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CHECK report for KEGGlincs on malbec1

This page was generated on 2019-04-16 11:52:23 -0400 (Tue, 16 Apr 2019).

Package 817/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGlincs 1.8.0
Shana White , Mario Medvedovic
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/KEGGlincs
Branch: RELEASE_3_8
Last Commit: 4c5235e
Last Changed Date: 2018-10-30 11:42:02 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: KEGGlincs
Version: 1.8.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings KEGGlincs_1.8.0.tar.gz
StartedAt: 2019-04-16 00:57:05 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:00:16 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 190.1 seconds
RetCode: 0
Status:  OK 
CheckDir: KEGGlincs.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings KEGGlincs_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/KEGGlincs.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGlincs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGlincs’ version ‘1.8.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
add_edge_data           21.600  0.416  23.126
overlap_info            19.444  0.440  20.196
edge_mapping_info       11.052  0.240  11.544
path_genes_by_cell_type 10.508  0.116  10.893
refine_mappings          9.636  0.136  10.021
get_graph_object         8.504  0.076   8.859
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/KEGGlincs.Rcheck/00check.log’
for details.



Installation output

KEGGlincs.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL KEGGlincs
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘KEGGlincs’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (KEGGlincs)

Tests output


Example timings

KEGGlincs.Rcheck/KEGGlincs-Ex.timings

nameusersystemelapsed
KEGG_lincs000
KL_compare000
add_edge_data21.600 0.41623.126
cyto_vis0.5880.0040.826
edge_mapping_info11.052 0.24011.544
expand_KEGG_edges0.4320.0200.704
expand_KEGG_mappings0.2240.0040.476
generate_mappings0.0040.0000.001
get_KGML0.2560.0000.959
get_fisher_info0.0040.0000.005
get_graph_object8.5040.0768.859
keggerize_edges000
node_mapping_info0.1560.0000.402
overlap_info19.444 0.44020.196
path_genes_by_cell_type10.508 0.11610.893
refine_mappings 9.636 0.13610.021
tidy_edge0.0040.0000.000