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This page was generated on 2024-03-18 11:37:14 -0400 (Mon, 18 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-06 r86056) -- "Unsuffered Consequences" 4685
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-06 r86056 ucrt) -- "Unsuffered Consequences" 4423
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-04 r86048) -- "Unsuffered Consequences" 4450
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-06 r86056) -- "Unsuffered Consequences" 4361
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

Package 74/2257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationHubData 1.33.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2024-03-17 14:00:14 -0400 (Sun, 17 Mar 2024)
git_url: https://git.bioconductor.org/packages/AnnotationHubData
git_branch: devel
git_last_commit: 088c3b2
git_last_commit_date: 2024-02-12 13:04:33 -0400 (Mon, 12 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for AnnotationHubData on palomino3


To the developers/maintainers of the AnnotationHubData package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: AnnotationHubData
Version: 1.33.1
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AnnotationHubData.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings AnnotationHubData_1.33.1.tar.gz
StartedAt: 2024-03-17 23:09:11 -0400 (Sun, 17 Mar 2024)
EndedAt: 2024-03-17 23:20:55 -0400 (Sun, 17 Mar 2024)
EllapsedTime: 703.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: AnnotationHubData.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AnnotationHubData.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings AnnotationHubData_1.33.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/AnnotationHubData.Rcheck'
* using R Under development (unstable) (2024-03-06 r86056 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'AnnotationHubData/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AnnotationHubData' version '1.33.1'
* 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 ... 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 whether startup messages can be suppressed ... 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'
  'GenomicFeatures:::lookup_organism_by_UCSC_genome'
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'
  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 ... NOTE
checkRd: (-1) makeAnnotationHubMetadata.Rd:31-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeAnnotationHubMetadata.Rd:40-187: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeGencodeFasta.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeGencodeFasta.Rd:31-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeGencodeFasta.Rd:35-38: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... NOTE
Invalid package aliases in Rd file 'AnnotationHubData-package.Rd':
  'AnnotationHubRecipes-package'
* 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 88.81   1.95   90.78
* 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 ... 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, 3 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/AnnotationHubData.Rcheck/00check.log'
for details.



Installation output

AnnotationHubData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL AnnotationHubData
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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) (2024-03-06 r86056 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, table, tapply,
    union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows

INFO [2024-03-17 23:16:43] Preparer Class: ChEAImportPreparer
complete!
INFO [2024-03-17 23:16:43] 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 [2024-03-17 23:16:47] 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 [2024-03-17 23:16:52] Preparer Class: EnsemblGtfImportPreparer
ftp://ftp.ensembl.org/pub/release-85/gtf/ailuropoda_melanoleuca/
ftp://ftp.ensembl.org/pub/release-85/gtf/anas_platyrhynchos/
INFO [2024-03-17 23:16:56] 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 [2024-03-17 23:17:09] Preparer Class: EnsemblTwoBitPreparer
INFO [2024-03-17 23:17:14] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2024-03-17 23:17:14] 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 [2024-03-17 23:17:26] Preparer Class: RefNetImportPreparer
complete!
INFO [2024-03-17 23:17:26] 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 -- Sun Mar 17 23:20:43 2024 
*********************************************** 
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 
 160.04    4.75  295.65 

Example timings

AnnotationHubData.Rcheck/AnnotationHubData-Ex.timings

nameusersystemelapsed
AnnotationHubMetadata-class000
ImportPreparer-class000
makeAnnotationHubMetadata0.000.020.02
makeEnsemblFasta000
makeGencodeFasta000
makeStandardOrgDbs000
updateResources000
upload_to_S3000
upload_to_azure000
validationFunctions88.81 1.9590.78