Package: DeconRNASeq

Version: 1.25.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:DeconRNASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DeconRNASeq_1.25.0.tar.gz

StartedAt: 2019-04-09 02:10:40 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:11:38 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 57.2 seconds

RetCode: 0

Status:  OK

CheckDir: DeconRNASeq.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:DeconRNASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DeconRNASeq_1.25.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DeconRNASeq.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DeconRNASeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DeconRNASeq' version '1.25.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'DeconRNASeq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
* 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 ... NOTE
'library' or 'require' call to 'grid' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'ggplot2' 'grid' 'pcaMethods'
  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
DeconRNASeq: no visible global function definition for 'prep'
DeconRNASeq: no visible global function definition for 'pca'
DeconRNASeq: no visible global function definition for 'R2cum'
DeconRNASeq: no visible global function definition for 'ggplot'
DeconRNASeq: no visible global function definition for 'aes'
DeconRNASeq: no visible global function definition for 'geom_point'
DeconRNASeq: no visible global function definition for 'labs'
DeconRNASeq: no visible global function definition for 'geom_abline'
DeconRNASeq: no visible global function definition for 'xlab'
DeconRNASeq: no visible global function definition for 'ylab'
condplot: no visible global function definition for 'plot'
condplot: no visible global function definition for 'rainbow'
condplot: no visible global function definition for 'lines'
condplot: no visible global function definition for 'axis'
condplot: no visible global function definition for 'title'
decon.bootstrap: no visible global function definition for 't.test'
multiplot: no visible global function definition for 'grid.newpage'
multiplot: no visible global function definition for 'pushViewport'
multiplot: no visible global function definition for 'viewport'
multiplot: no visible global function definition for 'grid.layout'
multiplot : vplayout: no visible global function definition for
  'viewport'
Undefined global functions or variables:
  R2cum aes axis geom_abline geom_point ggplot grid.layout grid.newpage
  labs lines pca plot prep pushViewport rainbow t.test title viewport
  xlab ylab
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "lines", "plot", "title")
  importFrom("stats", "t.test")
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
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/DeconRNASeq.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch DeconRNASeq
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* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
* installing *source* package 'DeconRNASeq' ...
** R
** data
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DeconRNASeq'
    finding HTML links ... done
    DeconRNASeq-package                     html  
    DeconRNASeq                             html  
    all.datasets                            html  
    array.proportions                       html  
    array.signatures                        html  
    condplot                                html  
    datasets                                html  
    decon.bootstrap                         html  
    fraction                                html  
    liver_kidney                            html  
    multi_tissue                            html  
    multiplot                               html  
    proportions                             html  
    rmse                                    html  
    signatures                              html  
    x.data                                  html  
    x.signature                             html  
    x.signature.filtered                    html  
    x.signature.filtered.optimal            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DeconRNASeq)
Making 'packages.html' ... done

name	user	system	elapsed
DeconRNASeq	0	0	0
all.datasets	0.09	0.00	0.10
array.proportions	0.07	0.00	0.08
array.signatures	0.08	0.00	0.07
condplot	0.08	0.00	0.07
datasets	0.17	0.01	0.19
fraction	0.44	0.00	0.44
liver_kidney	0.14	0.00	0.14
multi_tissue	0.42	0.00	0.42
multiplot	0	0	0
proportions	0.15	0.00	0.14
signatures	0.07	0.06	0.15
x.data	0.39	0.02	0.40
x.signature	0.41	0.02	0.42
x.signature.filtered	0.41	0.00	0.41
x.signature.filtered.optimal	0.29	0.03	0.32