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This page was generated on 2022-01-21 11:06:58 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 riesling1


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? here 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 61/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationHubData 1.25.4  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/AnnotationHubData
git_branch: master
git_last_commit: 93f75c2
git_last_commit_date: 2022-01-07 11:23:29 -0500 (Fri, 07 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'S4Vectors' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: AnnotationHubData
Version: 1.25.4
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AnnotationHubData.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings AnnotationHubData_1.25.4.tar.gz
StartedAt: 2022-01-20 18:13:38 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 18:21:19 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 461.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: AnnotationHubData.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AnnotationHubData.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings AnnotationHubData_1.25.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/AnnotationHubData.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.25.4'
* 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 ':::' 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 63.17   3.21   66.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'AnnotationHubData_unit_tests.R'
 ERROR
Running the tests in 'tests/AnnotationHubData_unit_tests.R' failed.
Last 13 lines of output:
   
  1 Test Suite : 
  AnnotationHubData RUnit Tests - 23 test functions, 1 error, 0 failures
  ERROR in test_ftpDirectoryInfo: Error in function (type, msg, asError = TRUE)  : 
    Failed to connect to ftp.ensembl.org port 21: Timed out
  
  Test files with failing tests
  
     test_webAccessFunctions.R 
       test_ftpDirectoryInfo 
  
  
  Error in BiocGenerics:::testPackage("AnnotationHubData") : 
    unit tests failed for package AnnotationHubData
  Execution halted
* 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 ERROR, 1 WARNING, 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/AnnotationHubData.Rcheck/00check.log'
for details.


Installation output

AnnotationHubData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL AnnotationHubData
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'AnnotationHubData' ...
** using staged installation
** 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  
    validationFunctions                     html  
** 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)
Making 'packages.html' ... done

Tests output

AnnotationHubData.Rcheck/tests/AnnotationHubData_unit_tests.Rout.fail


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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 [2022-01-20 18:18:29] Preparer Class: ChEAImportPreparer
complete!
INFO [2022-01-20 18:18:30] 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 [2022-01-20 18:18:33] 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 [2022-01-20 18:18:40] Preparer Class: EnsemblGtfImportPreparer
ftp://ftp.ensembl.org/pub/release-85/gtf/ailuropoda_melanoleuca/
ftp://ftp.ensembl.org/pub/release-85/gtf/anas_platyrhynchos/
INFO [2022-01-20 18:18:46] 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 [2022-01-20 18:19:01] Preparer Class: EnsemblTwoBitPreparer
INFO [2022-01-20 18:19:08] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2022-01-20 18:19:08] 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 [2022-01-20 18:19:14] Preparer Class: RefNetImportPreparer
complete!
INFO [2022-01-20 18:19:28] 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.
Timing stopped at: 0 0.02 21.59
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to ftp.ensembl.org port 21: Timed out
In addition: Warning messages:
1: In value[[3L]](cond) :
  gerstein-2012.tsv_0.0.1.RData: The TLS version of the connection is not permitted on this storage account.


2: In value[[3L]](cond) :
  hypoxiaSignaling-2006.tsv_0.0.1.RData: The TLS version of the connection is not permitted on this storage account.


3: In value[[3L]](cond) :
  stamlabTFs-2012.tsv_0.0.1.RData: The TLS version of the connection is not permitted on this storage account.


4: In value[[3L]](cond) :
  recon202.tsv_0.0.1.RData: The TLS version of the connection is not permitted on this storage account.


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 Jan 20 18:21:09 2022 
*********************************************** 
Number of test functions: 23 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHubData RUnit Tests - 23 test functions, 1 error, 0 failures
ERROR in test_ftpDirectoryInfo: Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to ftp.ensembl.org port 21: Timed out

Test files with failing tests

   test_webAccessFunctions.R 
     test_ftpDirectoryInfo 


Error in BiocGenerics:::testPackage("AnnotationHubData") : 
  unit tests failed for package AnnotationHubData
Execution halted

Example timings

AnnotationHubData.Rcheck/AnnotationHubData-Ex.timings

nameusersystemelapsed
AnnotationHubMetadata-class000
ImportPreparer-class000
makeAnnotationHubMetadata000
makeEnsemblFasta000
makeGencodeFasta000
makeStandardOrgDbs000
updateResources000
upload_to_S3000
validationFunctions63.17 3.2166.39