cran-comments.md

In andrewGhazi/malacoda: Bayesian Analysis of High-Throughput Genomic Assays

Resubmission

This is a resubmission of malacoda, which was previously released May 31 2019. In this submission:

• We have explained the acronyms in the description field.
• We have changed the not-easily-suppressed print() statements to use message() instead. We have also enclosed messages in if blocks with a "verbose"" condition that can be turned off by the user.
• We have removed the examples with commented out code, leaving just the parts necessary to run the example.
• We have tried to speed up the examples in order to reduce the check time.

Previous submission comments

• We have added runnable examples for all exported functions with one exception, count_barcodes(). count_barcodes() calls external bioinformatics software (the FAST-X toolkit mentioned in the SystemRequirements field) and hence we have still left it wrapped in \dontrun{}. However the example there will run if that software is installed. count_barcodes() is a convenient utility function but not essential to the core purpose of this package. count_barcodes() immediately checks if the FASTX-Toolkit is installed with Sys.which() and stops and gives an installation URL if it's not.
• We have corrected the URL in the documentation for u_deepsea
• There was a question with our previous submission if there was a method reference/citation we could put in the Description. We have not published this method yet but we were hoping to have it on CRAN before doing so. We have a manuscript in preparation that we aim to submit in the next few months.

Test environments

• local Linux Mint 19.1, R 3.6.1
• Ubuntu Linux 16.04 LTS, R-release, GCC via Rhub
• Fedora Linux, R-devel, clang, gfortran via Rhub
• macOS 10.11 El Capitan, R-release via Rhub

Windows is not a target platform for us, so Windows-related errors/warnings/build-failures do not bother us if they are not a problem for the CRAN maintainers.

R CMD check results

There were no ERRORs or WARNINGs.

There were 4 NOTEs: * checking CRAN incoming feasibility ... NOTE Maintainer: 'Andrew Ghazi [e-mail]'

New submission

Possibly mis-spelled words in DESCRIPTION: CRISPR (9:84, 9:144) MPRA (9:75, 9:127) barcodes (9:132) gRNAs (9:151)

This is a resubmission of this package (my first) after previous submission was rejected do to some initial problems.

The words CRISPR, MPRA, barcodes, and gRNAs are all spelled correctly. These seem to be false positives from the spell-checker. We have used devtools::spell_check() and didn't spot any problems.

• checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

GNU make was added as a system requirement by rstantools::rstan_package_skeleton(). Removing this requirement would likely interfere with the compilation of the Stan models in this package.

• on local Linux Mint 19.1, R 3.6.1: checking compilation flags used ... NOTE Compilation used the following non-portable flag(s): ‘-march=native’

The -march=native flag is recommended by the RStan team as part of our Stan installation. We have tried leaving off this flag and it doesn't seem to cause any problems, so we don't think its absence will cause issues.

• checking installed package size ... NOTE installed size is 41.7Mb sub-directories of 1Mb or more: doc 1.2Mb libs 39.2Mb

The large compiled libraries come from the package's Stan models and the associated pre-compiled C++ modules which are fairly large. There doesn't seem to be a way of reducing the size of these compiled Stan models, and they are essential to the function of the package.

Downstream dependencies

There are no downstream dependencies for this package.

Thank you! :)

andrewGhazi/malacoda documentation built on Aug. 2, 2020, 12:54 a.m.