BioC 3.3: CHECK report for AnnotationHubData on morelia

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationHubData_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/AnnotationHubData.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationHubData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnnotationHubData’ version ‘1.1.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AnnotationHubData’ can be installed ... [12s/14s] 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
Missing objects imported by ':::' calls:
  ‘AnnotationHub:::.db_connection’ ‘AnnotationHub:::.metadata’
Unexported object imported by a ':::' call: ‘OrganismDbi:::.packageTaxIds’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.NCBIMetadataFromUrl: no visible binding for global variable ‘results’
.NCBIMetadataFromUrl: no visible binding for global variable ‘specData’
.runRecipes: no visible binding for global variable ‘ahroot’
getAHTrackDates: no visible global function definition for
  ‘snapshotUrl’
trackWithAuxiliaryTablesToGRanges: no visible global function
  definition for ‘outputfile’
updateResources: no visible binding for global variable
  ‘listOfExistingResources’
Undefined global functions or variables:
  ahroot listOfExistingResources outputfile results snapshotUrl
  specData
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [42s/152s]
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  ERROR in test_PazarImportPreparer_recipe: Error in if (nchar(genome) > 30) { : 
    missing value where TRUE/FALSE needed
  
  Test files with failing tests
  
     test_recipe.R 
       test_ChEAPreparer_recipe 
       test_PazarImportPreparer_recipe 
  
  
  Error in BiocGenerics:::testPackage("AnnotationHubData") : 
    unit tests failed for package AnnotationHubData
  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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/AnnotationHubData.Rcheck/00check.log’
for details.


R Under development (unstable) (2015-10-08 r69496) -- "Unsuffered Consequences"
Copyright (C) 2015 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.

> BiocGenerics:::testPackage("AnnotationHubData")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
    eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unlist, unsplit


