CADStat - Provides a GUI to several statistical methods for making biological inferences - check results
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CADStat

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Version: 2.2-5
Result: WARNING
Check time: 2018-01-24 14:02
* 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 'CADStat/DESCRIPTION' ... OK
* this is package 'CADStat' version '2.2-5'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'JGR' 'XML' 'lattice' 'bio.infer' 'gdata' 'gmodels' 'car' 'MASS'
'quantreg' 'rpart' 'rJava'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... WARNING
Found the following executable file:
inst/scripts/jgr.exe
Source packages should not contain undeclared executable files.
See section 'Package structure' in the 'Writing R Extensions' manual.
* 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 'CADStat' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Non-standard license specification:
GPL Version 2 or newer
Standardizable: TRUE
Standardized license specification:
GPL (>= 2)
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
'version.number'
* 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
'library' or 'require' calls to packages already attached by Depends:
'XML' 'lattice'
Please remove these calls from your code.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
docbook.data.frame docbook.default docbook.glm docbook.glm.summary
docbook.hmtestp docbook.htest docbook.lm docbook.lm.summary
docbook.try text.rpart.JGR
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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'CADStat/R/zzz.R':
.First.lib calls:
cat(libname, "\n")

Package startup functions should use 'packageStartupMessage' to
generate messages.
See section 'Good practice' in '?.onAttach'.

CADStat.help: no visible global function definition for 'browseURL'
CADStat.update: no visible global function definition for
'available.packages'
CADStat.update: no visible global function definition for
'installed.packages'
CADStat.update: no visible global function definition for
'compareVersion'
CADStat.update: no visible global function definition for
'install.packages'
bioinfer.JGR: no visible global function definition for 'data'
browseHelp: no visible global function definition for 'browseURL'
bxplot.JGR: no visible global function definition for 'plot'
bxplot.JGR: no visible global function definition for 'text'
bxplot.JGR: no visible global function definition for 'formula'
bxplot.JGR: no visible global function definition for 'JavaGD'
conditionalprob.JGR: no visible global function definition for 'png'
conditionalprob.JGR: no visible global function definition for 'JavaGD'
conditionalprob.JGR: no visible global function definition for 'par'
conditionalprob.JGR: no visible global function definition for 'plot'
conditionalprob.JGR: no visible global function definition for 'points'
conditionalprob.JGR: no visible binding for global variable 'quantile'
conditionalprob.JGR: no visible global function definition for 'grid'
conditionalprob.JGR: no visible global function definition for
'dev.off'
cor.JGR: no visible global function definition for 'cor'
cor.JGR: no visible global function definition for 'cor.test'
cor.JGR: no visible global function definition for 'png'
cor.JGR: no visible global function definition for 'JavaGD'
cor.JGR: no visible global function definition for 'par'
cor.JGR: no visible global function definition for 'pairs'
cor.JGR: no visible global function definition for 'as.formula'
cor.JGR: no visible global function definition for 'dev.off'
datamerge.JGR: no visible global function definition for 'write.table'
docbook.glm: no visible global function definition for 'summary.lm'
docbook.glm.summary: no visible global function definition for 'coef'
docbook.glm.summary: no visible global function definition for 'pchisq'
docbook.lm.summary: no visible global function definition for 'coef'
genResultSpace: no visible global function definition for 'runif'
glm.JGR: no visible global function definition for 'glm'
glm.JGR: no visible global function definition for 'as.formula'
glm.JGR: no visible global function definition for 'confint'
glm.JGR: no visible global function definition for 'png'
glm.JGR: no visible global function definition for 'JavaGD'
glm.JGR: no visible global function definition for 'par'
glm.JGR: no visible global function definition for 'plot'
glm.JGR: no visible global function definition for 'dev.off'
glm.pred.JGR: no visible global function definition for 'as.formula'
glm.pred.JGR: no visible global function definition for 'glm'
glm.pred.JGR: no visible global function definition for 'predict'
glm.pred.JGR: no visible global function definition for 'pt'
glm.pred.JGR: no visible global function definition for 'pnorm'
glm.pred.JGR: no visible global function definition for 'model.matrix'
glm.pred.JGR: no visible global function definition for 'png'
glm.pred.JGR: no visible global function definition for 'JavaGD'
glm.pred.JGR: no visible global function definition for 'par'
glm.pred.JGR: no visible global function definition for 'plot'
glm.pred.JGR: no visible global function definition for 'abline'
glm.pred.JGR: no visible global function definition for 'legend'
glm.pred.JGR: no visible global function definition for 'points'
glm.pred.JGR: no visible global function definition for 'text'
glm.pred.JGR: no visible global function definition for 'dev.off'
pca.fa.JGR: no visible global function definition for 'as.formula'
pca.fa.JGR: no visible global function definition for 'prcomp'
pca.fa.JGR: no visible global function definition for 'JavaGD'
pca.fa.JGR: no visible global function definition for 'plot'
pca.fa.JGR: no visible global function definition for 'biplot'
pca.fa.JGR: no visible global function definition for 'factanal'
rpart.JGR: no visible global function definition for 'as.formula'
rpart.JGR: no visible global function definition for 'png'
rpart.JGR: no visible global function definition for 'JavaGD'
rpart.JGR: no visible global function definition for 'par'
rpart.JGR: no visible global function definition for 'plot'
rpart.JGR: no visible global function definition for 'text'
rpart.JGR: no visible global function definition for 'dev.off'
rq.JGR: no visible global function definition for 'as.formula'
rq.JGR: no visible global function definition for 'png'
rq.JGR: no visible global function definition for 'JavaGD'
rq.JGR: no visible global function definition for 'dev.off'
rq.JGR: no visible global function definition for 'plot'
rq.plot.JGR: no visible global function definition for 'plot'
rq.plot.JGR: no visible global function definition for 'points'
rq.plot.JGR: no visible global function definition for 'lm'
rq.plot.JGR: no visible global function definition for 'abline'
rq.plot.JGR: no visible global function definition for 'coef'
rq.plot.JGR: no visible global function definition for 'lines'
rq.plot.JGR: no visible global function definition for 'rainbow'
rq.plot.JGR: no visible global function definition for 'legend'
scatterplot2: no visible global function definition for 'JavaGD'
scatterplot2: no visible global function definition for 'plot'
scatterplot2: no visible global function definition for 'lm'
scatterplot2: no visible global function definition for 'predict'
scatterplot2: no visible global function definition for 'loess'
scatterplot2: no visible global function definition for 'qt'
scatterplot2: no visible global function definition for 'lines'
scatterplot2: no visible global function definition for 'text'
scatterplot2: no visible global function definition for 'legend'
text.rpart.JGR: no visible global function definition for 'rect'
text.rpart.JGR: no visible global function definition for 'text'
Undefined global functions or variables:
JavaGD abline as.formula available.packages biplot browseURL coef
compareVersion confint cor cor.test data dev.off factanal formula glm
grid install.packages installed.packages legend lines lm loess
model.matrix pairs par pchisq plot png pnorm points prcomp predict pt
qt quantile rainbow rect runif summary.lm text write.table
Consider adding
importFrom("grDevices", "dev.off", "png", "rainbow")
importFrom("graphics", "abline", "grid", "legend", "lines", "pairs",
"par", "plot", "points", "rect", "text")
importFrom("stats", "as.formula", "biplot", "coef", "confint", "cor",
"cor.test", "factanal", "formula", "glm", "lm", "loess",
"model.matrix", "pchisq", "pnorm", "prcomp", "predict",
"pt", "qt", "quantile", "runif", "summary.lm")
importFrom("utils", "available.packages", "browseURL",
"compareVersion", "data", "install.packages",
"installed.packages", "write.table")
to your NAMESPACE file.

