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CHECK report for KEGGlincs on tokay1

This page was generated on 2021-05-05 12:12:15 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the KEGGlincs package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 938/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGlincs 1.16.0  (landing page)
Shana White , Mario Medvedovic
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/KEGGlincs
Branch: RELEASE_3_12
Last Commit: cc5f8bd
Last Changed Date: 2020-10-27 11:18:22 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: KEGGlincs
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KEGGlincs.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings KEGGlincs_1.16.0.tar.gz
StartedAt: 2021-05-05 04:04:51 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 04:11:03 -0400 (Wed, 05 May 2021)
EllapsedTime: 372.6 seconds
RetCode: 0
Status:   OK   
CheckDir: KEGGlincs.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KEGGlincs.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings KEGGlincs_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/KEGGlincs.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.16.0'
* 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
add_edge_data           17.45   1.48   71.40
overlap_info            16.59   1.00   17.84
edge_mapping_info       11.13   0.39   11.74
refine_mappings         11.10   0.25   12.34
path_genes_by_cell_type  9.61   0.25   10.08
get_graph_object         6.30   0.09    6.60
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
overlap_info            15.48   0.62   16.33
add_edge_data           14.12   0.61   15.11
edge_mapping_info        9.50   0.27    9.97
path_genes_by_cell_type  7.95   0.22    8.39
refine_mappings          7.33   0.22    7.77
get_graph_object         6.58   0.14    6.92
* 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-3.12-bioc/meat/KEGGlincs.Rcheck/00check.log'
for details.



Installation output

KEGGlincs.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/KEGGlincs_1.16.0.tar.gz && rm -rf KEGGlincs.buildbin-libdir && mkdir KEGGlincs.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=KEGGlincs.buildbin-libdir KEGGlincs_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL KEGGlincs_1.16.0.zip && rm KEGGlincs_1.16.0.tar.gz KEGGlincs_1.16.0.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  35.1M      0 --:--:-- --:--:-- --:--:-- 35.5M

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_1.16.0.zip
* DONE (KEGGlincs)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'KEGGlincs' successfully unpacked and MD5 sums checked

Tests output


Example timings

KEGGlincs.Rcheck/examples_i386/KEGGlincs-Ex.timings

nameusersystemelapsed
KEGG_lincs000
KL_compare000
add_edge_data17.45 1.4871.40
cyto_vis0.250.000.86
edge_mapping_info11.13 0.3911.74
expand_KEGG_edges0.280.000.48
expand_KEGG_mappings0.800.051.06
generate_mappings000
get_KGML0.280.000.95
get_fisher_info000
get_graph_object6.300.096.60
keggerize_edges000
node_mapping_info0.220.000.45
overlap_info16.59 1.0017.84
path_genes_by_cell_type 9.61 0.2510.08
refine_mappings11.10 0.2512.34
tidy_edge000

KEGGlincs.Rcheck/examples_x64/KEGGlincs-Ex.timings

nameusersystemelapsed
KEGG_lincs000
KL_compare000
add_edge_data14.12 0.6115.11
cyto_vis0.30.00.5
edge_mapping_info9.500.279.97
expand_KEGG_edges0.140.000.36
expand_KEGG_mappings0.320.030.56
generate_mappings000
get_KGML0.290.000.94
get_fisher_info000
get_graph_object6.580.146.92
keggerize_edges000
node_mapping_info0.130.000.34
overlap_info15.48 0.6216.33
path_genes_by_cell_type7.950.228.39
refine_mappings7.330.227.77
tidy_edge0.020.000.01