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CHECK report for KEGGlincs on malbec2

This page was generated on 2019-10-16 12:09:45 -0400 (Wed, 16 Oct 2019).

Package 855/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGlincs 1.10.0
Shana White , Mario Medvedovic
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/KEGGlincs
Branch: RELEASE_3_9
Last Commit: 48cbf12
Last Changed Date: 2019-05-02 11:54:04 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: KEGGlincs
Version: 1.10.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings KEGGlincs_1.10.0.tar.gz
StartedAt: 2019-10-16 02:41:18 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:44:31 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 193.0 seconds
RetCode: 0
Status:  OK 
CheckDir: KEGGlincs.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings KEGGlincs_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/KEGGlincs.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.10.0’
* 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
overlap_info            19.439  0.652  20.440
add_edge_data           19.369  0.491  21.620
edge_mapping_info       10.512  0.276  11.022
path_genes_by_cell_type  9.354  0.124   9.721
refine_mappings          9.093  0.240   9.652
get_graph_object         7.357  0.028   7.625
* 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-3.9-bioc/meat/KEGGlincs.Rcheck/00check.log’
for details.



Installation output

KEGGlincs.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL KEGGlincs
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘KEGGlincs’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (KEGGlincs)

Tests output


Example timings

KEGGlincs.Rcheck/KEGGlincs-Ex.timings

nameusersystemelapsed
KEGG_lincs000
KL_compare000
add_edge_data19.369 0.49121.620
cyto_vis0.3980.0000.636
edge_mapping_info10.512 0.27611.022
expand_KEGG_edges0.3930.0200.643
expand_KEGG_mappings0.1870.0000.417
generate_mappings0.0010.0000.001
get_KGML0.2200.0000.904
get_fisher_info0.0020.0000.003
get_graph_object7.3570.0287.625
keggerize_edges0.0000.0000.001
node_mapping_info0.1540.0000.392
overlap_info19.439 0.65220.440
path_genes_by_cell_type9.3540.1249.721
refine_mappings9.0930.2409.652
tidy_edge0.0010.0000.001