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Beta versions of new DataSHIELD server functions

License: GNU General Public License v3.0

R 100.00%

dsbetatest's Introduction

datashield

DataSHIELD meta-package (server side)

dsbetatest's People

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stuartwheater tombisho patrickfischer1 intgren davraam rapus95

dsbetatest's Issues

unListDS.o - devtools::check note

devtools::check produces the following note

unListDS.o: no visible binding for global variable ‘newobj.class’

asListDS.o - devtools::check note

devtools::check produces the following note

asListDS.o: no visible binding for global variable ‘newobj.class’

lexisDS3.o - devtools::check note

devtools::check produces the following note

lexisDS3.o: no visible binding for global variable ‘messageobj’

tapplyDS.assign.o - devtools::check note

devtools::check produces the following note

tapplyDS.assign.o: no visible binding for global variable ‘current.factor’
tapplyDS.assign.o: no visible binding for global variable 'factor1.levels’
tapplyDS.assign.o: no visible binding for global variable ‘factor2.levels’
tapplyDS.assign.o: no visible binding for global variable ‘sd’
tapplyDS.assign.o: no visible binding for global variable ‘quantile’

tapplyDS.o - devtools::check note

devtools::check produces the following note

tapplyDS.o: no visible binding for global variable ‘current.factor’
tapplyDS.o: no visible binding for global variable ‘factor1.levels’
tapplyDS.o: no visible binding for global variable ‘factor2.levels’
tapplyDS.o: no visible binding for global variable ‘sd’
tapplyDS.o: no visible binding for global variable ‘quantile’

glmSLMADS2.o does not have disclosure traps in it

While working on SLMA of mixed models I have noticed that the glmSLMADS2.o function does not have the built in disclosure traps.
The glmDS2.o function has disclosure traps for things like over saturated models or categories with too few individuals.

Is this by design or does it need fixing? It would be useful to know if it is by design because then I won't have to do it for mixed models!

Package does not pass the devtools check

Running devtools::check() (or selecting Check in Build tab of Rstudio) reports the following:

* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --as-cran’
* checking for file ‘dsBetaTest/DESCRIPTION’ ... OK
* this is package ‘dsBetaTest’ version ‘0.4.3’
* package encoding: UTF-8
* 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 ‘dsBetaTest’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘dsBase’ ‘dsGraphics’ ‘dsModelling’ ‘dsStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BooleDS.o: no visible global function definition for ‘complete.cases’
asListDS.o: no visible binding for global variable ‘newobj.class’
covDS.o: no visible global function definition for ‘complete.cases’
covDS.o: no visible global function definition for ‘var’
dataFrameDS.o: no visible global function definition for
  ‘complete.cases’
glmDS1.o: no visible global function definition for ‘as.formula’
glmDS1.o: no visible global function definition for ‘glm’
glmDS1.o: no visible global function definition for ‘glm.control’
glmDS1.o: no visible global function definition for ‘complete.cases’
glmDS2.o: no visible global function definition for ‘complete.cases’
glmDS2.o: no visible global function definition for ‘as.formula’
glmDS2.o: no visible global function definition for ‘glm’
glmDS2.o: no visible global function definition for ‘glm.control’
glmSLMADS2.o: no visible global function definition for
  ‘complete.cases’
glmSLMADS2.o: no visible global function definition for ‘as.formula’
glmSLMADS2.o: no visible global function definition for ‘glm’
lexisDS1.o: no visible global function definition for ‘runif’
lexisDS2.o: no visible global function definition for ‘ave’
lexisDS2.o: no visible global function definition for ‘complete.cases’
lexisDS3.o: no visible binding for global variable ‘messageobj’
meanSdGpDS : FUN.var: no visible global function definition for ‘var’
meanSdGpDS: no visible global function definition for ‘complete.cases’
rBinomDS.o: no visible global function definition for ‘rbinom’
rNormDS.o: no visible global function definition for ‘rnorm’
rPoisDS.o: no visible global function definition for ‘rpois’
rUnifDS.o: no visible global function definition for ‘runif’
reShapeDS.o: no visible global function definition for ‘reshape’
recodeValuesDS1.o: no visible global function definition for
  ‘complete.cases’
recodeValuesDS2.o: no visible global function definition for
  ‘complete.cases’
rilmDS.b: no visible global function definition for ‘complete.cases’
tTestFDS2: no visible global function definition for ‘complete.cases’
tTestFDS2: no visible global function definition for ‘as.formula’
tTestFDS2: no visible global function definition for ‘glm’
tTestFDS2: no visible global function definition for ‘glm.control’
tapplyDS.assign.o: no visible global function definition for
  ‘complete.cases’
tapplyDS.assign.o: no visible binding for global variable
  ‘current.factor’
tapplyDS.assign.o: no visible binding for global variable
  ‘factor1.levels’
tapplyDS.assign.o: no visible binding for global variable
  ‘factor2.levels’
tapplyDS.assign.o: no visible binding for global variable ‘sd’
tapplyDS.assign.o: no visible binding for global variable ‘quantile’
tapplyDS.o: no visible global function definition for ‘complete.cases’
tapplyDS.o: no visible binding for global variable ‘current.factor’
tapplyDS.o: no visible binding for global variable ‘factor1.levels’
tapplyDS.o: no visible binding for global variable ‘factor2.levels’
tapplyDS.o: no visible binding for global variable ‘sd’
tapplyDS.o: no visible binding for global variable ‘quantile’
unListDS.o: no visible binding for global variable ‘newobj.class’
varDS.o: no visible global function definition for ‘var’
Undefined global functions or variables:
  as.formula ave complete.cases current.factor factor1.levels
  factor2.levels glm glm.control messageobj newobj.class quantile
  rbinom reshape rnorm rpois runif sd var
Consider adding
  importFrom("stats", "as.formula", "ave", "complete.cases", "glm",
             "glm.control", "quantile", "rbinom", "reshape", "rnorm",
             "rpois", "runif", "sd", "var")
to your NAMESPACE file.
* 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 ... WARNING
Undocumented arguments in documentation object 'asListDS.o'
  ‘newobj’

Undocumented arguments in documentation object 'messageDS.o'
  ‘message.object.name’
Documented arguments not in \usage in documentation object 'messageDS.o':
  ‘message.obj’

Undocumented arguments in documentation object 'unListDS.o'
  ‘recursive’ ‘newobj’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... NONE
* DONE
Status: 1 WARNING, 2 NOTEs

ds.levels and ds.summary

I think we need to make a new version of ds.levels that includes the disclosure trap for number of individuals in a group. If we have a numeric variable on the server side, this can be converted to a factor using ds.asFactor. Then the levels are the individual values, which can simply be returned with ds.levels.

Actually thinking about it, ds.summary will also return the level labels with NA in this scenario, I think, and should be modified not to return the labels.

glmSLMADS2.o - devtools::check note

devtools::check produces the following note

glmSLMADS2.o: no visible global function definition for ‘complete.cases’
glmSLMADS2.o: no visible global function definition for ‘as.formula’
glmSLMADS2.o: no visible global function definition for ‘glm’

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