Package: AnnotationHubData

Version: 1.16.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings AnnotationHubData_1.16.0.tar.gz

StartedAt: 2020-04-15 03:15:29 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:24:30 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 540.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: AnnotationHubData.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings AnnotationHubData_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/AnnotationHubData.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.16.0’
* 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 ‘AnnotationHubData’ 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 ... WARNING
'::' or ':::' import not declared from: ‘stringr’
Missing object imported by a ':::' call: ‘AnnotationHub:::.db_connection’
* 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’
.makeComplexGR: no visible binding for global variable ‘seqname’
needToRerunNonStandardOrgDb: no visible binding for global variable
  ‘results’
needToRerunNonStandardOrgDb: no visible binding for global variable
  ‘specData’
trackWithAuxiliaryTablesToGRanges: no visible binding for global
  variable ‘seqname’
Undefined global functions or variables:
  results seqname 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 include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
validationFunctions 75.884  0.476  76.542
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘AnnotationHubData_unit_tests.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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/AnnotationHubData.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL AnnotationHubData
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘AnnotationHubData’ ...
** using staged installation
** R
** 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 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 (AnnotationHubData)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, sd, var, xtabs

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

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


Attaching package: 'S4Vectors'

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

    expand.grid

INFO [2020-04-15 03:22:07] Preparer Class: ChEAImportPreparer
complete!
INFO [2020-04-15 03:22:08] Preparer Class: EncodeImportPreparer
getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878CellTotal.broadPeak.gz
getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878CytosolLongnonpolya.broadPeak.gz
getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878CytosolLongpolya.broadPeak.gz
getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878NucleolusTotal.broadPeak.gz
getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878NucleusLongnonpolya.broadPeak.gz
complete!
INFO [2020-04-15 03:22:10] Preparer Class: EnsemblGtfImportPreparer
ftp://ftp.ensembl.org/pub/release-84/gtf/ailuropoda_melanoleuca/
ftp://ftp.ensembl.org/pub/release-84/gtf/anas_platyrhynchos/
complete!
INFO [2020-04-15 03:22:23] Preparer Class: EnsemblTwoBitPreparer
complete!
INFO [2020-04-15 03:22:35] Preparer Class: EpigenomeRoadMapPreparer
trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/RRBS/FractionalMethylation_bigwig/'
downloaded 13 KB

trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/WGBS/FractionalMethylation_bigwig/'
downloaded 10 KB

trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/mCRF/FractionalMethylation_bigwig/'
Content type 'text/html;charset=UTF-8' length 5015 bytes
==================================================
downloaded 5015 bytes

getting file info: E002_RRBS_FractionalMethylation.bigwig
getting file info: E003_RRBS_FractionalMethylation.bigwig
complete!
INFO [2020-04-15 03:22:38] Preparer Class: GencodeFastaImportPreparer
getting file info: gencode.v23.chr_patch_hapl_scaff.transcripts.fa.gz
getting file info: gencode.v23.lncRNA_transcripts.fa.gz
complete!
INFO [2020-04-15 03:22:42] Preparer Class: GencodeGffImportPreparer
getting file info: gencode.v31.2wayconspseudos.gff3.gz
getting file info: gencode.v31.annotation.gff3.gz
complete!
INFO [2020-04-15 03:22:46] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2020-04-15 03:22:46] Preparer Class: NCBIImportPreparer
looking up value for: 3708
looking up value for: 3818
looking up value for: 90675
looking up value for: 3469
looking up value for: 7957
looking up value for: 4232
Processing 8 files.
complete!
INFO [2020-04-15 03:22:57] Preparer Class: RefNetImportPreparer
complete!
INFO [2020-04-15 03:22:58] Preparer Class: dbSNPVCFPreparer
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive_1.0/2016/
complete!
Found invalid DispatchClass.

[1] "somethingNotThere"

For currently available DispatchClass run
    'AnnotationHub::DispatchClassList()'

Found invalid DispatchClass.

[1] "somethingNotThere"

For currently available DispatchClass run
    'AnnotationHub::DispatchClassList()'

Loading valid species information.
ftp://ftp1.nci.nih.gov/pub/PID/BioPAX/
ftp://ftp1.nci.nih.gov/pub/PID/BioPAX/
ftp://ftp1.nci.nih.gov/pub/PID/BioPAX/


RUNIT TEST PROTOCOL -- Wed Apr 15 03:24:26 2020 
*********************************************** 
Number of test functions: 26 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHubData RUnit Tests - 26 test functions, 0 errors, 0 failures
Number of test functions: 26 
Number of errors: 0 
Number of failures: 0 
Warning message:
In value[[3L]](cond) : chea-background.zip: Service Unavailable

> 
> proc.time()
   user  system elapsed 
153.380   1.508 187.233 

name	user	system	elapsed
AnnotationHubMetadata-class	0.004	0.000	0.002
ImportPreparer-class	0.000	0.000	0.001
makeAnnotationHubMetadata	0.004	0.000	0.004
makeEnsemblFasta	0	0	0
makeGencodeFasta	0.000	0.000	0.001
makeStandardOrgDbs	0.004	0.000	0.000
updateResources	0	0	0
upload_to_S3	0	0	0
validationFunctions	75.884	0.476	76.542