BioC 3.5: CHECK report for clusterProfiler on oaxaca

Package: clusterProfiler

Version: 3.3.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clusterProfiler_3.3.6.tar.gz

StartedAt: 2017-03-04 00:44:32 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 00:48:27 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 234.9 seconds

RetCode: 1

Status:  ERROR

CheckDir: clusterProfiler.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clusterProfiler_3.3.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/clusterProfiler.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clusterProfiler/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘clusterProfiler’ version ‘3.3.6’
* 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 ‘clusterProfiler’ 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 ... OK
* 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
groupGO    60.455  5.505  77.643
enrichKEGG  0.697  0.024  41.282
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  2: expect(identical(as.vector(object), TRUE), sprintf("%s isn't true.", lab), info = info)
  3: as.expectation(exp, ..., srcref = srcref)
  4: identical(as.vector(object), TRUE)
  5: as.vector(object)
  6: "P22223" %in% bitr_kegg("1001", "ncbi-geneid", "uniprot", "hsa")[, 2]
  7: bitr_kegg("1001", "ncbi-geneid", "uniprot", "hsa")
  8: KEGG_convert(fromType, toType, organism)
  9: merge(fidconv, tidconv, by.x = "from", by.y = "from")
  
  testthat results ================================================================
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: bitr (@test-bitr.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
* 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 ERROR
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/clusterProfiler.Rcheck/00check.log’
for details.

R Under development (unstable) (2017-02-15 r72177) -- "Unsuffered Consequences"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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(clusterProfiler)
Loading required package: DOSE

DOSE v3.1.3  For help: https://guangchuangyu.github.io/DOSE

If you use DOSE in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609

clusterProfiler v3.3.6  For help: https://guangchuangyu.github.io/clusterProfiler

If you use clusterProfiler in published research, please cite:
Guangchuang Yu., Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
> 
> test_check("clusterProfiler")
1. Error: bitr (@test-bitr.R#7) ------------------------------------------------
object 'fidconv' not found
1: expect_true("P22223" %in% bitr_kegg("1001", "ncbi-geneid", "uniprot", "hsa")[, 2]) at testthat/test-bitr.R:7
2: expect(identical(as.vector(object), TRUE), sprintf("%s isn't true.", lab), info = info)
3: as.expectation(exp, ..., srcref = srcref)
4: identical(as.vector(object), TRUE)
5: as.vector(object)
6: "P22223" %in% bitr_kegg("1001", "ncbi-geneid", "uniprot", "hsa")[, 2]
7: bitr_kegg("1001", "ncbi-geneid", "uniprot", "hsa")
8: KEGG_convert(fromType, toType, organism)
9: merge(fidconv, tidconv, by.x = "from", by.y = "from")

testthat results ================================================================
OK: 1 SKIPPED: 0 FAILED: 1
1. Error: bitr (@test-bitr.R#7) 

Error: testthat unit tests failed
Execution halted

* installing *source* package ‘clusterProfiler’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (clusterProfiler)

name	user	system	elapsed
compareCluster	0	0	0
enrichGO	0.001	0.000	0.001
enrichKEGG	0.697	0.024	41.282
groupGO	60.455	5.505	77.643