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jirotubuyaki / hmds

hmds: An R Package for Heuristic High and Multi Dimensional Scaling

Home Page:https://jirotubuyaki.github.io/hmds/

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Resolve R CMD check warnings

kevinushey opened this issue · comments

commented

When running devtools::check() within RStudio, I see:

==> Rcpp::compileAttributes()

* Updated R/RcppExports.R

==> devtools::check(document = FALSE)

Setting env vars ---------------------------------------------------------------
CFLAGS  : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building hmds ------------------------------------------------------------------
'/Users/kevin/r/r-devel-sanitizers/lib/R/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD build '/Users/kevin/r/pkg/hmds'  \
  --no-resave-data --no-manual 

* checking for file ‘/Users/kevin/r/pkg/hmds/DESCRIPTION’ ... OK
* preparing ‘hmds’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
Warning: ‘inst/doc’ files
    ‘my-vignette.Rmd’, ‘my-vignette.R’
  ignored as vignettes have been rebuilt.
  Run R CMD build with --no-build-vignettes to prevent rebuilding.
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘hmds_1.0.tar.gz’

Setting env vars ---------------------------------------------------------------
_R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
_R_CHECK_CRAN_INCOMING_           : FALSE
_R_CHECK_FORCE_SUGGESTS_          : FALSE
Checking hmds ------------------------------------------------------------------
'/Users/kevin/r/r-devel-sanitizers/lib/R/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD check  \
  '/var/folders/tm/5dt8p5s50x58br1k6wpqnwx00000gn/T//RtmpDYP4R6/hmds_1.0.tar.gz'  \
  --as-cran --timings --no-manual 

* using log directory ‘/Users/kevin/r/pkg/hmds.Rcheck’
* using R Under development (unstable) (2017-04-22 r72596)
* using platform: x86_64-apple-darwin16.5.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --as-cran’
* checking for file ‘hmds/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘hmds’ version ‘1.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘hmds’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘paper’
* 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 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 ... 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘hmds/libs/hmds.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: 1 WARNING, 3 NOTEs

See
  ‘/Users/kevin/r/pkg/hmds.Rcheck/00check.log’
for details.


checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘paper’

checking compiled code ... NOTE
File ‘hmds/libs/hmds.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
 WARNING
‘qpdf’ is needed for checks on size reduction of PDFs
R CMD check results
0 errors | 0 warnings | 3 notes

R CMD check succeeded

You should resolve these if possible. The NOTEs related to .travis.yml, LICENSE and paper could be resolved by using a .Rbuildignore file to ensure that these files aren't included with the created R package. See https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Building-package-tarballs for more details.

In addition, the Read-and-delete-me file can be removed.