Anand K. Gavai
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/BiGGR |
| Branch: RELEASE_3_12 |
| Last Commit: dde16eb |
| Last Changed Date: 2020-10-27 10:52:29 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:30:00 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the BiGGR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 147/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiGGR 1.26.0 (landing page) Anand K. Gavai
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
| Package: BiGGR |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BiGGR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BiGGR_1.26.0.tar.gz |
| StartedAt: 2021-05-06 00:44:12 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 00:50:52 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 399.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BiGGR.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BiGGR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BiGGR_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BiGGR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.26.0'
* 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 ... WARNING
Found the following significant warnings:
Warning: multiple methods tables found for 'type'
Warning: multiple methods tables found for 'type<-'
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BiGGR.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 5.0Mb
sub-directories of 1Mb or more:
data 3.8Mb
* 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 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 176.89 0.05 177.02
gprMappingAvg 14.05 0.00 14.05
buildSBMLFromGenes 7.68 0.31 7.98
buildSBMLFromPathways 5.57 0.08 5.66
sbml2hyperdraw 2.47 0.01 29.16
* 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, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/BiGGR.Rcheck/00check.log'
for details.
BiGGR.Rcheck/00install.out
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch BiGGR
###
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* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/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
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
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)
Making 'packages.html' ... done
BiGGR.Rcheck/BiGGR-Ex.timings
| name | user | system | elapsed | |
| BiGGR-package | 3.36 | 0.06 | 3.42 | |
| E.coli_iAF1260 | 1.14 | 0.06 | 1.21 | |
| E.coli_iJR904 | 0.81 | 0.02 | 0.83 | |
| E.coli_textbook | 0.13 | 0.01 | 0.14 | |
| H.pylori_ilT341 | 0.25 | 0.06 | 0.31 | |
| H.sapiens_Recon1 | 1.59 | 0.11 | 1.71 | |
| M.barkeri_iAF692 | 0.46 | 0.19 | 0.64 | |
| M.tuberculosis_iNJ661 | 0.54 | 0.08 | 0.62 | |
| P.putida_iJN746 | 0.61 | 0.08 | 0.69 | |
| Recon2 | 2.61 | 0.11 | 2.72 | |
| S.aureus_iSB619 | 0.34 | 0.04 | 0.39 | |
| S.cerevisiae_iND750 | 0.47 | 0.13 | 0.60 | |
| buildSBMLFromBiGG | 0.12 | 0.05 | 0.17 | |
| buildSBMLFromGenes | 7.68 | 0.31 | 7.98 | |
| buildSBMLFromPathways | 5.57 | 0.08 | 5.66 | |
| buildSBMLFromReactionIDs | 2.22 | 0.00 | 2.21 | |
| createLIMFromBiGG | 0.09 | 0.00 | 0.10 | |
| createLIMFromSBML | 1.49 | 0.04 | 1.55 | |
| extractGeneAssociations | 3.57 | 0.00 | 3.63 | |
| extractPathways | 3.04 | 0.00 | 3.04 | |
| getPathwaysForSBML | 4.02 | 0.00 | 4.02 | |
| getRates | 0.00 | 0.02 | 0.01 | |
| gprMapping | 176.89 | 0.05 | 177.02 | |
| gprMappingAvg | 14.05 | 0.00 | 14.05 | |
| lying.tunell.data | 0.00 | 0.01 | 0.01 | |
| rmvSpliceVariant | 2.10 | 0.00 | 2.11 | |
| sampleFluxEnsemble | 2.52 | 0.30 | 2.81 | |
| sbml2hyperdraw | 2.47 | 0.01 | 29.16 | |