Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:37 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for AnnotationHubData on machv2


To the developers/maintainers of the AnnotationHubData package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AnnotationHubData.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 64/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationHubData 1.24.2  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/AnnotationHubData
git_branch: RELEASE_3_14
git_last_commit: fe8b582
git_last_commit_date: 2022-01-18 08:35:19 -0400 (Tue, 18 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: AnnotationHubData
Version: 1.24.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AnnotationHubData_1.24.2.tar.gz
StartedAt: 2022-04-12 10:19:23 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 10:32:24 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 781.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: AnnotationHubData.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AnnotationHubData_1.24.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/AnnotationHubData.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.24.2’
* 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 objects imported by ':::' calls:
  ‘AnnotationHub:::.db_connection’
  ‘GenomicFeatures:::.makeUCSCChrominfo’
* 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 (user + system) or elapsed time > 5s
                      user system elapsed
validationFunctions 93.648  1.102  94.869
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/AnnotationHubData.Rcheck/00check.log’
for details.



Installation output

AnnotationHubData.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: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.max, which.min


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

INFO [2022-04-12 10:27:55] Preparer Class: ChEAImportPreparer
complete!
INFO [2022-04-12 10:27:55] 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 [2022-04-12 10:27:57] Preparer Class: EnsemblGtfImportPreparer
ftp://ftp.ensembl.org/pub/release-96/gtf/acanthochromis_polyacanthus/
ftp://ftp.ensembl.org/pub/release-96/gtf/ailuropoda_melanoleuca/
acanthochromis_polyacanthus

acanthochromis_polyacanthus

ailuropoda_melanoleuca

ailuropoda_melanoleuca

acanthochromis_polyacanthus

acanthochromis_polyacanthus

ailuropoda_melanoleuca

ailuropoda_melanoleuca

complete!
INFO [2022-04-12 10:28:08] Preparer Class: EnsemblGtfImportPreparer
ftp://ftp.ensembl.org/pub/release-85/gtf/ailuropoda_melanoleuca/
ftp://ftp.ensembl.org/pub/release-85/gtf/anas_platyrhynchos/
INFO [2022-04-12 10:28:20] Preparer Class: EnsemblTwoBitPreparer
acanthochromis_polyacanthus

acanthochromis_polyacanthus

acanthochromis_polyacanthus

acanthochromis_polyacanthus

ailuropoda_melanoleuca

acanthochromis_polyacanthus

acanthochromis_polyacanthus

acanthochromis_polyacanthus

acanthochromis_polyacanthus

ailuropoda_melanoleuca

complete!
INFO [2022-04-12 10:29:19] Preparer Class: EnsemblTwoBitPreparer
INFO [2022-04-12 10:29:26] 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 [2022-04-12 10:29:30] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2022-04-12 10:29:30] Preparer Class: NCBIImportPreparer
looking up value for: 3708
looking up value for: 3818
looking up value for: 106335
looking up value for: 85692
looking up value for: 3635
looking up value for: 90675
Processing 11 files.
complete!
INFO [2022-04-12 10:29:41] Preparer Class: RefNetImportPreparer
complete!
INFO [2022-04-12 10:29:42] 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://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/
ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/
ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/


RUNIT TEST PROTOCOL -- Tue Apr 12 10:32:14 2022 
*********************************************** 
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHubData RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
176.752   2.922 322.927 

Example timings

AnnotationHubData.Rcheck/AnnotationHubData-Ex.timings

nameusersystemelapsed
AnnotationHubMetadata-class0.0040.0020.005
ImportPreparer-class0.0010.0010.002
makeAnnotationHubMetadata0.0070.0010.007
makeEnsemblFasta0.0010.0000.000
makeGencodeFasta000
makeStandardOrgDbs0.0000.0010.002
updateResources0.0010.0010.003
upload_to_S30.0000.0000.001
validationFunctions93.648 1.10294.869