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CHECK report for AnnotationHubData on tokay2

This page was generated on 2018-10-17 08:41:02 -0400 (Wed, 17 Oct 2018).

Package 56/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationHubData 1.10.3
Bioconductor Package Maintainer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/AnnotationHubData
Branch: RELEASE_3_7
Last Commit: fbc995e
Last Changed Date: 2018-10-12 12:35:02 -0400 (Fri, 12 Oct 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AnnotationHubData
Version: 1.10.3
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationHubData.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings AnnotationHubData_1.10.3.tar.gz
StartedAt: 2018-10-17 00:30:31 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:38:55 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 503.4 seconds
RetCode: 0
Status:  OK  
CheckDir: AnnotationHubData.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationHubData.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings AnnotationHubData_1.10.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/AnnotationHubData.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.10.3'
* 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.
Namespace in Imports field not imported from: 'GEOquery'
  All declared Imports should be used.
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'
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 include directives in Makefiles ... 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-3.7-bioc/meat/AnnotationHubData.Rcheck/00check.log'
for details.

Installation output

AnnotationHubData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/AnnotationHubData_1.10.3.tar.gz && rm -rf AnnotationHubData.buildbin-libdir && mkdir AnnotationHubData.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AnnotationHubData.buildbin-libdir AnnotationHubData_1.10.3.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL AnnotationHubData_1.10.3.zip && rm AnnotationHubData_1.10.3.tar.gz AnnotationHubData_1.10.3.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  182k  100  182k    0     0  3138k      0 --:--:-- --:--:-- --:--:-- 3518k

install for i386

* installing *source* package 'AnnotationHubData' ...
** R
** inst
** byte-compile and prepare 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_1.10.3.zip
* DONE (AnnotationHubData)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'AnnotationHubData' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

AnnotationHubData.Rcheck/tests_i386/AnnotationHubData_unit_tests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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


Attaching package: 'IRanges'

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

    windows

INFO [2018-10-17 00:36:16] Preparer Class: ChEAImportPreparer
complete!
INFO [2018-10-17 00:36:16] 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 [2018-10-17 00:36:19] Preparer Class: EnsemblGtfImportPreparer
complete!
INFO [2018-10-17 00:36:31] Preparer Class: EnsemblTwoBitPreparer
complete!
INFO [2018-10-17 00:36:38] Preparer Class: EpigenomeRoadMapPreparer
trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/RRBS/FractionalMethylation_bigwig/'
Content type 'text/html;charset=UTF-8' length unknown
.......... ...
downloaded 13 KB

trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/WGBS/FractionalMethylation_bigwig/'
Content type 'text/html;charset=UTF-8' length unknown
.......... 
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 [2018-10-17 00:36:41] 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 [2018-10-17 00:36:46] Preparer Class: GencodeGffImportPreparer
getting file info: gencode.v23.2wayconspseudos.gff3.gz
getting file info: gencode.v23.annotation.gff3.gz
complete!
INFO [2018-10-17 00:36:51] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2018-10-17 00:37:01] 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 [2018-10-17 00:37:09] Preparer Class: RefNetImportPreparer
complete!
INFO [2018-10-17 00:37:10] Preparer Class: dbSNPVCFPreparer
complete!


RUNIT TEST PROTOCOL -- Wed Oct 17 00:37:17 2018 
*********************************************** 
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHubData RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 
Warning message:
In value[[3L]](cond) : chea-background.zip: Service Unavailable


> 
> proc.time()
   user  system elapsed 
  58.40    3.00   99.37

AnnotationHubData.Rcheck/tests_x64/AnnotationHubData_unit_tests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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


Attaching package: 'IRanges'

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

    windows

INFO [2018-10-17 00:37:55] Preparer Class: ChEAImportPreparer
complete!
INFO [2018-10-17 00:37:55] 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 [2018-10-17 00:37:58] Preparer Class: EnsemblGtfImportPreparer
complete!
INFO [2018-10-17 00:38:10] Preparer Class: EnsemblTwoBitPreparer
complete!
INFO [2018-10-17 00:38:19] Preparer Class: EpigenomeRoadMapPreparer
trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/RRBS/FractionalMethylation_bigwig/'
Content type 'text/html;charset=UTF-8' length unknown
.......... ...
downloaded 13 KB

trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/WGBS/FractionalMethylation_bigwig/'
Content type 'text/html;charset=UTF-8' length unknown
.......... 
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 [2018-10-17 00:38:21] 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 [2018-10-17 00:38:26] Preparer Class: GencodeGffImportPreparer
getting file info: gencode.v23.2wayconspseudos.gff3.gz
getting file info: gencode.v23.annotation.gff3.gz
complete!
INFO [2018-10-17 00:38:31] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2018-10-17 00:38:31] 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 [2018-10-17 00:38:39] Preparer Class: RefNetImportPreparer
complete!
INFO [2018-10-17 00:38:40] Preparer Class: dbSNPVCFPreparer
complete!


RUNIT TEST PROTOCOL -- Wed Oct 17 00:38:49 2018 
*********************************************** 
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHubData RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 
Warning message:
In value[[3L]](cond) : chea-background.zip: Service Unavailable


> 
> proc.time()
   user  system elapsed 
  61.29    1.34   91.93

Example timings

AnnotationHubData.Rcheck/examples_i386/AnnotationHubData-Ex.timings

nameusersystemelapsed
AnnotationHubMetadata-class000
ImportPreparer-class0.010.000.02
makeAnnotationHubMetadata000
makeEnsemblFasta000
makeGencodeFasta000
makeStandardOrgDbs000
updateResources000
upload_to_S3000

AnnotationHubData.Rcheck/examples_x64/AnnotationHubData-Ex.timings

nameusersystemelapsed
AnnotationHubMetadata-class000
ImportPreparer-class0.010.000.02
makeAnnotationHubMetadata000
makeEnsemblFasta000
makeGencodeFasta000
makeStandardOrgDbs000
updateResources000
upload_to_S3000