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CHECK report for StarBioTrek on merida2

This page was generated on 2018-10-17 08:57:23 -0400 (Wed, 17 Oct 2018).

Package 1436/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
StarBioTrek 1.6.0
Claudia Cava
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/StarBioTrek
Branch: RELEASE_3_7
Last Commit: d0be5e0
Last Changed Date: 2018-04-30 10:35:44 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: StarBioTrek
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:StarBioTrek.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings StarBioTrek_1.6.0.tar.gz
StartedAt: 2018-10-17 00:18:02 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:23:44 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 341.8 seconds
RetCode: 0
Status:  OK 
CheckDir: StarBioTrek.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:StarBioTrek.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings StarBioTrek_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/StarBioTrek.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘StarBioTrek/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘StarBioTrek’ version ‘1.6.0’
* 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 ‘StarBioTrek’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getKEGGdata: no visible binding for global variable ‘Carbohydrate’
getKEGGdata: no visible binding for global variable ‘Energy’
getKEGGdata: no visible binding for global variable ‘Lipid’
getKEGGdata: no visible binding for global variable ‘Aminoacid’
getKEGGdata: no visible binding for global variable ‘Glybio_met’
getKEGGdata: no visible binding for global variable ‘Cofa_vita_met’
getKEGGdata: no visible binding for global variable ‘Transcription’
getKEGGdata: no visible binding for global variable ‘Translation’
getKEGGdata: no visible binding for global variable
  ‘Folding_sorting_and_degradation’
getKEGGdata: no visible binding for global variable
  ‘Replication_and_repair’
getKEGGdata: no visible binding for global variable
  ‘Signal_transduction’
getKEGGdata: no visible binding for global variable
  ‘Signaling_molecules_and_interaction’
getKEGGdata: no visible binding for global variable
  ‘Transport_and_catabolism’
getKEGGdata: no visible binding for global variable
  ‘Cell_growth_and_death’
getKEGGdata: no visible binding for global variable
  ‘Cellular_community’
getKEGGdata: no visible binding for global variable ‘Immune_system’
getKEGGdata: no visible binding for global variable ‘Endocrine_system’
getKEGGdata: no visible binding for global variable
  ‘Circulatory_system’
getKEGGdata: no visible binding for global variable ‘Digestive_system’
getKEGGdata: no visible binding for global variable ‘Excretory_system’
getKEGGdata: no visible binding for global variable ‘Nervous_system’
getKEGGdata: no visible binding for global variable ‘Sensory_system’
svm_classification: no visible binding for global variable ‘Target’
Undefined global functions or variables:
  Aminoacid Carbohydrate Cell_growth_and_death Cellular_community
  Circulatory_system Cofa_vita_met Digestive_system Endocrine_system
  Energy Excretory_system Folding_sorting_and_degradation Glybio_met
  Immune_system Lipid Nervous_system Replication_and_repair
  Sensory_system Signal_transduction
  Signaling_molecules_and_interaction Target Transcription Translation
  Transport_and_catabolism
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
IPPI        17.916  0.583  18.672
getKEGGdata  4.655  0.129   7.333
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/StarBioTrek.Rcheck/00check.log’
for details.



Installation output

StarBioTrek.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL StarBioTrek
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘StarBioTrek’ ...
** R
** data
*** moving datasets to lazyload DB
** 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 (StarBioTrek)

Tests output


Example timings

StarBioTrek.Rcheck/StarBioTrek-Ex.timings

nameusersystemelapsed
GE_matrix0.1610.0130.174
IPPI17.916 0.58318.672
SelectedSample0.1030.0300.134
average0.0120.0010.013
ds_score_crtlk0.0350.0080.044
euc_dist_crtlk0.0140.0030.018
getKEGGdata4.6550.1297.333
getNETdata1.3550.0923.451
list_path_net3.2020.2213.443
matrix_plot0.1080.0130.121
path_net2.9300.2043.154
plotting_cross_talk0.0370.0090.045
st_dv0.0180.0040.022
svm_classification1.8770.0301.918