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CHECK report for AnnotationHubData on tokay1

This page was generated on 2018-04-12 13:26:48 -0400 (Thu, 12 Apr 2018).

Package 55/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationHubData 1.8.1
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/AnnotationHubData
Branch: RELEASE_3_6
Last Commit: ec78bd8
Last Changed Date: 2018-03-14 09:18:28 -0400 (Wed, 14 Mar 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AnnotationHubData
Version: 1.8.1
Command: rm -rf AnnotationHubData.buildbin-libdir AnnotationHubData.Rcheck && mkdir AnnotationHubData.buildbin-libdir AnnotationHubData.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationHubData.buildbin-libdir AnnotationHubData_1.8.1.tar.gz >AnnotationHubData.Rcheck\00install.out 2>&1 && cp AnnotationHubData.Rcheck\00install.out AnnotationHubData-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=AnnotationHubData.buildbin-libdir --install="check:AnnotationHubData-install.out" --force-multiarch --no-vignettes --timings AnnotationHubData_1.8.1.tar.gz
StartedAt: 2018-04-11 22:12:55 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:21:41 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 526.3 seconds
RetCode: 0
Status:  OK  
CheckDir: AnnotationHubData.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf AnnotationHubData.buildbin-libdir AnnotationHubData.Rcheck && mkdir AnnotationHubData.buildbin-libdir AnnotationHubData.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationHubData.buildbin-libdir AnnotationHubData_1.8.1.tar.gz >AnnotationHubData.Rcheck\00install.out 2>&1 && cp AnnotationHubData.Rcheck\00install.out AnnotationHubData-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=AnnotationHubData.buildbin-libdir --install="check:AnnotationHubData-install.out" --force-multiarch --no-vignettes --timings AnnotationHubData_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/AnnotationHubData.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnnotationHubData/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AnnotationHubData' version '1.8.1'
* 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 whether package 'AnnotationHubData' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocInstaller'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
'library' or 'require' call to 'BiocInstaller' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing objects imported by ':::' calls:
  'AnnotationHub:::.db_connection'
  'GenomicFeatures:::UCSCGenomeToOrganism'
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'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'Title'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'Description'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'BiocVersion'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'Genome'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'SourceType'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'SourceUrl'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'SourceVersion'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'Species'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'TaxonomyId'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'Coordinate_1_based'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'DataProvider'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'Maintainer'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'RDataClass'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'RDataDateAdded'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'RDataPath'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'DispatchClass'
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
  binding for global variable 'Location_Prefix'
test_BioPaxImportPreparer_recipe: no visible binding for global
  variable 'ahroot'
test_BioPaxImportPreparer_recipe: no visible binding for global
  variable 'BiocVersion'
test_BioPaxImportPreparer_recipe: no visible global function definition
  for 'checkTrue'
test_Inparanoid8ImportPreparer_recipe: no visible global function
  definition for 'suppresWarnings'
test_Inparanoid8ImportPreparer_recipe: no visible binding for global
  variable 'ahroot'
test_Inparanoid8ImportPreparer_recipe: no visible binding for global
  variable 'BiocVersion'
test_Inparanoid8ImportPreparer_recipe: no visible global function
  definition for 'checkTrue'
trackWithAuxiliaryTablesToGRanges: no visible binding for global
  variable 'seqname'
Undefined global functions or variables:
  BiocVersion Coordinate_1_based DataProvider Description DispatchClass
  Genome Location_Prefix Maintainer RDataClass RDataDateAdded RDataPath
  SourceType SourceUrl SourceVersion Species TaxonomyId Title ahroot
  checkTrue results seqname specData suppresWarnings
* 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'AnnotationHubData_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/AnnotationHubData.Rcheck/00check.log'
for details.

Installation output

AnnotationHubData.Rcheck/00install.out


install for i386

* installing *source* package 'AnnotationHubData' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'AnnotationHubData'
    finding HTML links ... done
    AnnotationHubData-package               html  
    AnnotationHubMetadata-class             html  
    ImportPreparer-class                    html  
    flog                                    html  
    makeAnnotationHubMetadata               html  
    makeEnsemblFasta                        html  
    makeGencodeFasta                        html  
    makeStandardOrgDbs                      html  
    updateResources                         html  
    upload_to_S3                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'AnnotationHubData' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationHubData' as AnnotationHubData_1.8.1.zip
* DONE (AnnotationHubData)
In R CMD INSTALL
In R CMD INSTALL

Tests output

AnnotationHubData.Rcheck/tests_i386/AnnotationHubData_unit_tests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, cbind, colMeans, colSums, 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, 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

