Package: OmicCircos

Version: 1.16.0

Command: rm -rf OmicCircos.buildbin-libdir OmicCircos.Rcheck && mkdir OmicCircos.buildbin-libdir OmicCircos.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OmicCircos.buildbin-libdir OmicCircos_1.16.0.tar.gz >OmicCircos.Rcheck\00install.out 2>&1 && cp OmicCircos.Rcheck\00install.out OmicCircos-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=OmicCircos.buildbin-libdir --install="check:OmicCircos-install.out" --force-multiarch --no-vignettes --timings OmicCircos_1.16.0.tar.gz

StartedAt: 2018-04-12 01:53:52 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:55:53 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 121.4 seconds

RetCode: 0

Status:  OK

CheckDir: OmicCircos.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf OmicCircos.buildbin-libdir OmicCircos.Rcheck && mkdir OmicCircos.buildbin-libdir OmicCircos.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OmicCircos.buildbin-libdir OmicCircos_1.16.0.tar.gz >OmicCircos.Rcheck\00install.out 2>&1 && cp OmicCircos.Rcheck\00install.out OmicCircos-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=OmicCircos.buildbin-libdir --install="check:OmicCircos-install.out" --force-multiarch --no-vignettes --timings OmicCircos_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/OmicCircos.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OmicCircos/DESCRIPTION' ... OK
* this is package 'OmicCircos' version '1.16.0'
* 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 whether package 'OmicCircos' can be installed ... OK
* checking installed package size ... OK
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
circos: no visible global function definition for 'rainbow'
circos: no visible global function definition for 'start'
circos: no visible global function definition for 'end'
circos: no visible global function definition for 'dist'
circos: no visible global function definition for 'hclust'
circos: no visible global function definition for 'colorRampPalette'
circos: no visible global function definition for 'na.omit'
circos: no visible binding for global variable 'quantile'
circos : get.conf.int: no visible global function definition for
  't.test'
circos : var1: no visible global function definition for 'var'
circos: no visible global function definition for 'var'
circos : sd1: no visible global function definition for 'sd'
circos: no visible global function definition for 'sd'
circos: no visible global function definition for 'median'
color.bar: no visible global function definition for 'colorRampPalette'
color.bar: no visible global function definition for 'rect'
color.bar: no visible global function definition for 'text'
color.bar: no visible global function definition for 'segments'
do.scale: no visible global function definition for 'segments'
do.scale: no visible global function definition for 'text'
draw.arc.pg: no visible global function definition for 'polygon'
draw.arc.s: no visible global function definition for 'lines'
draw.line: no visible global function definition for 'segments'
draw.line2: no visible global function definition for 'segments'
draw.line3: no visible global function definition for 'segments'
draw.link: no visible global function definition for 'points'
draw.link.pg: no visible global function definition for 'polygon'
draw.link2: no visible global function definition for 'points'
draw.point.w: no visible global function definition for 'points'
draw.text.rt: no visible global function definition for 'text'
draw.text.w: no visible global function definition for 'text'
heatmap.cluster: no visible global function definition for 'dist'
heatmap.cluster: no visible global function definition for 'hclust'
heatmap.cluster: no visible global function definition for 'segments'
heatmap.cluster: no visible global function definition for 'text'
sim.circos: no visible global function definition for 'rnorm'
segAnglePo,GRanges: no visible global function definition for 'start'
segAnglePo,GRanges: no visible global function definition for 'end'
segAnglePo,GRanges: no visible global function definition for 'strand'
segAnglePo,GRanges: no visible binding for global variable 'seg'
segAnglePo,GRanges: no visible binding for global variable
  'angle.start'
segAnglePo,GRanges: no visible binding for global variable 'angle.end'
Undefined global functions or variables:
  angle.end angle.start colorRampPalette dist end hclust lines median
  na.omit points polygon quantile rainbow rect rnorm sd seg segments
  start strand t.test text var
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "lines", "points", "polygon", "rect",
             "segments", "text")
  importFrom("stats", "dist", "end", "hclust", "median", "na.omit",
             "quantile", "rnorm", "sd", "start", "t.test", "var")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/OmicCircos.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'OmicCircos' ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'OmicCircos'
    finding HTML links ... done
    OmicCircos                              html  
    TCGA.BC.cnv.2k.60                       html  
    TCGA.BC.fus                             html  
    TCGA.BC.gene.exp.2k.60                  html  
    TCGA.BC.sample60                        html  
    TCGA.BC_Her2_cnv_exp                    html  
    TCGA.PAM50_genefu_hg18                  html  
    UCSC.chr.colors                         html  
    UCSC.hg18                               html  
    UCSC.hg18.chr                           html  
    UCSC.hg19                               html  
    UCSC.hg19.chr                           html  
    UCSC.mm10                               html  
    UCSC.mm10.chr                           html  
    UCSC.mm9                                html  
    UCSC.mm9.chr                            html  
    circos                                  html  
    segAnglePo-methods                      html  
    segAnglePo                              html  
    sim.circos                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'OmicCircos' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OmicCircos' as OmicCircos_1.16.0.zip
* DONE (OmicCircos)
In R CMD INSTALL
In R CMD INSTALL