Multiple platform build/check report for BioC 3.9 - CHECK report for RITAN on tokay2

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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:RITAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RITAN_1.7.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RITAN.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RITAN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RITAN' version '1.7.0'
* 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 'RITAN' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'gplots::plotCI' by 'plotrix::plotCI' when loading 'RITAN'
  Warning: replacing previous import 'gplots::lowess' by 'stats::lowess' when loading 'RITAN'
  Warning: replacing previous import 'igraph::spectrum' by 'stats::spectrum' when loading 'RITAN'
  Warning: replacing previous import 'igraph::decompose' by 'stats::decompose' when loading 'RITAN'
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RITAN.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'sqldf'
A package should be listed in only one of these fields.
* 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 ... NOTE
Namespaces in Imports field not imported from:
  'BgeeDB' 'knitr'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
check_any_net_input: no visible binding for global variable
  'network_list'
enrichment_symbols: no visible binding for global variable
  'active_genesets'
icon_dual_between: no visible global function definition for 'ss2'
icon_dual_between: no visible binding for global variable 'all_symbols'
icon_dual_between: no visible binding for global variable 'all_net'
icon_single_within: no visible global function definition for 'ss2'
icon_single_within: no visible binding for global variable
  'all_symbols'
icon_single_within: no visible binding for global variable 'all_net'
load_geneset_symbols: no visible binding for global variable
  'geneset_list'
load_geneset_symbols: no visible binding for global variable 'f'
load_geneset_symbols: no visible binding for global variable
  'active_genesets'
network_overlap : <anonymous>: no visible binding for global variable
  'network_list'
network_overlap: no visible binding for global variable 'network_list'
network_overlap : select_edges: no visible binding for global variable
  'network_list'
plot.term_enrichment_by_subset: no visible binding for global variable
  'Var2'
plot.term_enrichment_by_subset: no visible binding for global variable
  'Var1'
show_active_genesets_hist: no visible binding for global variable
  'active_genesets'
term_enrichment : process_source: no visible binding for global
  variable 'active_genesets'
Undefined global functions or variables:
  Var1 Var2 active_genesets all_net all_symbols f geneset_list
  network_list ss2
* 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
Documented arguments not in \usage in documentation object 'resource_reduce':
  'mutual_overlap'

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 ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
summary.term_enrichment_by_subset 39.24  13.58   54.45
enrichment_symbols                21.33   9.62   33.63
term_enrichment                   20.56  10.17   31.52
plot.term_enrichment              20.36   6.86   28.00
summary.term_enrichment           18.81   7.81   27.44
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
summary.term_enrichment_by_subset 30.26  15.56   48.44
enrichment_symbols                19.22   8.69   29.06
term_enrichment                   16.60   9.43   26.78
summary.term_enrichment           15.02   9.28   25.06
plot.term_enrichment              14.73   9.17   24.69
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/RITAN.Rcheck/00check.log'
for details.

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###
### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/RITAN_1.7.0.tar.gz && rm -rf RITAN.buildbin-libdir && mkdir RITAN.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RITAN.buildbin-libdir RITAN_1.7.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RITAN_1.7.0.zip && rm RITAN_1.7.0.tar.gz RITAN_1.7.0.zip
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install for i386

* installing *source* package 'RITAN' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'gplots::plotCI' by 'plotrix::plotCI' when loading 'RITAN'
Warning: replacing previous import 'gplots::lowess' by 'stats::lowess' when loading 'RITAN'
Warning: replacing previous import 'igraph::spectrum' by 'stats::spectrum' when loading 'RITAN'
Warning: replacing previous import 'igraph::decompose' by 'stats::decompose' when loading 'RITAN'
** help
*** installing help indices
  converting help for package 'RITAN'
    finding HTML links ... done
    as.graph                                html  
    check_any_net_input                     html  
    check_net_input                         html  
    enrichment_symbols                      html  
    geneset_overlap                         html  
    icon_test                               html  
    load_all_protein_coding_symbols         html  
    load_geneset_symbols                    html  
    network_overlap                         html  
    plot.term_enrichment                    html  
    plot.term_enrichment_by_subset          html  
    readGMT                                 html  
    readSIF                                 html  
    resource_reduce                         html  
    show_active_genesets_hist               html  
    summary.term_enrichment                 html  
    summary.term_enrichment_by_subset       html  
    term_enrichment                         html  
    term_enrichment_by_subset               html  
    vac1.day0vs31.de.genes                  html  
    vac1.day0vs56.de.genes                  html  
    vac2.day0vs31.de.genes                  html  
    vac2.day0vs56.de.genes                  html  
    writeGMT                                html  
    write_simple_table                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'gplots::plotCI' by 'plotrix::plotCI' when loading 'RITAN'
Warning: replacing previous import 'gplots::lowess' by 'stats::lowess' when loading 'RITAN'
Warning: replacing previous import 'igraph::spectrum' by 'stats::spectrum' when loading 'RITAN'
Warning: replacing previous import 'igraph::decompose' by 'stats::decompose' when loading 'RITAN'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'gplots::plotCI' by 'plotrix::plotCI' when loading 'RITAN'
Warning: replacing previous import 'gplots::lowess' by 'stats::lowess' when loading 'RITAN'
Warning: replacing previous import 'igraph::spectrum' by 'stats::spectrum' when loading 'RITAN'
Warning: replacing previous import 'igraph::decompose' by 'stats::decompose' when loading 'RITAN'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'RITAN' ...
** testing if installed package can be loaded
Warning: replacing previous import 'gplots::plotCI' by 'plotrix::plotCI' when loading 'RITAN'
Warning: replacing previous import 'igraph::decompose' by 'stats::decompose' when loading 'RITAN'
Warning: replacing previous import 'gplots::lowess' by 'stats::lowess' when loading 'RITAN'
Warning: replacing previous import 'igraph::spectrum' by 'stats::spectrum' when loading 'RITAN'
* MD5 sums
packaged installation of 'RITAN' as RITAN_1.7.0.zip
* DONE (RITAN)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RITAN' successfully unpacked and MD5 sums checked

CHECK report for RITAN on tokay2

Summary

Command output

Installation output

Tests output

Example timings