Package: BiGGR

Version: 1.18.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BiGGR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BiGGR_1.18.0.tar.gz

StartedAt: 2019-04-13 00:44:08 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 00:49:34 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 326.6 seconds

RetCode: 0

Status:  OK

CheckDir: BiGGR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BiGGR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BiGGR_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BiGGR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiGGR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BiGGR' version '1.18.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'BiGGR' 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
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: 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 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
gprMapping         148.82   0.01  149.18
gprMappingAvg       13.31   0.00   13.32
buildSBMLFromGenes   5.62   0.20    5.83
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/BiGGR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch BiGGR
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
* installing *source* package 'BiGGR' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiGGR'
    finding HTML links ... done
    BiGGR-internal                          html  
    BiGGR-package                           html  
    E.coli_iAF1260                          html  
    E.coli_iJR904                           html  
    E.coli_textbook                         html  
    Glycolysis                              html  
    H.pylori_ilT341                         html  
    H.sapiens_Recon1                        html  
    M.barkeri_iAF692                        html  
    M.tuberculosis_iNJ661                   html  
    P.putida_iJN746                         html  
    Recon2                                  html  
    S.aureus_iSB619                         html  
    S.cerevisiae_iND750                     html  
    buildSBMLFromBiGG                       html  
    buildSBMLFromGenes                      html  
    finding level-2 HTML links ... done

    buildSBMLFromPathways                   html  
    buildSBMLFromReactionIDs                html  
    createLIMFromBiGG                       html  
    createLIMFromSBML                       html  
    extractGeneAssociations                 html  
    extractPathways                         html  
    getPathwaysForSBML                      html  
    getRates                                html  
    gprMapping                              html  
    gprMappingAvg                           html  
    lying.tunell.data                       html  
    rmvSpliceVariant                        html  
    sampleFluxEnsemble                      html  
    sbml2hyperdraw                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiGGR)
Making 'packages.html' ... done
In R CMD INSTALL

name	user	system	elapsed
BiGGR-package	2.66	0.06	2.84
E.coli_iAF1260	0.87	0.14	1.10
E.coli_iJR904	0.33	0.00	0.38
E.coli_textbook	0.04	0.03	0.09
H.pylori_ilT341	0.16	0.06	0.25
H.sapiens_Recon1	1.37	0.04	1.41
M.barkeri_iAF692	0.22	0.17	0.47
M.tuberculosis_iNJ661	0.39	0.09	0.50
P.putida_iJN746	0.41	0.11	0.54
Recon2	1.77	0.02	1.88
S.aureus_iSB619	0.18	0.07	0.33
S.cerevisiae_iND750	0.32	0.07	0.42
buildSBMLFromBiGG	0.14	0.00	0.14
buildSBMLFromGenes	5.62	0.20	5.83
buildSBMLFromPathways	3.60	0.19	3.78
buildSBMLFromReactionIDs	1.53	0.00	1.54
createLIMFromBiGG	0.09	0.00	0.10
createLIMFromSBML	1.16	0.08	1.23
extractGeneAssociations	2.15	0.00	2.16
extractPathways	2.28	0.00	2.28
getPathwaysForSBML	2.72	0.00	2.72
getRates	0.00	0.03	0.22
gprMapping	148.82	0.01	149.18
gprMappingAvg	13.31	0.00	13.32
lying.tunell.data	0.01	0.00	0.01
rmvSpliceVariant	1.78	0.02	1.80
sampleFluxEnsemble	2.40	0.28	2.69
sbml2hyperdraw	2.32	0.00	2.33