("cre", "aut")),
    person(given = "Nelle", 
family = "Varoquaux",
email = " nelle.varoquaux@univ-grenoble-alpes.fr",
role = c("aut")),
    person(given = "Thomas", 
family = "Burger",
email = "thomas.burger@cea.fr",
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

vjcitn commented 4 months ago

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.

lshep commented 3 months ago

may we expect updates to address the above concern?

samWieczorek commented 3 months ago

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

lshep commented 3 months ago

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.

samWieczorek commented 3 months ago

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

lshep commented 3 months ago

Please let us know when it is addressed and we will re-evaluate moving this forward in the process.

samWieczorek commented 3 months ago

Hi, I have fixed this warning with the set.seed() function. Please let me know if i have to do anything else ?

bioc-issue-bot commented 3 months ago

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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bioc-issue-bot commented 3 months ago

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lshep commented 3 months ago

Please fix the ERROR in the build report before the package will move into review.

samWieczorek commented 2 months ago

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 ?

lshep commented 2 months ago

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.

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vjcitn commented 2 months ago

make sure you remove any .Rproj files and bump version

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LiNk-NY commented 2 months ago

Hi @samWieczorek

Thank you for your submission. Please see the review below and respond to each item for the review to continue.

Best regards, Marcel

Pirat #3308

DESCRIPTION

Looks good.

NAMESPACE

Looks good.
There seems to be a shiny app provided as part of the package. Consider moving that functionality to a dedicated shiny package.

vignettes

Avoid using 1:N notation and use seq_len or seq instead in the "transcriptomic integration" section.
Minor: which is not needed for subsetting when a logical vector would work the same, e.g., in "samples-wise correlations" section. If there are NAs, use na.rm = TRUE with colSums, etc.
Minor: Consider wrapping text to a max character limit of 80 columns. It is easier to review and read.

R

Add a description to all fields in the data documentation (@format field in R/doc-data.R)
Remove or fix commented code in the estimate_gamma(), impute_block_llk_reset(), impute_block_llk_reset_PG() functions, etc.
It seems like mcar is not an override for gamma_1 to be 0 as it is in a multiple or | statement. Provide a more accurate description in the documentation for estimate_gamma.
Separate plots and calculation functions e.g., in estimate_psi_df
Rename install_Pirat to more accurately reflect the intention of the function.
Move the shiny app to another package. Not all users may want to use the shiny functionality.
Use more descriptive argument names e.g., ARG_VALUE_1 does not help the user.
Avoid using cat in functions that are not print or show methods, e.g., in pipeline_llkimpute.
Provide the full list options in the argument as a character vector and use match.arg in the body of the function, e.g., for extension argument in pipeline_llkimpute, set it to extension = c("a", "b", "c"). This way the user can see the full list of options in the usage section of the documentation.
Avoid using 1:N notation and use seq_len or seq for for loops; see get_indexes_embedded_prots
Consider moving plotting functions to another package. The package currently has basilisk / python deps, shiny, and ggplot. This would render the package fragile if any of those components begin to fail.
Avoid nested for loops where possible; see split_large_pg.
AFAIK, basilisk and reticulate operate differently yet you use them both. Can you explain why both are needed?
Resolve the following R CMD check NOTE:

* checking R code for possible problems ... NOTE
estimate_gamma: no visible global function definition for ‘lm’
estimate_psi_df: no visible binding for global variable ‘var’
estimate_psi_df: no visible binding for global variable ‘x’
mod_Pirat_server : <anonymous>: no visible global function definition
  for ‘observe’
plot_pep_correlations: no visible global function definition for ‘cor’
plot_pep_correlations: no visible binding for global variable ‘group’
remove_NA_pep_reset: no visible global function definition for
  ‘remove_pep_from_idx’
Undefined global functions or variables:
  cor group lm observe remove_pep_from_idx var x
Consider adding
  importFrom("stats", "cor", "lm", "var")
to your NAMESPACE file.

/

Add .github folder to .Rbuildignore

tests

Increase coverage where needed:

> covr::package_coverage(type = "all")
Pirat Coverage: 68.83%
R/mod_Pirat.R: 0.00%
R/reset_data.R: 0.00%
R/split_funcs.R: 48.28%
R/plots.R: 63.46%
R/pirat_utils.R: 82.29%
R/pipeline_impute.R: 92.78%
R/estimate_funcs.R: 93.88%
R/install.R: 100.00%
R/SE.R: 100.00%
R/utils.R: 100.00%

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samWieczorek commented 2 months ago

Hi, I've corrected almost half of your comments. The rest are in the hands of a colleague who looks after certain parts of the code in Pirat.

I have 2 questions if I don't manage to fix everything by the time of release: what will the status of the package be?

Is it accepted and remains in development?
it's not put into development and its acceptance process is blocked?

About your question relative to the use of the reticulate package. I need it for two reasons:

In the documentation of the package basilisk, there is an example on how to use their package an they explicitely use a function from the reticulate package to import Python libraries into the environment -Pirat uses the python package Torch but we have modified two files of this package. Theses files are in the inst/python directory. When I load the Python environment with functions of the package basilisk, I have to source those two customized Python scripts to overwrite the ones tha come with the library Torch. The function to do that does not exist in the basilisk package

Bioconductor / Contributions

Package Pirat #3308

Pirat #3308

DESCRIPTION

NAMESPACE

vignettes

R

/

tests