Category talk:OpasnetUtils

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CRAN submission -- Teemu R 13:06, 4 June 2013 (EEST)

Links:

To get a package hosted on CRAN, it should be well documented and pass R CMD check --as-cran with no errors and preferably no warnings.

"Please ensure that R CMD check --as-cran has been run on the tarball to be uploaded before submission. This should be done with the current release of R or (preferably) R-devel or R-patched. As “Writing R Extensions” used to say: Please ensure that you can run through the complete procedure with only warnings that you understand and have reasons not to eliminate. In principle, packages must pass R CMD check without warnings or significant notes to be admitted to the main CRAN package area. If there are warnings or notes you cannot eliminate (for example because you believe them to be spurious) send an explanatory note as part of your covering email. "

Current output of R CMD check --as-cran: 

C:\Users\Teemu\workspace\opasnet_utils>R CMD check trunk --as-cran
* using log directory 'C:/Users/Teemu/workspace/opasnet_utils/trunk.Rcheck'
* using R version 2.15.2 (2012-10-26)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* checking for file 'trunk/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OpasnetUtils' version '0.1.10'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Einari Happonen <einari.happonen@thl.fi>'
New submission
Non-FOSS package license (CC BY-SA 3.0)
* 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:
  .svn
  R/.svn
  man/.svn
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking whether package 'OpasnetUtils' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... WARNING
Found the following file(s) with non-portable file names:
  R/.svn/text-base/GIS methods.r.svn-base
  R/GIS methods.r
These are not fully portable file names.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  CC BY-SA 3.0
Standardizable: FALSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Found the following directory(s) with names of version control directories:
  ./.svn
  ./R/.svn
  ./man/.svn
These should not be in a package tarball.
* checking R files for non-ASCII characters ... WARNING
Found the following files with non-ASCII characters:
  Tidy.r
Portable packages must use only ASCII characters in their R code,
except perhaps in comments.
Use \uxxxx escapes for other characters.
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
summary:
  function(object, ...)
summary.bring:
  function(page, base)

See section 'Generic functions and methods' of the 'Writing R
Extensions' manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
WriteData: no visible binding for global variable 'asd'
WriteData: no visible binding for global variable 'indices'
objects.decode: no visible global function definition for 'AES'
objects.encode: no visible global function definition for 'AES'
opbase.old.locations.read: no visible global function definition for
  'odbcConnect'
opbase.old.locations.read: no visible global function definition for
  'sqlQuery'
opbase.old.locations.read: no visible global function definition for
  'odbcClose'
opbase.old.read: no visible global function definition for
  'odbcConnect'
opbase.old.read: no visible global function definition for 'sqlQuery'
opbase.old.read: no visible global function definition for 'odbcClose'
opbase.old.write: no visible global function definition for
  'odbcConnect'
opbase.old.write: no visible global function definition for 'sqlQuery'
opbase.old.write: no visible global function definition for 'odbcClose'
convert.units,data.frame: no visible binding for global variable
  'tounit'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object 'C:/Users/Teemu/workspace/opasnet_utils/
trunk/man/op_base.Rd':
  'RODBC'

See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'CheckCollapse' 'CheckDecisions' 'CheckInput' 'CheckMarginals'
  'CollapseMarginal' 'CollapseTableParser' 'ComputeDependencies'
  'DecisionTableParser' 'EvalOutput' 'Fetch2'
  'GIS.Concentration.matrix' 'GIS.Exposure' 'Ovariable' 'PTable'
  'apply.decisions' 'convert.units' 'ddata_apply' 'decisions.apply'
  'dropall' 'fetch' 'fillna' 'init.assessment' 'interpret'
  'make.oassessment' 'make.ovariable' 'movariable' 'oapply'
  'objects.decode' 'objects.encode' 'objects.get' 'objects.latest'
  'objects.put' 'objects.store' 'opasnet.csv' 'opasnet.data'
  'opbase.data' 'opbase.locations' 'opbase.obj.exists'
  'opbase.old.data' 'opbase.old.locations' 'opbase.old.upload'
  'opbase.series' 'opbase.upload' 'oprint' 'orbind' 'result'
  'summary.bring' 'tidy' 'xtable'
Undocumented S4 methods:
  generic 'Math' and siglist 'ovariable'
  generic 'Ops' and siglist 'numeric,ovariable'
  generic 'Ops' and siglist 'ovariable,numeric'
  generic 'Ops' and siglist 'ovariable,ovariable'
  generic 'convert.units' and siglist 'data.frame'
  generic 'convert.units' and siglist 'ovariable'
  generic 'interpret' and siglist 'character'
  generic 'make.ovariable' and siglist 'data.frame'
  generic 'make.ovariable' and siglist 'list'
  generic 'make.ovariable' and siglist 'ovariable'
  generic 'make.ovariable' and siglist 'vector'
  generic 'merge' and siglist 'data.frame,ovariable'
  generic 'merge' and siglist 'numeric,ovariable'
  generic 'merge' and siglist 'ovariable,data.frame'
  generic 'merge' and siglist 'ovariable,numeric'
  generic 'merge' and siglist 'ovariable,ovariable'
  generic 'oprint' and siglist 'ovariable'
  generic 'plot' and siglist 'oassessment'
  generic 'plot' and siglist 'ovariable'
  generic 'print' and siglist 'oassessment'
  generic 'print' and siglist 'ovariable'
  generic 'summary' and siglist 'ovariable'
  generic 'update' and siglist 'ovariable'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Functions/methods with usage in documentation object 'DataframeToArray' but not
in code:
  DataframeToArray

Codoc mismatches from documentation object 'op_base':
op_baseGetData
  Code: function(dsn, ident, ...)
  Docs: function(dsn, ident, include = NULL, exclude = NULL, series_id
                 = NULL, iterations = NULL)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    include exclude series_id iterations
  Mismatches in argument names:
    Position: 3 Code: ... Docs: include
op_baseGetLocs
  Code: function(dsn, ident, ...)
  Docs: function(dsn, ident, series_id = NULL)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    series_id
  Mismatches in argument names:
    Position: 3 Code: ... Docs: series_id
op_baseWrite
  Code: function(dsn, input, ...)
  Docs: function(dsn, input, ident = NULL, name = NULL, unit = NULL,
                 objtype_id = NULL, who = NULL, acttype = NULL, sort =
                 TRUE)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    ident name unit objtype_id who acttype sort
  Mismatches in argument names:
    Position: 3 Code: ... Docs: ident

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... ERROR
Running examples in 'OpasnetUtils-Ex.R' failed
The error most likely occurred in:

> ### Name: DataframeToArray
> ### Title: Transform data.frames of certain structure to arrays
> ### Aliases: DataframeToArray
> ### Keywords: methods
>
> ### ** Examples
>
>   DataframeToArray(data.frame(Country=rep(c("Finland", "Sweden"),each=4),
+   Age=rep(c("<4","5-14", "15-59", ">60"),2), Result=runif(2*4, 2, 11)))
Error: could not find function "DataframeToArray"
Execution halted

Issues:

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