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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Sushi.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Sushi_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/Sushi.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 'Sushi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Sushi' 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 'Sushi' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... WARNING
Undocumented arguments in documentation object 'plotBedpe'
  'border'

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 ... WARNING
  Warning: large data file saved inefficiently:
                      size ASCII compress
  Sushi_5C.bedpe.rda 321Kb  TRUE     none
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                  old_size new_size compress
  Sushi_5C.bedpe.rda                 321Kb     62Kb       xz
  Sushi_ChIAPET_pol2.bedpe.rda       846Kb    449Kb       xz
  Sushi_ChIPExo_CTCF.bedgraph.rda     29Kb     13Kb       xz
  Sushi_ChIPSeq_CTCF.bedgraph.rda    160Kb     37Kb       xz
  Sushi_ChIPSeq_pol2.bedgraph.rda     28Kb     11Kb       xz
  Sushi_DNaseI.bedgraph.rda           23Kb     12Kb       xz
  Sushi_GWAS.bed.rda                 515Kb    241Kb       xz
  Sushi_HiC.matrix.rda                40Kb     31Kb       xz
* 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: 2 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/Sushi.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/Sushi_1.26.0.tar.gz && rm -rf Sushi.buildbin-libdir && mkdir Sushi.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Sushi.buildbin-libdir Sushi_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Sushi_1.26.0.zip && rm Sushi_1.26.0.tar.gz Sushi_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
  0 4024k    0 16384    0     0  32687      0  0:02:06 --:--:--  0:02:06 33032
100 4024k  100 4024k    0     0  7323k      0 --:--:-- --:--:-- --:--:-- 7397k

install for i386

* installing *source* package 'Sushi' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Sushi'
    finding HTML links ... done
    SushiColors                             html  
    Sushi_5C.bedpe                          html  
    Sushi_ChIAPET_pol2.bedpe                html  
    Sushi_ChIPExo_CTCF.bedgraph             html  
    Sushi_ChIPSeq_CTCF.bedgraph             html  
    Sushi_ChIPSeq_pol2.bed                  html  
    Sushi_ChIPSeq_pol2.bedgraph             html  
    Sushi_ChIPSeq_severalfactors.bed        html  
    Sushi_DNaseI.bedgraph                   html  
    Sushi_GWAS.bed                          html  
    Sushi_HiC.matrix                        html  
    Sushi_RNASeq_K562.bedgraph              html  
    Sushi_genes.bed                         html  
    Sushi_hg18_genome                       html  
    Sushi_transcripts.bed                   html  
    addlegend                               html  
    chromOffsets                            html  
    convertstrandinfo                       html  
    labelgenome                             html  
    labelplot                               html  
    maptocolors                             html  
    maptolwd                                html  
    opaque                                  html  
    plotBed                                 html  
    plotBedgraph                            html  
    plotBedpe                               html  
    plotGenes                               html  
    finding level-2 HTML links ... done

    plotHic                                 html  
    plotManhattan                           html  
    sortChrom                               html  
    zoombox                                 html  
    zoomsregion                             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 'Sushi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Sushi' as Sushi_1.26.0.zip
* DONE (Sushi)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'Sushi' successfully unpacked and MD5 sums checked