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
INFO [2015-10-22 03:28:10] Preparer Class: BioPaxImportPreparer
BioCarta.owl.gz
KEGG.bp2.owl.gz
KEGG.bp3.owl.gz
NCI-Nature_Curated.bp2.owl.gz
NCI-Nature_Curated.owl.gz
Reactome.owl.gz
BioCarta.bp2.owl.gz
KEGG.bp2.owl.gz
NCI-Nature_Curated.bp2.owl.gz
Reactome.bp2.owl.gz
INFO [2015-10-22 03:28:16] Preparer Class: ChEAImportPreparer
Timing stopped at: 0.015 0 4.368 
Error in if (nchar(genome) > 30) { : 
  missing value where TRUE/FALSE needed
INFO [2015-10-22 03:28:21] Preparer Class: EncodeImportPreparer
wgEncodeAffyRnaChipFiltTransfragsGm12878CellTotal.broadPeak.gz
wgEncodeAffyRnaChipFiltTransfragsGm12878CytosolLongnonpolya.broadPeak.gz
wgEncodeAffyRnaChipFiltTransfragsGm12878CytosolLongpolya.broadPeak.gz
wgEncodeAffyRnaChipFiltTransfragsGm12878NucleolusTotal.broadPeak.gz
wgEncodeAffyRnaChipFiltTransfragsGm12878NucleusLongnonpolya.broadPeak.gz
wgEncodeAwgDnaseDuke8988tUniPk.narrowPeak.gz
wgEncodeAwgDnaseDukeAosmcUniPk.narrowPeak.gz
wgEncodeAwgDnaseDukeChorionUniPk.narrowPeak.gz
wgEncodeAwgDnaseDukeCllUniPk.narrowPeak.gz
wgEncodeAwgDnaseDukeFibroblUniPk.narrowPeak.gz
wgEncodeCshlLongRnaSeqA549CellPamContigs.bedRnaElements.gz
wgEncodeCshlLongRnaSeqA549CellPamExonsGencV7.gtf.gz
wgEncodeCshlLongRnaSeqA549CellPamGeneDeNovo.gtf.gz
wgEncodeCshlLongRnaSeqA549CellPamGeneGencV7.gtf.gz
wgEncodeCshlLongRnaSeqA549CellPamJunctions.bedRnaElements.gz
wgEncodeGencode2wayConsPseudoV4.gtf.gz
wgEncodeGencodeAutoV4.gtf.gz
wgEncodeGencodeManualV4.gtf.gz
wgEncodeGencodePolyAV4.gtf.gz
INFO [2015-10-22 03:28:31] Preparer Class: EnsemblGtfImportPreparer
Ailuropoda_melanoleuca.ailMel1.69.gtf.gz
Anolis_carolinensis.AnoCar2.0.69.gtf.gz
Bos_taurus.UMD3.1.69.gtf.gz
Caenorhabditis_elegans.WBcel215.69.gtf.gz
Callithrix_jacchus.C_jacchus3.2.1.69.gtf.gz
Ailuropoda_melanoleuca.ailMel1.69.gtf.gz
Anolis_carolinensis.AnoCar2.0.69.gtf.gz
Bos_taurus.UMD3.1.69.gtf.gz
Caenorhabditis_elegans.WBcel215.69.gtf.gz
Callithrix_jacchus.C_jacchus3.2.1.69.gtf.gz
INFO [2015-10-22 03:28:54] Preparer Class: EpigenomeRoadMapPreparer
E002_RRBS_FractionalMethylation.bigwig
E003_RRBS_FractionalMethylation.bigwig
INFO [2015-10-22 03:28:56] Preparer Class: GencodeFastaImportPreparer
gencode.vM6.chr_patch_hapl_scaff.transcripts.fa.gz
gencode.vM6.lncRNA_transcripts.fa.gz
gencode.vM6.pc_transcripts.fa.gz
gencode.vM6.pc_translations.fa.gz
gencode.vM6.transcripts.fa.gz
INFO [2015-10-22 03:29:04] Preparer Class: GencodeGffImportPreparer
gencode.v23.2wayconspseudos.gff3.gz
gencode.v23.annotation.gff3.gz
gencode.v23.basic.annotation.gff3.gz
gencode.v23.chr_patch_hapl_scaff.annotation.gff3.gz
gencode.v23.chr_patch_hapl_scaff.basic.annotation.gff3.gz
INFO [2015-10-22 03:29:13] Preparer Class: Grasp2ImportPreparer
INFO [2015-10-22 03:29:13] Preparer Class: HaemCodeImportPreparer
CTCF_GSM546526_Pro-B-Cells.bw
CTCF_GSM644975_Pro-B-Cells.bw
FoxO1_GSM860926_Pre-B-Cells.bed
Oct2_GSM537990_B-Cells.bed
EBF_GSM499030_Pro-B-Cells.csv
EBF1_GSE35857_B-Cells.csv
INFO [2015-10-22 03:29:20] Preparer Class: NCBIImportPreparer
looking up value for: 90675
looking up value for: 3847
looking up value for: 3750
looking up value for: 4577
looking up value for: 3711
looking up value for: 3880
INFO [2015-10-22 03:29:30] Preparer Class: PazarImportPreparer
pazar_ABS_20120522.csv
pazar_AP2g_E2_tan_20120522.csv
pazar_AP2g_tan_20120522.csv
pazar_AREs_20120522.csv
pazar_Atoh1_Klisch_20120522.csv
Timing stopped at: 0.069 0.004 0.255 
Error in if (nchar(genome) > 30) { : 
  missing value where TRUE/FALSE needed
INFO [2015-10-22 03:29:31] Preparer Class: RefNetImportPreparer
INFO [2015-10-22 03:29:35] Preparer Class: UCSC2BitPreparer
hg38.2bit
INFO [2015-10-22 03:29:57] Preparer Class: UCSCChainPreparer
hg38ToBosTau8.over.chain.gz
hg38ToCalJac3.over.chain.gz
hg38ToCanFam3.over.chain.gz
hg38ToDanRer10.over.chain.gz
hg38ToHg19.over.chain.gz
hg38ToMm10.over.chain.gz
hg38ToMonDom5.over.chain.gz
hg38ToOviAri3.over.chain.gz
hg38ToPanPan1.over.chain.gz
hg38ToPanTro4.over.chain.gz
hg38ToRheMac3.over.chain.gz
hg38ToRn5.over.chain.gz
hg38ToSaiBol1.over.chain.gz
hg38ToTarSyr2.over.chain.gz
INFO [2015-10-22 03:30:21] Preparer Class: dbSNPVCFPreparer
All_20150603.vcf.gz
common_all_20150603.vcf.gz
All_20150603_papu.vcf.gz
common_all_20150603_papu.vcf.gz


RUNIT TEST PROTOCOL -- Thu Oct 22 03:30:25 2015 
*********************************************** 
Number of test functions: 19 
Number of errors: 2 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHubData RUnit Tests - 19 test functions, 2 errors, 0 failures
ERROR in test_ChEAPreparer_recipe: Error in if (nchar(genome) > 30) { : 
  missing value where TRUE/FALSE needed
ERROR in test_PazarImportPreparer_recipe: Error in if (nchar(genome) > 30) { : 
  missing value where TRUE/FALSE needed

Test files with failing tests

   test_recipe.R 
     test_ChEAPreparer_recipe 
     test_PazarImportPreparer_recipe 


Error in BiocGenerics:::testPackage("AnnotationHubData") : 
  unit tests failed for package AnnotationHubData
Execution halted

name	user	system	elapsed
AnnotationHubMetadata-class	0.002	0.000	0.002
ImportPreparer-class	0.001	0.001	0.001
upload_to_S3	0.000	0.000	0.001

BioC 3.3: CHECK report for AnnotationHubData on morelia

Summary

Command output