Deducer - A graphical data analysis system for use with JGR - check results
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Deducer

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Package R docs

Version: 0.7-7
Result: ERROR
Check time: 2018-01-24 14:12
* using log directory ''
* using R Under development (unstable) (2018-01-24 r74156)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'Deducer/DESCRIPTION' ... OK
* this is package 'Deducer' version '0.7-7'
* 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 serialized R objects in the sources ... OK
* checking whether package 'Deducer' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Checking should be performed on sources prepared by 'R CMD build'.
* 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 ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
as.matrix.cor.matrix plot.cor.matrix print.contin.table
print.contin.tests print.contingency.tables print.cor.matrix
print.freq.table print.multi.test sort.data.frame summary.lm
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
add.chi.squared : : no visible global function definition
for 'chisq.test'
add.correlation : corr: no visible global function definition for
'cor.test'
add.fishers.exact : : no visible global function definition
for 'fisher.test'
add.kruskal : krusk.rows: no visible global function definition for
'kruskal.test'
add.kruskal : krusk.cols: no visible global function definition for
'kruskal.test'
add.mantel.haenszel : : no visible global function
definition for 'mantelhaen.test'
chi.noncentral.conf: no visible global function definition for 'pchisq'
contingency.tables : single.table: no visible global function
definition for 'chisq.test'
cor.matrix: no visible binding for global variable 'cor.test'
cor.matrix: no visible global function definition for 'na.omit'
deducer: no visible global function definition for 'menu'
descriptive.table : : no visible global function definition
for 'sd'
descriptive.table : : no visible global function definition
for 'median'
descriptive.table : : no visible global function definition
for 'quantile'
ggcorplot : ezLev: no visible global function definition for 'relevel'
ggcorplot: no visible global function definition for 'sd'
ggcorplot: no visible global function definition for 'na.omit'
ggcorplot: possible error in layer(geom = "line", geom_params =
list(colour = "red"), stat = "smooth", stat_params = list(method =
line.method), data = z, mapping = aes(x = x_var, y = y_var)): unused
arguments (geom_params = list(colour = "red"), stat_params =
list(method = line.method))
ggcorplot: possible error in layer(geom = "ribbon", geom_params =
list(fill = "green", alpha = 0.5), stat = "smooth", stat_params =
list(method = line.method), data = z, mapping = aes(x = x_var, y =
y_var)): unused arguments (geom_params = list(fill = "green", alpha =
0.5), stat_params = list(method = line.method))
ggcorplot: no visible binding for global variable 'cor'
ggcorplot: possible error in layer(geom = "text", geom_params =
list(size = var_text_size), data = diag, mapping = aes(x = y_mid, y =
x_mid, label = x_label)): unused argument (geom_params = list(size =
var_text_size))
k.sample.test: no visible binding for global variable 'oneway.test'
k.sample.test: no visible global function definition for 'na.omit'
likelihood.test: no visible global function definition for
'complete.cases'
likelihood.test: no visible global function definition for 'pchisq'
one.sample.test: no visible binding for global variable 't.test'
one.sample.test: no visible global function definition for 'na.omit'
onesample.plot: no visible global function definition for 'sd'
onesample.plot: no visible global function definition for 'na.omit'
oneway.plot: no visible global function definition for 'sd'
oneway.plot: no visible global function definition for 'na.omit'
perm.t.test: no visible global function definition for 'na.omit'
perm.t.test: no visible binding for global variable 'var'
plot.cor.matrix: no visible binding for global variable 'cor'
print.contin.table: no visible global function definition for
'capture.output'
sort.data.frame: no visible global function definition for 'as.formula'
summary.lm: no visible global function definition for 'coef'
summary.lm: no visible global function definition for 'pt'
two.sample.test: no visible binding for global variable 't.test'
two.sample.test: no visible global function definition for 'na.omit'
Undefined global functions or variables:
as.formula capture.output chisq.test coef complete.cases cor cor.test
fisher.test kruskal.test mantelhaen.test median menu na.omit
oneway.test pchisq pt quantile relevel sd t.test var
Consider adding
importFrom("stats", "as.formula", "chisq.test", "coef",
"complete.cases", "cor", "cor.test", "fisher.test",
"kruskal.test", "mantelhaen.test", "median", "na.omit",
"oneway.test", "pchisq", "pt", "quantile", "relevel", "sd",
"t.test", "var")
importFrom("utils", "capture.output", "menu")
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... ERROR
Running examples in 'Deducer-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggcorplot
> ### Title: Correlation matrix
> ### Aliases: ggcorplot
>
> ### ** Examples
>
> data(mtcars)
> corr.mat1<-cor.matrix(variables=d(mpg,carb,carb+rnorm(length(carb))),,
+ data=mtcars,
+ test=cor.test,
+ method='spearman',
+ alternative="two.sided",exact=FALSE)
>
> p<-ggcorplot(corr.mat1,data = mtcars)
Error: Attempted to create layer with no stat.
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
'/00check.log'
for details.


