CRAN checks failed

[bnaras]

@mlinderm You submitted this on CRAN , I approved, and it did not pass pretest checks. See message below. It passes on Windows, however, without that warning.

using log directory ‘/srv/hornik/tmp/CRAN/Rclusterpp.Rcheck’
* using R Under development (unstable) (2022-08-11 r82712)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘Rclusterpp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rclusterpp’ version ‘0.2.6’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Balasubramanian Narasimhan <naras@stanford.edu>’

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  Linkable (3:8)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2018-05-09 as check problems were not
    corrected despite reminders.
* 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 for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘Rclusterpp’ can be installed ... [10s/10s] WARNING
Found the following significant warnings:
  ../inst/include/Rclusterpp/util.h:9:51: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  ../inst/include/Rclusterpp/method.h:64:64: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
See ‘/srv/hornik/tmp/CRAN/Rclusterpp.Rcheck/00install.out’ for details.
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... 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 ... [2s/2s] OK
* checking Rd files ... [0s/0s] 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [0s/0s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [1s/0s] OK
  Running ‘doRUnit.R’ [0s/0s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [1s/1s] OK
* checking PDF version of manual ... OK
* checking HTML 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, 1 NOTE

[mlinderm]

I am not sure why those deprecation warnings weren't flagged before, maybe R/compiler versions? I fixed those, rebuilt and resubmitted.

[bnaras]

More issues noted by CRAN. @mlinderm Please fix what you can and make a PR for review, but don't merge. I will review and merge and submit it.

Please always write package names, software names and API (application programming interface) names in single quotes in title and description. e.g: --> 'C++'

If there are references describing the methods in your package, please add these in the description field of your DESCRIPTION file in the form
authors (year) <doi:...>
authors (year) <arXiv:...>
authors (year, ISBN:...)
or if those are not available: [<https:...>](https://github.com/nolanlab/Rclusterpp/issues/...)
with no space after 'doi:', 'arXiv:', 'https:' and angle brackets for auto-linking.
(If you want to add a title as well please put it in quotes: "Title")

The Description field is intended to be a (one paragraph) description of what the package does and why it may be useful. Please add a few more details about the package functionality and implemented methods in your Description text.


Please always make sure to reset to user's options(), working directory or par() after you changed it in examples and vignettes and demos. -> tests/doRUnit.R
e.g.:
...
oldwd <- getwd()
...
setwd(...)
...
setwd(oldwd)
...

Please ensure that your functions do not write by default or in your examples/vignettes/tests in the user's home filespace (including the package directory and getwd()). This is not allowed by CRAN policies.
Please omit any default path in writing functions. In your examples/vignettes/tests you can write to tempdir().

Please do not modifiy the .GlobalEnv. This is not allowed by the CRAN policies.

Please fix and resubmit.

[mlinderm]

I addressed the first set of issues, but was not sure about:

Please ensure that your functions do not write by default or in your examples/vignettes/tests in the user's home filespace (including the package directory and getwd()). This is not allowed by CRAN policies.
Please omit any default path in writing functions. In your examples/vignettes/tests you can write to tempdir().

The only function I can think of that has paths is the skeleton function, but there we use the same default arguments as the package.skeleton function in utils.