CHECK report for DTA on malbec1
This page was generated on 2019-04-16 11:49:22 -0400 (Tue, 16 Apr 2019).
DTA 2.28.0
Bjoern Schwalb
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/DTA |
| Branch: RELEASE_3_8 |
| Last Commit: 4b7f7b1 |
| Last Changed Date: 2018-10-30 11:41:48 -0400 (Tue, 30 Oct 2018) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
Summary
Command output
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DTA.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DTA_2.28.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/DTA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DTA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DTA’ version ‘2.28.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DTA’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.2Mb
sub-directories of 1Mb or more:
data 6.8Mb
* checking package directory ... OK
* checking ‘build’ 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 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 ... NOTE
DTA.dynamic.estimate : ellipse.coordinates: no visible global function
definition for ‘qchisq’
DTA.dynamic.estimate : plotsfkt: no visible global function definition
for ‘par’
DTA.dynamic.estimate: no visible global function definition for
‘quantile’
DTA.dynamic.estimate : plotsfkt: no visible global function definition
for ‘plot’
DTA.dynamic.estimate : plotsfkt: no visible global function definition
for ‘points’
DTA.dynamic.estimate : plotsfkt: no visible global function definition
for ‘sd’
DTA.dynamic.estimate : plotsfkt: no visible global function definition
for ‘legend’
DTA.dynamic.generate: no visible global function definition for ‘rf’
DTA.dynamic.generate: no visible global function definition for
‘median’
DTA.dynamic.generate : <anonymous>: no visible global function
definition for ‘rnorm’
DTA.dynamic.generate: no visible binding for global variable ‘median’
DTA.dynamic.singlegenerate : plotsfkt: no visible global function
definition for ‘par’
DTA.dynamic.singlegenerate : plotsfkt: no visible global function
definition for ‘plot’
DTA.dynamic.singlegenerate : plotsfkt: no visible global function
definition for ‘points’
DTA.dynamic.singlegenerate : plotsfkt: no visible global function
definition for ‘abline’
DTA.dynamic.singlegenerate : plotsfkt: no visible global function
definition for ‘legend’
DTA.generate: no visible global function definition for ‘rf’
DTA.generate: no visible global function definition for ‘rnorm’
DTA.map.it: no visible global function definition for ‘aggregate’
DTA.map.it : <anonymous>: no visible global function definition for
‘median’
DTA.plot.it: no visible global function definition for ‘jpeg’
DTA.plot.it: no visible global function definition for ‘png’
DTA.plot.it: no visible global function definition for ‘bmp’
DTA.plot.it: no visible global function definition for ‘tiff’
DTA.plot.it: no visible global function definition for ‘postscript’
DTA.plot.it: no visible global function definition for ‘pdf’
DTA.plot.it: no visible global function definition for ‘dev.off’
DTA.plot.it: no visible global function definition for ‘dev.new’
DTA.singleestimate: no visible global function definition for ‘median’
DTA.singleestimate : lossfct: no visible global function definition for
‘median’
DTA.singleestimate: no visible global function definition for
‘optimize’
DTA.singleestimate: no visible global function definition for ‘lm’
DTA.singleestimate: no visible global function definition for
‘coefficients’
DTA.singleestimate: no visible global function definition for
‘quantile’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘par’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘points’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘abline’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘median’
DTA.singleestimate: no visible binding for global variable ‘median’
DTA.singleestimate : plotsfkt: no visible binding for global variable
‘median’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘plot’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘hist’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘text’
DTA.singleestimate: no visible global function definition for ‘cor’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘layout’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘image’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘colorRampPalette’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘axis’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘box’
DTA.singleestimate: no visible binding for global variable ‘sd’
DTA.singleestimate: no visible global function definition for ‘loess’
DTA.singleestimate : <anonymous>: no visible global function definition
for ‘optimize’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘persp’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘polygon’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘trans3d’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘lines’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘dgamma’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘mtext’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘legend’
DTA.singleestimate : <anonymous>: no visible global function definition
for ‘rnorm’
DTA.singleestimate : <anonymous>: no visible global function definition
for ‘quantile’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘quantile’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘coefficients’
DTA.singleestimate : plotsfkt: no visible global function definition
for ‘density’
DTA.singlegenerate: no visible global function definition for ‘median’
DTA.singlegenerate: no visible global function definition for ‘rnorm’
gridfkt: no visible global function definition for ‘abline’
gridfkt: no visible global function definition for ‘text’
likelihood: no visible global function definition for ‘dnorm’
likelihood: no visible global function definition for ‘dgamma’
medctr: no visible binding for global variable ‘median’
medctr: no visible global function definition for ‘median’
mediancenter: no visible binding for global variable ‘median’
mediancenter: no visible global function definition for ‘median’
mtextfkt: no visible global function definition for ‘mtext’
parfkt: no visible global function definition for ‘par’
pcor: no visible global function definition for ‘cor’
scor: no visible global function definition for ‘cor’
tls: no visible global function definition for ‘model.response’
tls: no visible global function definition for ‘model.matrix’
tls: no visible binding for global variable ‘contrasts’
toquantiles: no visible global function definition for ‘quantile’
wtls.solve: no visible global function definition for ‘lm’
wtls.solve: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
abline aggregate axis bmp box coefficients colorRampPalette contrasts
cor density dev.new dev.off dgamma dnorm hist image jpeg layout
legend lines lm loess median model.matrix model.response mtext
optimize par pdf persp plot png points polygon postscript qchisq
quantile rf rnorm sd text tiff trans3d uniroot
Consider adding
importFrom("grDevices", "bmp", "colorRampPalette", "dev.new",
"dev.off", "jpeg", "pdf", "png", "postscript", "tiff",
"trans3d")
importFrom("graphics", "abline", "axis", "box", "hist", "image",
"layout", "legend", "lines", "mtext", "par", "persp",
"plot", "points", "polygon", "text")
importFrom("stats", "aggregate", "coefficients", "contrasts", "cor",
"density", "dgamma", "dnorm", "lm", "loess", "median",
"model.matrix", "model.response", "optimize", "qchisq",
"quantile", "rf", "rnorm", "sd", "uniroot")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
DTA.dynamic.generate 68.996 3.816 72.965
DTA.estimate 50.440 1.012 51.553
DTA.generate 48.852 0.520 49.464
DTA.dynamic.estimate 35.632 0.024 35.715
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/DTA.Rcheck/00check.log’
for details.
Installation output
DTA.Rcheck/00install.out
Tests output
Example timings
DTA.Rcheck/DTA-Ex.timings