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This page was generated on 2021-06-18 14:06:43 -0400 (Fri, 18 Jun 2021).

CHECK results for fobitools on machv2

To the developers/maintainers of the fobitools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fobitools.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 672/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fobitools 1.0.0  (landing page)
Pol Castellano-Escuder
Snapshot Date: 2021-06-17 06:50:12 -0400 (Thu, 17 Jun 2021)
URL: https://git.bioconductor.org/packages/fobitools
Branch: RELEASE_3_13
Last Commit: ad1d5ca
Last Changed Date: 2021-05-19 12:59:34 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: fobitools
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:fobitools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings fobitools_1.0.0.tar.gz
StartedAt: 2021-06-17 18:54:20 -0400 (Thu, 17 Jun 2021)
EndedAt: 2021-06-17 18:59:13 -0400 (Thu, 17 Jun 2021)
EllapsedTime: 292.7 seconds
RetCode: 0
Status:   OK  
CheckDir: fobitools.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:fobitools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings fobitools_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/fobitools.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fobitools/DESCRIPTION’ ... OK
* this is package ‘fobitools’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘fobitools’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotate_foods: no visible binding for global variable ‘FOOD_NAME’
annotate_foods: no visible binding for global variable ‘FOOD_ID’
annotate_foods: no visible binding for global variable ‘words’
annotate_foods: no visible binding for global variable ‘words_joint’
annotate_foods: no visible binding for global variable ‘id_code’
annotate_foods: no visible binding for global variable ‘name’
annotate_foods: no visible binding for global variable ‘ref’
annotate_foods: no visible binding for global variable ‘detect’
annotate_foods: no visible binding for global variable ‘.’
annotate_foods: no visible binding for global variable ‘match_score’
fobi_graph: no visible binding for global variable ‘is_a_code’
fobi_graph: no visible binding for global variable ‘id_code’
fobi_graph: no visible binding for global variable ‘Contains’
fobi_graph: no visible binding for global variable ‘Property’
fobi_graph: no visible binding for global variable ‘name’
fobi_graph: no visible binding for global variable ‘BiomarkerOf’
fobi_graph: no visible binding for global variable ‘is_a_name’
fobi_graph: no visible binding for global variable ‘subOntology’
id_convert: no visible binding for global variable ‘BiomarkerOf’
id_convert: no visible binding for global variable ‘name’
id_convert: no visible binding for global variable ‘FOBI’
id_convert: no visible binding for global variable ‘HMDB’
id_convert: no visible binding for global variable ‘KEGG’
id_convert: no visible binding for global variable ‘PubChemCID’
id_convert: no visible binding for global variable ‘InChIKey’
id_convert: no visible binding for global variable ‘InChICode’
id_convert: no visible binding for global variable ‘ChemSpider’
id_convert: no visible binding for global variable ‘metaboliteNames’
id_convert: no visible binding for global variable ‘presence’
id_convert: no visible binding for global variable ‘.’
msea: no visible binding for global variable ‘BiomarkerOf’
msea: no visible binding for global variable ‘id_BiomarkerOf’
msea: no visible binding for global variable ‘name’
msea: no visible binding for global variable ‘FOBI’
msea: no visible binding for global variable ‘is_a_code’
msea: no visible binding for global variable ‘is_a_name’
msea: no visible binding for global variable ‘.’
msea: no visible global function definition for ‘unstack’
msea: no visible binding for global variable ‘pathway’
msea: no visible binding for global variable ‘size’
msea: no visible binding for global variable ‘className’
msea: no visible binding for global variable ‘classSize’
msea: no visible binding for global variable ‘log2err’
msea: no visible binding for global variable ‘ES’
msea: no visible binding for global variable ‘NES’
msea: no visible binding for global variable ‘pval’
msea: no visible binding for global variable ‘padj’
msea: no visible binding for global variable ‘leadingEdge’
ora: no visible binding for global variable ‘BiomarkerOf’
ora: no visible binding for global variable ‘id_BiomarkerOf’
ora: no visible binding for global variable ‘name’
ora: no visible binding for global variable ‘FOBI’
ora: no visible binding for global variable ‘is_a_code’
ora: no visible binding for global variable ‘is_a_name’
ora: no visible binding for global variable ‘.’
ora: no visible global function definition for ‘unstack’
ora: no visible binding for global variable ‘pathway’
ora: no visible binding for global variable ‘size’
ora: no visible binding for global variable ‘overlapGenes’
ora: no visible binding for global variable ‘className’
ora: no visible binding for global variable ‘classSize’
ora: no visible binding for global variable ‘overlap’
ora: no visible binding for global variable ‘pval’
ora: no visible binding for global variable ‘padj’
ora: no visible binding for global variable ‘overlapMetabolites’
parse_fobi: no visible binding for global variable ‘V2’
parse_fobi: no visible binding for global variable ‘V1’
parse_fobi: no visible binding for global variable ‘gf’
parse_fobi: no visible binding for global variable ‘name’
parse_fobi: no visible binding for global variable ‘id_code’
parse_fobi: no visible binding for global variable ‘Contains’
parse_fobi: no visible binding for global variable ‘is_a_code’
parse_fobi: no visible binding for global variable ‘id_BiomarkerOf’
parse_fobi: no visible binding for global variable ‘id_Contains’
Undefined global functions or variables:
  . BiomarkerOf ChemSpider Contains ES FOBI FOOD_ID FOOD_NAME HMDB
  InChICode InChIKey KEGG NES Property PubChemCID V1 V2 className
  classSize detect gf id_BiomarkerOf id_Contains id_code is_a_code
  is_a_name leadingEdge log2err match_score metaboliteNames name
  overlap overlapGenes overlapMetabolites padj pathway presence pval
  ref size subOntology unstack words words_joint
Consider adding
  importFrom("methods", "className")
  importFrom("utils", "unstack")
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 ... NOTE
  Note: found 199 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
parse_fobi 30.024  1.732  34.779
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/fobitools.Rcheck/00check.log’
for details.



Installation output

fobitools.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL fobitools
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘fobitools’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (fobitools)

Tests output

fobitools.Rcheck/tests/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(fobitools)
> 
> test_check("fobitools")
100% annotated
0.515 sec elapsed
100% annotated
0.447 sec elapsed
100% annotated
9.41 sec elapsed
[ FAIL 0 | WARN 20 | SKIP 0 | PASS 73 ]
> 
> proc.time()
   user  system elapsed 
133.858   6.114 152.198 

Example timings

fobitools.Rcheck/fobitools-Ex.timings

nameusersystemelapsed
ORA2.4410.0742.547
annotate_foods0.5230.0110.536
fobi_graph0.7210.0140.736
id_convert0.1140.0000.115
msea2.8040.2472.943
parse_fobi30.024 1.73234.779