Package: MADSEQ

Version: 1.10.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MADSEQ.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MADSEQ_1.10.0.tar.gz

StartedAt: 2019-10-16 04:53:13 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:00:05 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 412.0 seconds

RetCode: 0

Status:  OK

CheckDir: MADSEQ.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MADSEQ.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MADSEQ_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MADSEQ.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MADSEQ/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MADSEQ' version '1.10.0'
* 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 'MADSEQ' 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
removeRE: no visible global function definition for 'seqlevelsStyle<-'
Undefined global functions or variables:
  seqlevelsStyle<-
* 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
normalizeCoverage 10.54   2.29   13.94
runMadSeq         11.14   0.07   11.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
normalizeCoverage 10.46   1.09   11.56
runMadSeq         10.10   0.12   10.58
* 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-3.9-bioc/meat/MADSEQ.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MADSEQ_1.10.0.tar.gz && rm -rf MADSEQ.buildbin-libdir && mkdir MADSEQ.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MADSEQ.buildbin-libdir MADSEQ_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MADSEQ_1.10.0.zip && rm MADSEQ_1.10.0.tar.gz MADSEQ_1.10.0.zip
###
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100 2126k  100 2126k    0     0  25.5M      0 --:--:-- --:--:-- --:--:-- 28.0M

install for i386

* installing *source* package 'MADSEQ' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MADSEQ'
    finding HTML links ... done
    MADSEQ-package                          html  
    MadSeq                                  html  
    aneuploidy_chr18                        html  
    deltaBIC                                html  
    normalizeCoverage                       html  
    finding level-2 HTML links ... done

    plotFraction                            html  
    plotMadSeq                              html  
    plotMixture                             html  
    posterior                               html  
    prepareCoverageGC                       html  
    prepareHetero                           html  
    runMadSeq                               html  
    summary-method                          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 'MADSEQ' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MADSEQ' as MADSEQ_1.10.0.zip
* DONE (MADSEQ)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MADSEQ' successfully unpacked and MD5 sums checked