cran-comments.md

In osmose-model/osmose: Object Oriented Simulator of Marine Ecosystems

version 3.3.4

round 3

Remove reference to vignette, leave only package URL

round 2

Make URL for startup canonical

round 1

No more use of the user cache dir, which is contrary to CRAN policies and prevents a built for Mac Os X. Instead, data are either downloaded on a temporary directory or in the one defined in the OSMOSE_DIR directory (set from .Renviron file.

version 3.3.3

round 5

The cache flushing of the Java executables is forced in the vignettes. This is to force the flushing of the corrupted JAR file that may have remained on CRAN cache directory.

round 4

Jar files are now downloaded through Zip files. Direct downloading of the jar files caused errors in Windows.

round 3

Size has been reduced by removing the heavy data files and Java libraries. These are downloaded into the user cache file, following what is done in the BIOMASS package.

round 2

` Found the following (possibly) invalid URLs: URL: https://cran.rstudio.com/web/packages/osmose/index.html From: README.md Status: 200 Message: OK CRAN URL not in canonical form

Canonical: https://CRAN.R-project.org/package=osmose

Size of tarball: 33864553 bytes

Not more than 5 MB for a CRAN package, please. `

The URL has been corrected as suggested.

Regarding the size of the package, as we said in our previous message, we were not able to reduce the size of the package, since its heavy size is mainly due to an external Java library needed to run the package (netcdfAll-4.6.6.jar) and to external data needed to run the demo scripts (NetCDF forcings).

We therefore have no possibility to reduce the size of the package. Since there are already packages on the CRAN (geomapdata for instance is 26 Mo), we therefore ask for the possibility to submit the package with its actual size.

round 1

Package has FOSS license, installs .class/.jar but has no 'java' directory.

Found the following (possibly) invalid URLs: URL: http://cran.r-project.org/package=osmose From: README.md CRAN URL not in canonical form URL: http://cran.rstudio.com/web/packages/osmose/index.html From: README.md Status: 200 Message: OK CRAN URL not in canonical form Canonical CRAN.R-project.org URLs use https.

Size of tarball: 32817276 bytes

Not more than 5 MB for a CRAN package, please.

Please fix and resubmit.

The "java" directory has been added and put to .Rinstignore.

The CRAN URLs have been corrected.

However, we were not able to reduce the size of the package, since its heavy size is mainly due to an external Java library needed to run the package (netcdfAll-4.6.6.jar) and to external data needed to run the demo scripts (NetCDF forcings).

version 0.1.2

Adding more plot functions Correction of a bug in the call to Java Update in the java code (v3u3)

version 0.1.1

round 8

Removing of the 0.1.0 version tar.gz file which is responsible for a note on the automatic check

round 7

Update in version name

version 0.1.0

round 6

Update in Java version name, as suggested by Brian Ripley

round 5

Thanks, please add more small executable examples in your Rd-files (code coverage 30.35%).

This has been done (sizeSpectrum, getMortality, getAverageMortality, getMortalityDeviation, getFishingMortality, getFishingBaseRate functions)

round 4

Sample CSV files have been added to run examples.

round 3

Thanks, please write the title in title case: Object-Oriented Simulator of Marine Ecosystems

This has been done

Please write package names and software names in single quotes (e.g. 'FishBase').

Please add an URL for 'FishBase' in your description text in the form or with angle brackets for auto-linking and no space after 'http:' and 'https:'.

Please add a reference for the OSMOSE model in the 'Description' field of your DESCRIPTION file in the form authors (year) authors (year) authors (year, ISBN:...) with no space after 'doi:', 'arXiv:' and angle brackets for auto-linking.

The FishBase website has been added and single quotes have been added around names. References have been added.

Your examples are wrapped in \dontrun{}, hence nothing gets tested. Please unwrap the examples if that is feasible and if they can be executed in < 5 sec for each Rd file or create additionally small toy examples. Something like \examples{ examples for users: executable in < 5 sec for checks \dontshow{ examples for checks: executable in < 5 sec together with the examples above not shown to users } donttest{ further examples for users (not used for checks) } } would be desirable.