Found the following assignments to the global environment:
File 'CADStat/R/bioinfer.JGR.R':
assign(globenv[["resultName"]], result, envir = .GlobalEnv)
File 'CADStat/R/datamerge.JGR.R':
assign(rName, mergedData, pos = 1)
File 'CADStat/R/glm.JGR.R':
assign(saveLMName, my.fit, pos = 1)
assign("my_glm.fit", my.fit, pos = 1)
File 'CADStat/R/pca.fa.JGR.R':
assign("PCA.scores", PCA.scores, pos = 1)
assign("FA.scores", FA.scores, pos = 1)

Found the following calls to data() loading into the global environment:
File 'CADStat/R/bioinfer.JGR.R':
data(list = coefBioInferDataName)
See section 'Good practice' in '?data'.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
'benthicCount' 'envdata.or' 'eptpctfn' 'fish.lwr' 'refids.or'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... WARNING
Files not of a type allowed in a 'data' directory:
'forTest'
Please use e.g. 'inst/extdata' for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
WARNING
'qpdf' is needed for checks on size reduction of PDFs
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 6 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 'CADStat/DESCRIPTION' ... OK
* preparing 'CADStat':
* 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 'CADStat' ...

Using auto-selected zip option '--use-zip-data'

** R
** data
** inst
** preparing package for lazy loading
Loading required package: rJava
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 in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
there is no package called 'XML'
Error : package 'XML' could not be loaded
ERROR: lazy loading failed for package 'CADStat'
* removing 'c:/tmp/Rinst59222225/CADStat'
ERROR
* installation failed


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

* checking for file 'CADStat/DESCRIPTION' ... OK
* preparing 'CADStat':
* 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 'CADStat' ...

Using auto-selected zip option '--use-zip-data'

** R
** data
** inst
** preparing package for lazy loading
Loading required package: rJava
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 in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
there is no package called 'XML'
Error : package 'XML' could not be loaded
ERROR: lazy loading failed for package 'CADStat'
* removing 'c:/tmp/Rinst215684982/CADStat'
ERROR
* installation failed


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

ERROR: dependencies 'JGR', 'XML', 'bio.infer', 'gdata', 'gmodels', 'car', 'quantreg' are not available for package 'CADStat'
* removing '/Volumes/Tiger/Builds/rforge/Rlib/osx9-2.16/CADStat'

Build log for Windows 7 (R 3.0.x)

(CADStat 2.2-5)
* installing to library 'z:/rforge/Rlib/win7-3.0'
* installing *source* package 'CADStat' ...
** R
** data
** inst
** preparing package for lazy loading
File type 'perl' not found or no open command associated with it.
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
File type 'perl' not found or no open command associated with it.
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
File type 'perl' not found or no open command associated with it.
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
File type 'perl' not found or no open command associated with it.
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
Warning: ignoring .First.lib() for package 'CADStat'
*** arch - x64
File type 'perl' not found or no open command associated with it.
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
File type 'perl' not found or no open command associated with it.
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
Warning: ignoring .First.lib() for package 'CADStat'
* MD5 sums
packaged installation of 'CADStat' as CADStat_2.2-5.zip
* DONE (CADStat)