Package: DTA

Version: 2.28.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DTA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DTA_2.28.0.tar.gz

StartedAt: 2019-04-13 01:56:13 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 02:05:19 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 545.9 seconds

RetCode: 0

Status:  OK

CheckDir: DTA.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DTA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DTA_2.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DTA.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'DTA' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.4Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
DTA.dynamic.generate 64.66   4.80   69.45
DTA.estimate         56.08   1.27   57.36
DTA.generate         50.20   0.92   51.12
DTA.dynamic.estimate 29.47   0.03   29.50
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
DTA.dynamic.generate 73.33   5.36   78.69
DTA.generate         53.57   0.84   54.44
DTA.estimate         51.60   1.13   52.72
DTA.dynamic.estimate 38.42   0.04   38.50
* 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/DTA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DTA_2.28.0.tar.gz && rm -rf DTA.buildbin-libdir && mkdir DTA.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DTA.buildbin-libdir DTA_2.28.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DTA_2.28.0.zip && rm DTA_2.28.0.tar.gz DTA_2.28.0.zip
###
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100 7015k  100 7015k    0     0  54.6M      0 --:--:-- --:--:-- --:--:-- 56.1M

install for i386

* installing *source* package 'DTA' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DTA'
    finding HTML links ... done
    DTA-package                             html  
    DTA.dynamic.estimate                    html  
    DTA.dynamic.generate                    html  
    DTA.estimate                            html  
    DTA.generate                            html  
    DTA.map.it                              html  
    DTA.normalize                           html  
    DTA.phenomat                            html  
    DTA.plot.it                             html  
    Dm.tnumber                              html  
    Doelken2008                             html  
    Hs.datamat                              html  
    Hs.enst2ensg                            html  
    Hs.phenomat                             html  
    Hs.reliable                             html  
    Hs.tnumber                              html  
    Miller2011                              html  
    Miller2011dynamic                       html  
    Mm.datamat                              html  
    Mm.enst2ensg                            html  
    Mm.phenomat                             html  
    Mm.reliable                             html  
    Mm.tnumber                              html  
    Pol.phenomat                            html  
    Raw.datamat                             html  
    Sc.affy2ensg                            html  
    Sc.datamat                              html  
    Sc.datamat.dynamic                      html  
    Sc.ensg.reliable                        html  
    Sc.phenomat                             html  
    Sc.phenomat.dynamic                     html  
    Sc.reliable                             html  
    Sc.reliable.dynamic                     html  
    Sc.ribig.ensg                           html  
    Sc.rpg.ensg                             html  
    Sc.stress.ensg                          html  
    Sc.tf.ensg                              html  
    Sc.tnumber                              html  
    Sp.affy.reliable                        html  
    Sp.tnumber                              html  
    Sun2011                                 html  
    Wt.phenomat                             html  
    tls                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DTA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DTA' as DTA_2.28.0.zip
* DONE (DTA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DTA' successfully unpacked and MD5 sums checked
In R CMD INSTALL