There is an example for you function buildConfiguration(), but it looks like the function is not exported. Please check.

Please ensure that your function do not write by default or in your examples in the user's home filespace. tempdir() is allowed.

@examples statements have been replaced by @usage statements. The buildconfiguration function was not exported since not yet finished. It has thus been commented out.

License: CeCILL Imports: graphics, grDevices, rlist, stats, stringr, utils

The maintainer confirms that he or she has read and agrees to the CRAN policies.

Submitter's comment: The title has been changed as suggested

=================================================

Original content of DESCRIPTION file:

Package: osmose Type: Package Title: Object-oriented Simulator of Marine Ecosystems Version: 0.1.0 Date: 2017-12-06 Authors@R: c( person("Yunne-Jai", "Shin", role="aut"), person("Travers", "Morgane", role="aut"), person("Verley", "Philippe", role="aut"), person("Ricardo", "Oliveros-Ramos", role = "aut"), person("Laure", "Velez", role = "aut"), person("Nicolas", "Barrier", email="[e-mail]", role="cre"), person("Criscely", "Lujan", role="ctb"), person("Michael", "Hurtado", role = "ctb") ) Description: The multispecies and Individual-based model (IBM) OSMOSE focuses on fish species. This model assumes opportunistic predation based on spatial co-occurrence and size adequacy between a predator and its prey (size-based opportunistic predation). It represents fish individuals grouped into schools, which are characterized by their size, weight, age, taxonomy and geographical location (2D model), and which undergo major processes of fish life cycle (growth, explicit predation, natural and starvation mortalities, reproduction and migration) and fishing exploitation. The model needs basic biological parameters that are often available for a wide range of species, and which can be found in FishBase for instance, and fish spatial distribution data. This package provides tools to build a model and run simulations using the OSMOSE model. See http://www.osmose-model.org/ for more details. License: CeCILL Encoding: UTF-8 Depends: R (>= 2.15) Imports: graphics, grDevices, rlist, stats, stringr, utils URL: http://www.osmose-model.org/ LazyData: FALSE BugReports: https://github.com/osmose-model/osmose/issues SystemRequirements: Java JDK 1.7 or higher RoxygenNote: 6.0.1 NeedsCompilation: no Packaged: 2017-12-08 12:12:37 UTC; nbarrier Author: Yunne-Jai Shin [aut], Travers Morgane [aut], Verley Philippe [aut], Ricardo Oliveros-Ramos [aut], Laure Velez [aut], Nicolas Barrier [cre], Criscely Lujan [ctb], Michael Hurtado [ctb] Maintainer: Nicolas Barrier [e-mail]

round 2

Dear maintainer,

package osmose_0.1.0.tar.gz does not pass the incoming checks automatically, please see the pre-test at: https://win-builder.r-project.org/incoming_pretest/171207_074550_osmose_010/00check.log Status: 3 WARNINGs, 3 NOTEs

Best regards, CRAN teams' auto-check service

Upss.

round 1

Thanks, we see:

Non-FOSS package license (file LICENSE)

The license has be updated to CeCILL

Suggests or Enhances not in mainstream repositories: kali

Removed from Suggests.

Found the following (possibly) invalid URLs: URL: http://cran.r-project.org/package=osmose From: README.md CRAN URL not in canonical form URL: http://cran.rstudio.com/web/packages/osmose/index.html (moved to https://cran.rstudio.com/web/packages/osmose/index.html) From: README.md Status: 404 Message: Not Found CRAN URL not in canonical form Canonical CRAN.R-project.org URLs use https.

README.md added to .Rbuildignore

The Title field starts with the package name.

The Description field should not start with the package name, 'This package' or similar.

DESCRIPTION file has been edited.

The Date field is over a month old.

Updated.

• checking package dependencies ... NOTE Package suggested but not available for checking: 'kali'

Kali imports has been removed.

Please fix and resubmit. Best, Uwe Ligges

Thanks for the comments.

osmose-model/osmose documentation built on Feb. 16, 2023, 5 a.m.