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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Oscope.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Oscope_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/Oscope.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 'Oscope/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Oscope' version '1.18.0'
* 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 'Oscope' 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
AbsCor: no visible global function definition for 'cor'
CalcMV: no visible binding for global variable 'median'
CalcMV: no visible global function definition for 'lm'
CalcMV: no visible global function definition for 'coef'
CalcMV: no visible global function definition for 'lines'
CalcMV: no visible global function definition for 'points'
CalcMV: no visible global function definition for 'abline'
FlagCluster: no visible global function definition for 'quantile'
ImpShift: no visible global function definition for 'txtProgressBar'
ImpShift: no visible global function definition for 'setTxtProgressBar'
NISFun: no visible global function definition for 'str'
NormForSine : <anonymous>: no visible global function definition for
  'quantile'
PipeR : <anonymous>: no visible global function definition for
  'residuals'
PipeR : <anonymous>: no visible global function definition for 'lm'
PipeShiftCDF : <anonymous>: no visible global function definition for
  'quantile'
PipeShiftCDF : <anonymous>: no visible global function definition for
  'ecdf'
SineOptim: no visible global function definition for 'optim'
scanK: no visible global function definition for 'quantile'
scanK: no visible global function definition for 'dist'
scanK : <anonymous>: no visible global function definition for 'median'
Undefined global functions or variables:
  abline coef cor dist ecdf lines lm median optim points quantile
  residuals setTxtProgressBar str txtProgressBar
Consider adding
  importFrom("graphics", "abline", "lines", "points")
  importFrom("stats", "coef", "cor", "dist", "ecdf", "lm", "median",
             "optim", "quantile", "residuals")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
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 (user + system) or elapsed time > 5s
         user system elapsed
PermuCut 5.23      0    5.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
PermuCut 5.82      0    5.83
* 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-3.11-bioc/meat/Oscope.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/Oscope_1.18.0.tar.gz && rm -rf Oscope.buildbin-libdir && mkdir Oscope.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Oscope.buildbin-libdir Oscope_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Oscope_1.18.0.zip && rm Oscope_1.18.0.tar.gz Oscope_1.18.0.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  533k  100  533k    0     0  5675k      0 --:--:-- --:--:-- --:--:-- 6064k

install for i386

* installing *source* package 'Oscope' ...
** using staged installation
** R
** data
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Oscope'
    finding HTML links ... done
    AbsCor                                  html  
    CalcMV                                  html  
    FlagCluster                             html  
    FormatSineOut                           html  
    ImpShift                                html  
    NISFun                                  html  
    NormForSine                             html  
    Opt2Shift                               html  
    Oscope-package                          html  
    OscopeENI                               html  
    OscopeExampleData                       html  
    OscopeKM                                html  
    OscopeSine                              html  
    PermuCut                                html  
    PipeR                                   html  
    PipeShiftCDF                            html  
    SineFun                                 html  
    SineOptim                               html  
    scanK                                   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 'Oscope' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Oscope' as Oscope_1.18.0.zip
* DONE (Oscope)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'Oscope' successfully unpacked and MD5 sums checked