Package: CNVRanger

Version: 1.2.2

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVRanger.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CNVRanger_1.2.2.tar.gz

StartedAt: 2020-04-15 02:13:05 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:19:24 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 378.8 seconds

RetCode: 0

Status:  OK

CheckDir: CNVRanger.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVRanger.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CNVRanger_1.2.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/CNVRanger.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNVRanger/DESCRIPTION' ... OK
* this is package 'CNVRanger' version '1.2.2'
* package encoding: UTF-8
* 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 'CNVRanger' 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 ... NOTE
Unexported object imported by a ':::' call: 'rappdirs:::get_os'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotRecurrentRegions: no visible binding for global variable 'type'
plotRecurrentRegions: no visible binding for global variable 'pvalue'
Undefined global functions or variables:
  pvalue type
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
plotEQTL             18.14   1.40   34.14
plotRecurrentRegions 14.64   0.13   28.35
plotManhattan         6.86   0.11    7.23
cnvGWAS               6.67   0.06    7.64
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
plotEQTL             18.21   0.27   34.34
plotRecurrentRegions 14.61   0.02   37.63
cnvGWAS               6.31   0.05    6.67
plotManhattan         5.07   0.12    5.44
* 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-3.10-bioc/meat/CNVRanger.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/CNVRanger_1.2.2.tar.gz && rm -rf CNVRanger.buildbin-libdir && mkdir CNVRanger.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNVRanger.buildbin-libdir CNVRanger_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL CNVRanger_1.2.2.zip && rm CNVRanger_1.2.2.tar.gz CNVRanger_1.2.2.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  892k  100  892k    0     0   9.9M      0 --:--:-- --:--:-- --:--:-- 10.5M

install for i386

* installing *source* package 'CNVRanger' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CNVRanger'
    finding HTML links ... done
    cnvEQTL                                 html  
    finding level-2 HTML links ... done

    cnvGWAS                                 html  
    generateGDS                             html  
    importLrrBaf                            html  
    plotEQTL                                html  
    plotManhattan                           html  
    plotRecurrentRegions                    html  
    populationRanges                        html  
    setupCnvGWAS                            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 'CNVRanger' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNVRanger' as CNVRanger_1.2.2.zip
* DONE (CNVRanger)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'CNVRanger' successfully unpacked and MD5 sums checked