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This page was generated on 2022-01-17 13:06:28 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for KEGGlincs on tokay2


To the developers/maintainers of the KEGGlincs package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/KEGGlincs.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 980/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGlincs 1.20.0  (landing page)
Shana White , Mario Medvedovic
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/KEGGlincs
git_branch: RELEASE_3_14
git_last_commit: 65205d4
git_last_commit_date: 2021-10-26 12:30:32 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: KEGGlincs
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KEGGlincs.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings KEGGlincs_1.20.0.tar.gz
StartedAt: 2022-01-16 22:53:17 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 22:58:11 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 294.0 seconds
RetCode: 0
Status:   OK  
CheckDir: KEGGlincs.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KEGGlincs.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings KEGGlincs_1.20.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/KEGGlincs.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.20.0'
* 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           13.89   1.88   16.70
overlap_info            13.73   1.08   15.01
edge_mapping_info        8.42   0.30    8.93
path_genes_by_cell_type  8.05   0.30    8.55
refine_mappings          7.63   0.33    8.46
get_graph_object         5.47   0.14    5.81
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
add_edge_data           14.50   0.92   15.98
overlap_info            14.58   0.56   15.34
edge_mapping_info        9.22   0.20    9.63
path_genes_by_cell_type  8.11   0.41    8.72
refine_mappings          6.98   0.23    7.42
get_graph_object         6.36   0.12    6.70
* 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-3.14-bioc/meat/KEGGlincs.Rcheck/00check.log'
for details.



Installation output

KEGGlincs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/KEGGlincs_1.20.0.tar.gz && rm -rf KEGGlincs.buildbin-libdir && mkdir KEGGlincs.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=KEGGlincs.buildbin-libdir KEGGlincs_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL KEGGlincs_1.20.0.zip && rm KEGGlincs_1.20.0.tar.gz KEGGlincs_1.20.0.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 2149k  100 2149k    0     0  4932k      0 --:--:-- --:--:-- --:--:-- 4941k

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_1.20.0.zip
* DONE (KEGGlincs)
* installing to library 'C:/Users/biocbuild/bbs-3.14-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_data13.89 1.8816.70
cyto_vis0.440.000.64
edge_mapping_info8.420.308.93
expand_KEGG_edges0.260.000.47
expand_KEGG_mappings0.670.030.92
generate_mappings000
get_KGML0.300.000.92
get_fisher_info0.010.000.02
get_graph_object5.470.145.81
keggerize_edges000
node_mapping_info0.240.010.46
overlap_info13.73 1.0815.01
path_genes_by_cell_type8.050.308.55
refine_mappings7.630.338.46
tidy_edge000

KEGGlincs.Rcheck/examples_x64/KEGGlincs-Ex.timings

nameusersystemelapsed
KEGG_lincs000
KL_compare000
add_edge_data14.50 0.9215.98
cyto_vis0.420.000.64
edge_mapping_info9.220.209.63
expand_KEGG_edges0.250.000.45
expand_KEGG_mappings0.340.040.58
generate_mappings000
get_KGML0.310.000.92
get_fisher_info000
get_graph_object6.360.126.70
keggerize_edges000
node_mapping_info0.240.000.45
overlap_info14.58 0.5615.34
path_genes_by_cell_type8.110.418.72
refine_mappings6.980.237.42
tidy_edge000