BioC 3.4: CHECK report for StarBioTrek on morelia

Package: StarBioTrek

Version: 1.0.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings StarBioTrek_1.0.3.tar.gz

StartedAt: 2017-04-15 08:35:34 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 08:42:32 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 418.5 seconds

RetCode: 0

Status:  OK

CheckDir: StarBioTrek.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings StarBioTrek_1.0.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/StarBioTrek.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.0.3’
* 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 11.0Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
    doc    2.0Mb
* 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 loading without being on the library search path ... 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
GE_matrix: no visible binding for global variable ‘path’
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’
matrix_plot: no visible binding for global variable ‘path’
plotting_cross_talk: no visible binding for global variable ‘path’
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 path
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
getKEGGdata   7.225  0.141   9.761
list_path_net 6.571  0.208   6.785
* 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-3.4-bioc/meat/StarBioTrek.Rcheck/00check.log’
for details.

* installing *source* package ‘StarBioTrek’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (StarBioTrek)

name	user	system	elapsed
GE_matrix	0.677	0.013	0.690
SelectedSample	0.614	0.021	0.635
average	0.011	0.001	0.011
ds_score_crtlk	0.038	0.006	0.044
euc_dist_crtlk	0.522	0.009	0.531
getKEGGdata	7.225	0.141	9.761
getNETdata	2.174	0.078	4.172
list_path_net	6.571	0.208	6.785
matrix_plot	0.050	0.009	0.061
path_net	4.085	0.170	4.262
plotting_cross_talk	0.044	0.011	0.055
st_dv	0.020	0.005	0.025
svm_classification	1.991	0.056	2.047