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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmicCircos.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings OmicCircos_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/OmicCircos.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.26.0'
* 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
* 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
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 ... WARNING
Documented arguments not in \usage in documentation object 'circos':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
** 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/OmicCircos.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/OmicCircos_1.26.0.tar.gz && rm -rf OmicCircos.buildbin-libdir && mkdir OmicCircos.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OmicCircos.buildbin-libdir OmicCircos_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL OmicCircos_1.26.0.zip && rm OmicCircos_1.26.0.tar.gz OmicCircos_1.26.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  111k  100  111k    0     0  1722k      0 --:--:-- --:--:-- --:--:-- 1924k

install for i386

* installing *source* package 'OmicCircos' ...
** using staged installation
** R
** data
** demo
** byte-compile and prepare 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'OmicCircos' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OmicCircos' as OmicCircos_1.26.0.zip
* DONE (OmicCircos)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'OmicCircos' successfully unpacked and MD5 sums checked