Package: BiGGR

Version: 1.23.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiGGR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiGGR_1.23.0.tar.gz

StartedAt: 2019-12-19 01:49:24 -0500 (Thu, 19 Dec 2019)

EndedAt: 2019-12-19 01:56:14 -0500 (Thu, 19 Dec 2019)

EllapsedTime: 409.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiGGR.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiGGR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiGGR_1.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/BiGGR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiGGR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiGGR’ version ‘1.23.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BiGGR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for ‘type’
  Warning: multiple methods tables found for ‘type<-’
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/BiGGR.Rcheck/00install.out’ for details.
* 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
Package in Depends field not imported from: ‘stringr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.buildSubModel: no visible global function definition for ‘new’
buildSBMLFromBiGG: no visible global function definition for
  ‘read.delim’
buildSBMLFromBiGG : <anonymous>: no visible global function definition
  for ‘new’
buildSBMLFromBiGG: no visible global function definition for ‘new’
createLIMFromSBML: no visible global function definition for ‘hasArg’
gprMapping: no visible global function definition for ‘str_detect’
gprMapping: no visible global function definition for ‘na.omit’
gprMappingAvg: no visible global function definition for ‘na.omit’
sampleFluxEnsemble: no visible global function definition for ‘Xsample’
sbml2hyperdraw : <anonymous>: no visible binding for global variable
  ‘species’
sbml2hyperdraw: no visible global function definition for ‘hasArg’
sbml2hyperdraw: no visible global function definition for ‘graphLayout’
sbml2hyperdraw: no visible global function definition for
  ‘nodeDataDefaults<-’
sbml2hyperdraw: no visible global function definition for
  ‘edgeDataDefaults<-’
sbml2hyperdraw: no visible global function definition for
  ‘graphDataDefaults<-’
sbml2hyperdraw : <anonymous>: no visible global function definition for
  ‘edgeData<-’
Undefined global functions or variables:
  Xsample edgeData<- edgeDataDefaults<- graphDataDefaults<- graphLayout
  hasArg na.omit new nodeDataDefaults<- read.delim species str_detect
Consider adding
  importFrom("methods", "hasArg", "new")
  importFrom("stats", "na.omit")
  importFrom("utils", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 (user + system) or elapsed time > 5s
                         user system elapsed
gprMapping            155.915  5.297 161.466
gprMappingAvg          27.391  2.817  30.211
buildSBMLFromGenes      8.354  0.102   8.456
buildSBMLFromPathways   6.738  0.047   6.787
* 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 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/BiGGR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiGGR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘BiGGR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: multiple methods tables found for ‘type’ 
2: multiple methods tables found for ‘type<-’ 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: multiple methods tables found for ‘type’
Warning: multiple methods tables found for ‘type<-’
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for ‘type’
Warning: multiple methods tables found for ‘type<-’
** testing if installed package keeps a record of temporary installation path
* DONE (BiGGR)

name	user	system	elapsed
BiGGR-package	4.672	0.200	4.886
E.coli_iAF1260	1.565	0.072	1.636
E.coli_iJR904	0.801	0.035	0.836
E.coli_textbook	0.049	0.007	0.055
H.pylori_ilT341	0.328	0.016	0.343
H.sapiens_Recon1	2.16	0.13	2.29
M.barkeri_iAF692	0.366	0.020	0.386
M.tuberculosis_iNJ661	0.618	0.020	0.637
P.putida_iJN746	0.643	0.045	0.687
Recon2	2.639	0.324	2.962
S.aureus_iSB619	0.464	0.018	0.481
S.cerevisiae_iND750	0.817	0.069	0.886
buildSBMLFromBiGG	0.275	0.055	0.330
buildSBMLFromGenes	8.354	0.102	8.456
buildSBMLFromPathways	6.738	0.047	6.787
buildSBMLFromReactionIDs	2.598	0.069	2.668
createLIMFromBiGG	0.183	0.018	0.201
createLIMFromSBML	2.141	0.055	2.199
extractGeneAssociations	3.594	0.026	3.620
extractPathways	3.422	0.038	3.506
getPathwaysForSBML	4.154	0.060	4.282
getRates	0.006	0.005	0.011
gprMapping	155.915	5.297	161.466
gprMappingAvg	27.391	2.817	30.211
lying.tunell.data	0.004	0.006	0.009
rmvSpliceVariant	3.362	0.019	3.381
sampleFluxEnsemble	3.606	0.257	3.866
sbml2hyperdraw	3.924	0.080	4.007