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CHECK report for AnnotationHubData on celaya2

This page was generated on 2019-04-09 13:14:44 -0400 (Tue, 09 Apr 2019).

Package 62/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationHubData 1.13.10
Bioconductor Package Maintainer
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/AnnotationHubData
Branch: master
Last Commit: 22d0b7a
Last Changed Date: 2019-03-29 12:07:16 -0400 (Fri, 29 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: AnnotationHubData
Version: 1.13.10
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AnnotationHubData_1.13.10.tar.gz
StartedAt: 2019-04-08 23:52:00 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-09 00:04:08 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 727.1 seconds
RetCode: 0
Status:  OK 
CheckDir: AnnotationHubData.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AnnotationHubData_1.13.10.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AnnotationHubData.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.13.10’
* 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 ... NOTE
Missing object imported by a ':::' call: ‘AnnotationHub:::.db_connection’
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’
.makeComplexGR: no visible binding for global variable ‘seqname’
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 97.87  2.843 100.717
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/AnnotationHubData.Rcheck/00check.log’
for details.



Installation output

AnnotationHubData.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AnnotationHubData
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)

Tests output

AnnotationHubData.Rcheck/tests/AnnotationHubData_unit_tests.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, 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, rowMeans, rowSums,
    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 [2019-04-09 00:00:09] Preparer Class: ChEAImportPreparer
complete!
INFO [2019-04-09 00:00:11] 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 [2019-04-09 00:00:13] 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 [2019-04-09 00:00:28] Preparer Class: EnsemblTwoBitPreparer
complete!
INFO [2019-04-09 00:00:40] 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 [2019-04-09 00:00:43] 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 [2019-04-09 00:00:51] Preparer Class: GencodeGffImportPreparer
getting file info: gencode.v23.2wayconspseudos.gff3.gz
getting file info: gencode.v23.annotation.gff3.gz
complete!
INFO [2019-04-09 00:00:58] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2019-04-09 00:00:58] 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
complete!
INFO [2019-04-09 00:01:08] Preparer Class: RefNetImportPreparer
complete!
INFO [2019-04-09 00:01:09] 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 -- Tue Apr  9 00:04:00 2019 
*********************************************** 
Number of test functions: 25 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHubData RUnit Tests - 25 test functions, 0 errors, 0 failures
Number of test functions: 25 
Number of errors: 0 
Number of failures: 0 
Warning message:
In value[[3L]](cond) : chea-background.zip: Service Unavailable

> 
> proc.time()
   user  system elapsed 
193.116   6.330 294.143 

Example timings

AnnotationHubData.Rcheck/AnnotationHubData-Ex.timings

nameusersystemelapsed
AnnotationHubMetadata-class0.0060.0020.008
ImportPreparer-class0.0020.0020.002
makeAnnotationHubMetadata0.0080.0010.009
makeEnsemblFasta0.0010.0000.001
makeGencodeFasta0.0000.0000.001
makeStandardOrgDbs0.0010.0020.003
updateResources0.0010.0010.002
upload_to_S30.0010.0000.000
validationFunctions 97.870 2.843100.717