Installation log: 00install.out

Distribution log

SVN checkout/GIT clone log


Build log for Windows (R 2.11.x)

* checking for file 'Deducer/DESCRIPTION' ... OK
* preparing 'Deducer':
* checking DESCRIPTION meta-information ... OK
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building binary distribution
WARNING: some HTML links may not be found
* installing *source* package 'Deducer' ...
** R
** inst
** preparing package for lazy loading
Warning: package 'ggplot2' was built under R version 2.11.1
Loading required package: reshape
Loading required package: plyr
Warning: package 'plyr' was built under R version 2.11.1
Loading required package: grid
Loading required package: proto
Loading required package: JavaGD
Loading required package: iplots

Please use the corresponding JGR launcher to start JGR.
Run JGR() for details. You can also use JGR(update=TRUE) to update JGR.

Warning: package 'car' was built under R version 2.11.1
Loading required package: MASS
Warning: package 'MASS' was built under R version 2.11.1
Loading required package: nnet
Loading required package: survival
Loading required package: splines
Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
there is no package called 'multcomp'
Error : package 'multcomp' could not be loaded
ERROR: lazy loading failed for package 'Deducer'
* removing 'c:/tmp/Rinst190019869/Deducer'
ERROR
* installation failed


Build log for Windows 64-bit (R 2.11.x)

* checking for file 'Deducer/DESCRIPTION' ... OK
* preparing 'Deducer':
* checking DESCRIPTION meta-information ... OK
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building binary distribution
WARNING: some HTML links may not be found
* installing *source* package 'Deducer' ...
** R
** inst
** preparing package for lazy loading
Warning: package 'ggplot2' was built under R version 2.11.1
Loading required package: reshape
Loading required package: plyr
Warning: package 'plyr' was built under R version 2.11.1
Loading required package: grid
Loading required package: proto
Loading required package: JavaGD
Loading required package: iplots

Please use the corresponding JGR launcher to start JGR.
Run JGR() for details. You can also use JGR(update=TRUE) to update JGR.

Loading required package: mvtnorm
Warning: package 'mvtnorm' was built under R version 2.11.1
Loading required package: survival
Loading required package: splines
Loading required package: lattice
Loading required package: MASS
Warning: package 'MASS' was built under R version 2.11.1
Loading required package: nnet
Loading required package: colorspace

Attaching package: 'effects'

The following object(s) are masked from 'package:datasets':

Titanic

** help
*** installing help indices
** building package indices ...
** MD5 sums
** testing if installed package can be loaded
packaged installation of 'Deducer' as Deducer_0.4-1.zip

* DONE (Deducer)


Build log for Mac OS X 10.5 (R 2.16.x)

ERROR: dependencies 'ggplot2', 'scales', 'JGR', 'plyr' are not available for package 'Deducer'
* removing '/Volumes/Tiger/Builds/rforge/Rlib/osx9-2.16/Deducer'

Build log for Windows 7 (R 3.0.x)

(Deducer 0.7-6)
* installing to library 'z:/rforge/Rlib/win7-3.0'
* installing *source* package 'Deducer' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Error : .onLoad failed in loadNamespace() for 'Deducer', details:
call: .jfindClass(as.character(class))
error: class not found
Error: loading failed
Execution halted
*** arch - x64
Error : .onLoad failed in loadNamespace() for 'Deducer', details:
call: .jfindClass(as.character(class))
error: class not found
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing 'z:/rforge/Rlib/win7-3.0/Deducer'