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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KEGGlincs.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings KEGGlincs_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/KEGGlincs.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 'KEGGlincs/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KEGGlincs' version '1.14.0'
* 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 'KEGGlincs' 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 ... NOTE
Namespace in Imports field not imported from: 'XML'
  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 ... 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 ... 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
overlap_info            19.37   1.03   20.62
add_edge_data           16.18   1.22   30.48
path_genes_by_cell_type  9.99   0.38   10.56
edge_mapping_info        9.74   0.45   10.38
refine_mappings          8.86   0.39    9.89
get_graph_object         6.77   0.19    7.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
overlap_info            16.60   0.75   17.53
add_edge_data           15.58   0.61   16.55
edge_mapping_info       10.78   0.51   11.50
refine_mappings          9.22   0.14    9.55
path_genes_by_cell_type  8.17   0.19    8.56
get_graph_object         7.06   0.19    7.43
* 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/KEGGlincs.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/KEGGlincs_1.14.0.tar.gz && rm -rf KEGGlincs.buildbin-libdir && mkdir KEGGlincs.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=KEGGlincs.buildbin-libdir KEGGlincs_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL KEGGlincs_1.14.0.zip && rm KEGGlincs_1.14.0.tar.gz KEGGlincs_1.14.0.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
100 2148k  100 2148k    0     0  19.8M      0 --:--:-- --:--:-- --:--:-- 20.9M

install for i386

* installing *source* package 'KEGGlincs' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'KEGGlincs'
    finding HTML links ... done
    KEGG_lincs                              html  
    KEGGlincs                               html  
    KL_compare                              html  
    add_edge_data                           html  
    cyto_vis                                html  
    edge_mapping_info                       html  
    expand_KEGG_edges                       html  
    expand_KEGG_mappings                    html  
    generate_mappings                       html  
    get_KGML                                html  
    get_fisher_info                         html  
    get_graph_object                        html  
    keggerize_edges                         html  
    node_mapping_info                       html  
    overlap_info                            html  
    path_genes_by_cell_type                 html  
    refine_mappings                         html  
    tidy_edge                               html  
    toCytoscape                             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 'KEGGlincs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'KEGGlincs' as KEGGlincs_1.14.0.zip
* DONE (KEGGlincs)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'KEGGlincs' successfully unpacked and MD5 sums checked