Release/5.0.2

[dcollins15]

Release SeuratObject v5.0.2

• Bump version
• Update CRAN comments
• Update changelog
• Win-builder
• Mac-builder
• Submit to CRAN
• Resolve issues with submission
• Re-submit to CRAN

Additional Changes:

• Added an entry for the ... param in the docstring for the Radius generic - this seems to be required for CRAN checks to pass, at least on my local machine

[dcollins15]

CRAN rejected our initial submission with the following message:

Package has help file(s) containing install/render-stage \Sexpr{}
expressions but no prebuilt PDF manual.

Any idea what's going on here @mojaveazure? Maybe related to r-lib/lifecycle#39?

[mojaveazure]

The PDF is bundled in /build, not /inst; my guess is there's an issue with LaTeX on your system. Check the logs from R CMD build to see why the PDF failed to build. In the mean time, here's a tarball built from release/5.0.2 with the manual in it (sorry for the mix of \ and /; I'm on Windows so I get to deal with all sorts of Windows vs *nix oddities)

 PS C:\Users\Paul Hoffman> tar -tvzf .\SeuratObject_5.0.2.tar.gz SeuratObject/build/*.pdf
-rw-rw-rw-  0 0      0      416556 May 07 11:10 SeuratObject/build/SeuratObject.pdf

SeuratObject_5.0.2.tar.gz

[mojaveazure]

For reference, R CMD check output

PDF check:

* checking PDF version of manual ... OK

Full log:

PS C:\Users\Paul Hoffman> R.exe CMD check --as-cran .\SeuratObject_5.0.2.tar.gz
* using log directory 'C:/Users/Paul Hoffman/SeuratObject.Rcheck'
* using R version 4.2.2 (2022-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--as-cran'
* checking for file 'SeuratObject/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeuratObject' version '5.0.2'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Rahul Satija <[email protected]>'

New maintainer:
  Rahul Satija <seurat@nygenome.org>
Old maintainer(s):
  Paul Hoffman <seurat@nygenome.org>

Suggests or Enhances not in mainstream repositories:
  BPCells
Availability using Additional_repositories specification:
  BPCells   yes   https://bnprks.r-universe.dev
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'SeuratObject' can be installed ... [54s] WARNING
Found the following significant warnings:
  Warning: package 'sp' was built under R version 4.2.3
See 'C:/Users/Paul Hoffman/SeuratObject.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [27s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [39s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
SaveSeuratRds 2.51   0.14       6
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'C:/Users/Paul Hoffman/SeuratObject.Rcheck/00check.log'
for details.

Ignore the warning, that's just due to Windows binary builds

[dcollins15]

v5.0.2 is on its way to CRAN! See https://cran.r-project.org/web/packages/SeuratObject/index.html