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
INFO [2018-04-11 22:18:19] Preparer Class: ChEAImportPreparer
complete!
INFO [2018-04-11 22:18:21] 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 [2018-04-11 22:18:24] Preparer Class: EnsemblGtfImportPreparer
complete!
INFO [2018-04-11 22:18:32] Preparer Class: EnsemblTwoBitPreparer
complete!
INFO [2018-04-11 22:19:06] Preparer Class: EpigenomeRoadMapPreparer
getting file info: E002_RRBS_FractionalMethylation.bigwig
getting file info: E003_RRBS_FractionalMethylation.bigwig
complete!
INFO [2018-04-11 22:19:08] 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 [2018-04-11 22:19:15] Preparer Class: GencodeGffImportPreparer
getting file info: gencode.v23.2wayconspseudos.gff3.gz
getting file info: gencode.v23.annotation.gff3.gz
complete!
INFO [2018-04-11 22:19:20] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2018-04-11 22:19:21] Preparer Class: NCBIImportPreparer
looking up value for: 3708
looking up value for: 90675
looking up value for: 4232
looking up value for: 3635
looking up value for: 4097
looking up value for: 7962
complete!
INFO [2018-04-11 22:19:43] Preparer Class: PazarImportPreparer
getting file info: pazar_ABS_20120522.csv
getting file info: pazar_AP2g_E2_tan_20120522.csv
getting file info: pazar_AP2g_tan_20120522.csv
getting file info: pazar_AREs_20120522.csv
getting file info: pazar_Atoh1_Klisch_20120522.csv
complete!
INFO [2018-04-11 22:19:45] Preparer Class: RefNetImportPreparer
complete!
INFO [2018-04-11 22:19:47] Preparer Class: dbSNPVCFPreparer
complete!


RUNIT TEST PROTOCOL -- Wed Apr 11 22:19:57 2018 
*********************************************** 
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHubData RUnit Tests - 21 test functions, 0 errors, 0 failures
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 
Warning message:
In value[[3L]](cond) : chea-background.zip: Service Unavailable


> 
> proc.time()
   user  system elapsed 
  55.75    1.09  119.07

AnnotationHubData.Rcheck/tests_x64/AnnotationHubData_unit_tests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, cbind, colMeans, colSums, 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, 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

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
INFO [2018-04-11 22:20:25] Preparer Class: ChEAImportPreparer
complete!
INFO [2018-04-11 22:20:26] 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 [2018-04-11 22:20:30] Preparer Class: EnsemblGtfImportPreparer
complete!
INFO [2018-04-11 22:20:36] Preparer Class: EnsemblTwoBitPreparer
complete!
INFO [2018-04-11 22:20:40] Preparer Class: EpigenomeRoadMapPreparer
getting file info: E002_RRBS_FractionalMethylation.bigwig
getting file info: E003_RRBS_FractionalMethylation.bigwig
complete!
INFO [2018-04-11 22:20:42] 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 [2018-04-11 22:20:49] Preparer Class: GencodeGffImportPreparer
getting file info: gencode.v23.2wayconspseudos.gff3.gz
getting file info: gencode.v23.annotation.gff3.gz
complete!
INFO [2018-04-11 22:20:54] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2018-04-11 22:20:55] Preparer Class: NCBIImportPreparer
looking up value for: 3708
looking up value for: 90675
looking up value for: 4232
looking up value for: 3635
looking up value for: 4097
looking up value for: 7962
complete!
INFO [2018-04-11 22:21:17] Preparer Class: PazarImportPreparer
getting file info: pazar_ABS_20120522.csv
getting file info: pazar_AP2g_E2_tan_20120522.csv
getting file info: pazar_AP2g_tan_20120522.csv
getting file info: pazar_AREs_20120522.csv
getting file info: pazar_Atoh1_Klisch_20120522.csv
complete!
INFO [2018-04-11 22:21:21] Preparer Class: RefNetImportPreparer
complete!
INFO [2018-04-11 22:21:22] Preparer Class: dbSNPVCFPreparer
complete!


RUNIT TEST PROTOCOL -- Wed Apr 11 22:21:35 2018 
*********************************************** 
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHubData RUnit Tests - 21 test functions, 0 errors, 0 failures
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 
Warning message:
In value[[3L]](cond) : chea-background.zip: Service Unavailable


> 
> proc.time()
   user  system elapsed 
  67.76    1.25   97.28

Example timings

AnnotationHubData.Rcheck/examples_i386/AnnotationHubData-Ex.timings

nameusersystemelapsed
AnnotationHubMetadata-class000
ImportPreparer-class000
makeAnnotationHubMetadata000
makeEnsemblFasta000
makeGencodeFasta000
makeStandardOrgDbs000
updateResources000
upload_to_S3000

AnnotationHubData.Rcheck/examples_x64/AnnotationHubData-Ex.timings

nameusersystemelapsed
AnnotationHubMetadata-class000
ImportPreparer-class000
makeAnnotationHubMetadata000
makeEnsemblFasta000
makeGencodeFasta000
makeStandardOrgDbs000
updateResources000
upload_to_S3000