Package: iCNV

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iCNV.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings iCNV_1.6.0.tar.gz

StartedAt: 2020-04-15 03:58:46 -0400 (Wed, 15 Apr 2020)

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

EllapsedTime: 317.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: iCNV.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iCNV.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings iCNV_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/iCNV.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 'iCNV/DESCRIPTION' ... OK
* this is package 'iCNV' version '1.6.0'
* 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 'iCNV' can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/iCNV.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* 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 ... OK
* 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 or elapsed time > 5s
                user system elapsed
iCNV_detection  9.00   0.30    9.32
bambaf_from_vcf 3.24   0.71   13.47
get_array_input 0.16   0.04    5.64
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
iCNV_detection 12.62   0.09   14.13
* 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
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/iCNV.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/iCNV_1.6.0.tar.gz && rm -rf iCNV.buildbin-libdir && mkdir iCNV.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iCNV.buildbin-libdir iCNV_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL iCNV_1.6.0.zip && rm iCNV_1.6.0.tar.gz iCNV_1.6.0.zip
###
##############################################################################
##############################################################################


  % 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 1207k  100 1207k    0     0  9424k      0 --:--:-- --:--:-- --:--:-- 9815k

install for i386

* installing *source* package 'iCNV' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: break used in wrong context: no loop is visible 
** help
*** installing help indices
  converting help for package 'iCNV'
    finding HTML links ... done
    bambaf_from_vcf                         html  
    bed_generator                           html  
    chr                                     html  
    filenm                                  html  
    get_array_input                         html  
    iCNV_detection                          html  
    icnv_output_to_gb                       html  
    icnv_res0                               html  
    ngs_baf                                 html  
    ngs_baf.chr                             html  
    ngs_baf.id                              html  
    ngs_baf.nm                              html  
    ngs_baf.pos                             html  
    ngs_plr                                 html  
    ngs_plr.pos                             html  
    normObj                                 html  
    output_list                             html  
    plotHMMscore                            html  
    plot_intensity                          html  
    plotindi                                html  
    projname                                html  
    qcObj                                   html  
    sampname                                html  
    sampname_qc                             html  
    snp_baf                                 html  
    snp_baf.pos                             html  
    snp_lrr                                 html  
    snp_lrr.pos                             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 'iCNV' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iCNV' as iCNV_1.6.0.zip
* DONE (iCNV)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'iCNV' successfully unpacked and MD5 sums checked