Package: EMDomics

Version: 2.14.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EMDomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings EMDomics_2.14.0.tar.gz

StartedAt: 2019-10-16 03:29:19 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:31:33 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 134.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: EMDomics.Rcheck

Warnings: 1

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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:EMDomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings EMDomics_2.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/EMDomics.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 'EMDomics/DESCRIPTION' ... OK
* this is package 'EMDomics' version '2.14.0'
* 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 'EMDomics' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMzMAK6/R.INSTALLf7c45294999/EMDomics/man/calculate_emd.Rd:101: file link 'emd2d' in package 'emdist' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMzMAK6/R.INSTALLf7c45294999/EMDomics/man/calculate_emd_gene.Rd:31: file link 'emd2d' in package 'emdist' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMzMAK6/R.INSTALLf7c45294999/EMDomics/man/calculate_emd_gene.Rd:47: file link 'emd2d' in package 'emdist' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/EMDomics.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
  Sadhika Malladi  [aut, cre]
  Daniel Schmolze  [aut, cre]
* 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
.cvm_pairwise_q: no visible global function definition for 'combn'
.cvm_pairwise_q : : no visible global function definition
  for 'median'
.emd_gene_pairwise: no visible global function definition for 'hist'
.emd_pairwise_q: no visible global function definition for 'combn'
.emd_pairwise_q : : no visible global function definition
  for 'median'
.ks_pairwise_table: no visible global function definition for 'ks.test'
calculate_cvm: no visible global function definition for 'combn'
calculate_cvm : : no visible global function definition for
  'median'
calculate_cvm_gene: no visible global function definition for 'combn'
calculate_emd: no visible global function definition for 'combn'
calculate_emd : : no visible global function definition for
  'median'
calculate_emd_gene: no visible global function definition for 'combn'
calculate_ks: no visible global function definition for 'combn'
calculate_ks : : no visible global function definition for
  'p.adjust'
calculate_ks : : no visible global function definition for
  'median'
calculate_ks_gene: no visible global function definition for 'combn'
calculate_ks_gene: no visible global function definition for 'ks.test'
Undefined global functions or variables:
  combn hist ks.test median p.adjust
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "ks.test", "median", "p.adjust")
  importFrom("utils", "combn")
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 or elapsed time > 5s
                 user system elapsed
plot_cvm_density 6.32   0.03    6.35
calculate_cvm    5.25   0.02    5.27
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plot_cvm_density 9.19   0.01    9.20
plot_cvmperms    9.02   0.03    9.05
calculate_cvm    7.94   0.02    7.95
calculate_emd    5.61   0.02    5.64
plot_emd_density 5.43   0.01    5.45
plot_emdperms    5.30   0.02    5.31
* 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/EMDomics.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/EMDomics_2.14.0.tar.gz && rm -rf EMDomics.buildbin-libdir && mkdir EMDomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EMDomics.buildbin-libdir EMDomics_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL EMDomics_2.14.0.zip && rm EMDomics_2.14.0.tar.gz EMDomics_2.14.0.zip
###
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100 96830  100 96830    0     0   495k      0 --:--:-- --:--:-- --:--:--  516k

install for i386

* installing *source* package 'EMDomics' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'EMDomics'
    finding HTML links ... done
    CVMomics                                html  
    EMDomics                                html  
    KSomics                                 html  
    calculate_cvm                           html  
    calculate_cvm_gene                      html  
    calculate_emd                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMzMAK6/R.INSTALLf7c45294999/EMDomics/man/calculate_emd.Rd:101: file link 'emd2d' in package 'emdist' does not exist and so has been treated as a topic
    calculate_emd_gene                      html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMzMAK6/R.INSTALLf7c45294999/EMDomics/man/calculate_emd_gene.Rd:31: file link 'emd2d' in package 'emdist' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMzMAK6/R.INSTALLf7c45294999/EMDomics/man/calculate_emd_gene.Rd:47: file link 'emd2d' in package 'emdist' does not exist and so has been treated as a topic
    calculate_ks                            html  
    calculate_ks_gene                       html  
    emdomics-package                        html  
    plot_cvm_density                        html  
    plot_cvmnull                            html  
    plot_cvmperms                           html  
    plot_emd_density                        html  
    plot_emdnull                            html  
    plot_emdperms                           html  
    plot_ks_density                         html  
    plot_ksnull                             html  
    plot_ksperms                            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 'EMDomics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EMDomics' as EMDomics_2.14.0.zip
* DONE (EMDomics)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'EMDomics' successfully unpacked and MD5 sums checked