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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethTargetedNGS.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MethTargetedNGS_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MethTargetedNGS.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 'MethTargetedNGS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethTargetedNGS' version '1.20.0'
* 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 'MethTargetedNGS' 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
compare_samples: no visible global function definition for 'par'
compare_samples: no visible global function definition for 'lines'
fishertest_cpg: no visible global function definition for 'fisher.test'
fishertest_cpg: no visible global function definition for 'p.adjust'
fishertest_cpg: no visible global function definition for 'barplot'
fishertest_cpg: no visible global function definition for 'abline'
methAlign: no visible global function definition for 'subject'
methAlign: no visible global function definition for 'pattern'
nhmmer: no visible global function definition for 'read.table'
nhmmer: no visible global function definition for 'setNames'
Undefined global functions or variables:
  abline barplot fisher.test lines p.adjust par pattern read.table
  setNames subject
Consider adding
  importFrom("graphics", "abline", "barplot", "lines", "par")
  importFrom("stats", "fisher.test", "p.adjust", "setNames")
  importFrom("utils", "read.table")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
fishertest_cpg  5.28   0.01    5.30
odd_ratio       5.16   0.00    5.16
compare_samples 4.96   0.18    5.16
** 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/MethTargetedNGS.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/MethTargetedNGS_1.20.0.tar.gz && rm -rf MethTargetedNGS.buildbin-libdir && mkdir MethTargetedNGS.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MethTargetedNGS.buildbin-libdir MethTargetedNGS_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL MethTargetedNGS_1.20.0.zip && rm MethTargetedNGS_1.20.0.tar.gz MethTargetedNGS_1.20.0.zip
###
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100 14231  100 14231    0     0   212k      0 --:--:-- --:--:-- --:--:--  239k

install for i386

* installing *source* package 'MethTargetedNGS' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MethTargetedNGS'
    finding HTML links ... done
    MethTargetedNGS-package                 html  
    bconv                                   html  
    compare_samples                         html  
    fishertest_cpg                          html  
    hmmbuild                                html  
    methAlign                               html  
    methAvg                                 html  
    methEntropy                             html  
    methHeatmap                             html  
    nhmmer                                  html  
    odd_ratio                               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 'MethTargetedNGS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MethTargetedNGS' as MethTargetedNGS_1.20.0.zip
* DONE (MethTargetedNGS)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'MethTargetedNGS' successfully unpacked and MD5 sums checked