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BioC 3.4: CHECK report for BiGGR on zin1

This page was generated on 2016-09-21 03:38:33 -0700 (Wed, 21 Sep 2016).

Package 101/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.9.0
Anand K. Gavai , Hannes Hettling
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiGGR
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  ERROR  ERROR 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiGGR
Version: 1.9.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings BiGGR_1.9.0.tar.gz
StartedAt: 2016-09-20 03:40:49 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 03:44:57 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 247.8 seconds
RetCode: 0
Status:  OK 
CheckDir: BiGGR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings BiGGR_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/BiGGR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.9.0’
* 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 ‘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 loading without being on the library search path ... 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’
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 xsample
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 or elapsed time > 5s
                      user system elapsed
gprMapping         134.436  0.028 134.476
gprMappingAvg       15.124  0.004  15.128
buildSBMLFromGenes   5.608  0.068   5.676
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/BiGGR.Rcheck/00check.log’
for details.


BiGGR.Rcheck/00install.out:

* installing *source* package ‘BiGGR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiGGR)

BiGGR.Rcheck/BiGGR-Ex.timings:

nameusersystemelapsed
BiGGR-package2.5480.0642.641
E.coli_iAF12600.6480.0280.677
E.coli_iJR9040.3800.0000.378
E.coli_textbook0.0360.0040.040
H.pylori_ilT3410.1480.0120.158
H.sapiens_Recon10.9120.0240.937
M.barkeri_iAF6920.2200.0400.258
M.tuberculosis_iNJ6610.2600.0240.285
P.putida_iJN7460.2920.0240.315
Recon22.3680.0602.425
S.aureus_iSB6190.2120.0080.218
S.cerevisiae_iND7500.3040.0160.322
buildSBMLFromBiGG0.1240.0000.126
buildSBMLFromGenes5.6080.0685.676
buildSBMLFromPathways3.7960.0083.806
buildSBMLFromReactionIDs1.4400.0001.443
createLIMFromBiGG0.1120.0000.112
createLIMFromSBML0.8480.0080.856
extractGeneAssociations2.1400.0002.139
extractPathways2.0360.0042.042
getPathwaysForSBML2.5120.0002.514
getRates0.0040.0000.008
gprMapping134.436 0.028134.476
gprMappingAvg15.124 0.00415.128
lying.tunell.data0.0040.0000.003
rmvSpliceVariant2.0520.0002.052
sampleFluxEnsemble2.5840.0282.612
sbml2hyperdraw2.3200.0002.322