Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:11:29 -0400 (Thu, 12 Apr 2018).
Package 113/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
BiGGR 1.14.0 Anand K. Gavai
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: BiGGR |
Version: 1.14.0 |
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BiGGR_1.14.0.tar.gz |
StartedAt: 2018-04-11 21:44:41 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 21:48:36 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 235.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BiGGR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BiGGR_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/BiGGR.Rcheck’ * using R version 3.4.4 (2018-03-15) * 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 ‘1.14.0’ * 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 ... 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’ 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 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 113.288 0.100 113.458 gprMappingAvg 14.132 0.004 14.150 buildSBMLFromGenes 6.084 0.160 6.246 * 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 ‘/home/biocbuild/bbs-3.6-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
name | user | system | elapsed | |
BiGGR-package | 3.176 | 0.064 | 3.319 | |
E.coli_iAF1260 | 0.936 | 0.056 | 0.997 | |
E.coli_iJR904 | 0.28 | 0.00 | 0.28 | |
E.coli_textbook | 0.024 | 0.040 | 0.065 | |
H.pylori_ilT341 | 0.164 | 0.028 | 0.189 | |
H.sapiens_Recon1 | 1.148 | 0.060 | 1.210 | |
M.barkeri_iAF692 | 0.272 | 0.060 | 0.333 | |
M.tuberculosis_iNJ661 | 0.252 | 0.044 | 0.297 | |
P.putida_iJN746 | 0.26 | 0.04 | 0.30 | |
Recon2 | 2.084 | 0.060 | 2.144 | |
S.aureus_iSB619 | 0.208 | 0.036 | 0.244 | |
S.cerevisiae_iND750 | 0.344 | 0.020 | 0.363 | |
buildSBMLFromBiGG | 0.108 | 0.000 | 0.108 | |
buildSBMLFromGenes | 6.084 | 0.160 | 6.246 | |
buildSBMLFromPathways | 4.104 | 0.044 | 4.150 | |
buildSBMLFromReactionIDs | 1.928 | 0.000 | 1.932 | |
createLIMFromBiGG | 0.184 | 0.000 | 0.186 | |
createLIMFromSBML | 0.908 | 0.020 | 0.926 | |
extractGeneAssociations | 2.096 | 0.000 | 2.099 | |
extractPathways | 2.104 | 0.008 | 2.113 | |
getPathwaysForSBML | 2.800 | 0.000 | 2.801 | |
getRates | 0.304 | 0.000 | 0.304 | |
gprMapping | 113.288 | 0.100 | 113.458 | |
gprMappingAvg | 14.132 | 0.004 | 14.150 | |
lying.tunell.data | 0.004 | 0.000 | 0.003 | |
rmvSpliceVariant | 2.196 | 0.008 | 2.206 | |
sampleFluxEnsemble | 3.324 | 0.028 | 3.374 | |
sbml2hyperdraw | 2.824 | 0.004 | 2.831 | |