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This page was generated on 2023-01-28 11:08:14 -0500 (Sat, 28 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4465
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4246
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4269
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 merida1


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 59/2162HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationHubData 1.29.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2023-01-27 14:00:19 -0500 (Fri, 27 Jan 2023)
git_url: https://git.bioconductor.org/packages/AnnotationHubData
git_branch: master
git_last_commit: 3214594
git_last_commit_date: 2022-12-13 10:09:22 -0500 (Tue, 13 Dec 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: AnnotationHubData
Version: 1.29.1
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_1.29.1.tar.gz
StartedAt: 2023-01-27 22:22:18 -0500 (Fri, 27 Jan 2023)
EndedAt: 2023-01-27 22:41:07 -0500 (Fri, 27 Jan 2023)
EllapsedTime: 1129.4 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_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/AnnotationHubData.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationHubData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnnotationHubData’ version ‘1.29.1’
* 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 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 ':::' imports not declared from:
  ‘AzureStor’ ‘stringr’
'loadNamespace' or 'requireNamespace' call not declared from: ‘AzureStor’
Missing objects imported by ':::' calls:
  ‘AnnotationHub:::.db_connection’
  ‘GenomicFeatures:::.makeUCSCChrominfo’
Unexported objects imported by ':::' calls:
  ‘BiocCheck:::getParent’ ‘GenomeInfoDb:::check_tax_id’
  ‘GenomeInfoDb:::fetch_species_index_from_Ensembl_FTP’
  ‘GenomeInfoDb:::lookup_organism_by_tax_id’
  ‘GenomeInfoDb:::lookup_tax_id_by_organism’
  ‘GenomicFeatures:::lookup_organism_by_UCSC_genome’
  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’
needToRerunNonStandardOrgDb: no visible binding for global variable
  ‘results’
needToRerunNonStandardOrgDb: no visible binding for global variable
  ‘specData’
oldAWSS3_needToRerunNonStandardOrgDb: no visible binding for global
  variable ‘results’
oldAWSS3_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 117.423  1.336 157.428
* 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-3.17-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/4.3/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) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 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, aperm, 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 [2023-01-27 22:36:37] Preparer Class: ChEAImportPreparer
complete!
INFO [2023-01-27 22:36:43] 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 [2023-01-27 22:36:45] 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 [2023-01-27 22:36:51] Preparer Class: EnsemblGtfImportPreparer
ftp://ftp.ensembl.org/pub/release-85/gtf/ailuropoda_melanoleuca/
ftp://ftp.ensembl.org/pub/release-85/gtf/anas_platyrhynchos/
INFO [2023-01-27 22:36:57] 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 [2023-01-27 22:37:20] Preparer Class: EnsemblTwoBitPreparer
INFO [2023-01-27 22:37:29] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2023-01-27 22:37:29] Preparer Class: NCBIImportPreparer
looking up value for: 4565
looking up value for: 3708
looking up value for: 3818
looking up value for: 106335
looking up value for: 274614
looking up value for: 85692
AzureStor not installed.
  Regenerating all files
Processing 11 files.
complete!
INFO [2023-01-27 22:37:48] Preparer Class: RefNetImportPreparer
complete!
INFO [2023-01-27 22:37:52] 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 -- Fri Jan 27 22:40:53 2023 
*********************************************** 
Number of test functions: 23 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHubData RUnit Tests - 23 test functions, 0 errors, 0 failures
Number of test functions: 23 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
202.564   3.156 358.963 

Example timings

AnnotationHubData.Rcheck/AnnotationHubData-Ex.timings

nameusersystemelapsed
AnnotationHubMetadata-class0.0040.0010.009
ImportPreparer-class0.0000.0010.005
makeAnnotationHubMetadata0.0070.0010.012
makeEnsemblFasta000
makeGencodeFasta0.0000.0000.001
makeStandardOrgDbs0.0000.0000.001
updateResources0.0010.0000.001
upload_to_S3000
upload_to_azure0.0000.0000.001
validationFunctions117.423 1.336157.428