Anand K. Gavai
| Snapshot Date: 2019-03-29 17:01:00 -0400 (Fri, 29 Mar 2019) |
| URL: https://git.bioconductor.org/packages/BiGGR |
| Branch: master |
| Last Commit: fcab01b |
| Last Changed Date: 2018-10-30 11:54:31 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-03-30 11:39:39 -0400 (Sat, 30 Mar 2019).
| Package 129/1686 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiGGR 1.19.0 Anand K. Gavai
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: BiGGR |
| Version: 1.19.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BiGGR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BiGGR_1.19.0.tar.gz |
| StartedAt: 2019-03-30 01:58:28 -0400 (Sat, 30 Mar 2019) |
| EndedAt: 2019-03-30 02:04:04 -0400 (Sat, 30 Mar 2019) |
| EllapsedTime: 336.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiGGR.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BiGGR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BiGGR_1.19.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BiGGR.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.19.0'
* 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 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 169.26 0.07 171.53
gprMappingAvg 18.31 0.03 18.35
buildSBMLFromGenes 6.34 0.42 6.77
* 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-3.9-bioc/meat/BiGGR.Rcheck/00check.log'
for details.
BiGGR.Rcheck/00install.out
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch BiGGR
###
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* installing to library 'C:/Users/biocbuild/bbs-3.9-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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiGGR)
Making 'packages.html' ... done
BiGGR.Rcheck/BiGGR-Ex.timings
| name | user | system | elapsed | |
| BiGGR-package | 2.84 | 0.08 | 3.09 | |
| E.coli_iAF1260 | 1.41 | 0.14 | 1.55 | |
| E.coli_iJR904 | 0.60 | 0.01 | 0.61 | |
| E.coli_textbook | 0.06 | 0.10 | 0.19 | |
| H.pylori_ilT341 | 0.39 | 0.09 | 0.48 | |
| H.sapiens_Recon1 | 1.78 | 0.02 | 1.80 | |
| M.barkeri_iAF692 | 0.29 | 0.20 | 0.50 | |
| M.tuberculosis_iNJ661 | 0.52 | 0.11 | 0.65 | |
| P.putida_iJN746 | 0.48 | 0.06 | 0.55 | |
| Recon2 | 2.44 | 0.05 | 2.48 | |
| S.aureus_iSB619 | 0.33 | 0.08 | 0.41 | |
| S.cerevisiae_iND750 | 0.47 | 0.06 | 0.53 | |
| buildSBMLFromBiGG | 0.11 | 0.05 | 0.25 | |
| buildSBMLFromGenes | 6.34 | 0.42 | 6.77 | |
| buildSBMLFromPathways | 3.92 | 0.15 | 4.07 | |
| buildSBMLFromReactionIDs | 1.94 | 0.00 | 2.07 | |
| createLIMFromBiGG | 0.16 | 0.00 | 0.60 | |
| createLIMFromSBML | 1.64 | 0.04 | 1.68 | |
| extractGeneAssociations | 2.17 | 0.02 | 2.19 | |
| extractPathways | 2.43 | 0.00 | 2.44 | |
| getPathwaysForSBML | 3.73 | 0.01 | 3.78 | |
| getRates | 0.02 | 0.00 | 0.01 | |
| gprMapping | 169.26 | 0.07 | 171.53 | |
| gprMappingAvg | 18.31 | 0.03 | 18.35 | |
| lying.tunell.data | 0.00 | 0.01 | 0.01 | |
| rmvSpliceVariant | 2.79 | 0.00 | 2.78 | |
| sampleFluxEnsemble | 2.92 | 0.24 | 3.64 | |
| sbml2hyperdraw | 3.10 | 0.04 | 3.14 | |