Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:06:04 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 palomino4


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 60/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationHubData 1.27.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/AnnotationHubData
git_branch: master
git_last_commit: e630772
git_last_commit_date: 2022-04-28 10:36:19 -0400 (Thu, 28 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: AnnotationHubData
Version: 1.27.1
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationHubData.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings AnnotationHubData_1.27.1.tar.gz
StartedAt: 2022-06-23 23:09:58 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 23:18:36 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 517.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: AnnotationHubData.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationHubData.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings AnnotationHubData_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/AnnotationHubData.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.27.1'
* 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 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'
* 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 73.27   0.73      74
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/AnnotationHubData.Rcheck/00check.log'
for details.



Installation output

AnnotationHubData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/AnnotationHubData_1.27.1.tar.gz && rm -rf AnnotationHubData.buildbin-libdir && mkdir AnnotationHubData.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AnnotationHubData.buildbin-libdir AnnotationHubData_1.27.1.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL AnnotationHubData_1.27.1.zip && rm AnnotationHubData_1.27.1.tar.gz AnnotationHubData_1.27.1.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  186k  100  186k    0     0  2239k      0 --:--:-- --:--:-- --:--:-- 2272k
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'AnnotationHubData' as AnnotationHubData_1.27.1.zip
* DONE (AnnotationHubData)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'AnnotationHubData' successfully unpacked and MD5 sums checked

Tests output

AnnotationHubData.Rcheck/tests/AnnotationHubData_unit_tests.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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: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


Attaching package: 'IRanges'

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

    windows

INFO [2022-06-23 23:15:52] Preparer Class: ChEAImportPreparer
complete!
INFO [2022-06-23 23:15:52] 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 [2022-06-23 23:15:54] 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 [2022-06-23 23:16:01] Preparer Class: EnsemblGtfImportPreparer
ftp://ftp.ensembl.org/pub/release-85/gtf/ailuropoda_melanoleuca/
ftp://ftp.ensembl.org/pub/release-85/gtf/anas_platyrhynchos/
INFO [2022-06-23 23:16:09] 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 [2022-06-23 23:16:34] Preparer Class: EnsemblTwoBitPreparer
INFO [2022-06-23 23:16:43] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2022-06-23 23:16:43] 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: 85692
looking up value for: 3635
AzureStor not installed.
  Regenerating all files
Processing 13 files.
complete!
INFO [2022-06-23 23:16:51] Preparer Class: RefNetImportPreparer
complete!
INFO [2022-06-23 23:16:51] 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 -- Thu Jun 23 23:18:24 2022 
*********************************************** 
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 
 118.67    1.78  197.26 

Example timings

AnnotationHubData.Rcheck/AnnotationHubData-Ex.timings

nameusersystemelapsed
AnnotationHubMetadata-class000
ImportPreparer-class000
makeAnnotationHubMetadata000
makeEnsemblFasta000
makeGencodeFasta000
makeStandardOrgDbs000
updateResources000
upload_to_S3000
upload_to_azure000
validationFunctions73.27 0.7374.00