Package: MethTargetedNGS

Version: 1.18.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethTargetedNGS.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MethTargetedNGS_1.18.0.tar.gz

StartedAt: 2020-04-15 04:38:22 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:40:52 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 150.4 seconds

RetCode: 0

Status:  OK

CheckDir: MethTargetedNGS.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethTargetedNGS.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MethTargetedNGS_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/MethTargetedNGS.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 'MethTargetedNGS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethTargetedNGS' version '1.18.0'
* 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 'plot'
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 plot read.table
  setNames subject
Consider adding
  importFrom("graphics", "abline", "barplot", "lines", "par", "plot")
  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
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
odd_ratio 5.34      0    5.34
* 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-3.10-bioc/meat/MethTargetedNGS.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/MethTargetedNGS_1.18.0.tar.gz && rm -rf MethTargetedNGS.buildbin-libdir && mkdir MethTargetedNGS.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MethTargetedNGS.buildbin-libdir MethTargetedNGS_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL MethTargetedNGS_1.18.0.zip && rm MethTargetedNGS_1.18.0.tar.gz MethTargetedNGS_1.18.0.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 13299  100 13299    0     0   226k      0 --:--:-- --:--:-- --:--:--  245k

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_1.18.0.zip
* DONE (MethTargetedNGS)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'MethTargetedNGS' successfully unpacked and MD5 sums checked