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CHECK report for AnnotationHub on merida2

This page was generated on 2019-04-09 13:28:04 -0400 (Tue, 09 Apr 2019).

Package 61/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationHub 2.15.12
Bioconductor Package Maintainer
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/AnnotationHub
Branch: master
Last Commit: 1e1d17b
Last Changed Date: 2019-03-29 14:21:32 -0400 (Fri, 29 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: AnnotationHub
Version: 2.15.12
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AnnotationHub.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AnnotationHub_2.15.12.tar.gz
StartedAt: 2019-04-08 23:13:58 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:18:05 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 247.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: AnnotationHub.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AnnotationHub.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AnnotationHub_2.15.12.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AnnotationHub.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationHub/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnnotationHub’ version ‘2.15.12’
* 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 ‘AnnotationHub’ 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: ‘ensembldb’
Unexported objects imported by ':::' calls:
  ‘BiocFileCache:::.get_tbl_rid’ ‘BiocManager:::.version_bioc’
  ‘BiocManager:::isDevel’
  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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
AnnotationHub-class 58.47  2.805  68.088
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/AnnotationHub.Rcheck/00check.log’
for details.



Installation output

AnnotationHub.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AnnotationHub
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘AnnotationHub’ ...
** 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
* DONE (AnnotationHub)

Tests output

AnnotationHub.Rcheck/tests/runTests.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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("AnnotationHub")

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
snapshotDate(): 2019-04-03
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
snapshotDate(): 2019-04-03
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
snapshotDate(): 2019-04-03
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
snapshotDate(): 2019-04-03
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
snapshotDate(): 2019-04-03
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
snapshotDate(): 2019-04-03
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
snapshotDate(): 2019-04-03
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
snapshotDate(): 2019-04-03
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
snapshotDate(): 2019-04-03
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
snapshotDate(): 2019-04-03
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
snapshotDate(): 2019-04-03
Using temporary cache /tmp/Rtmprvu1U3/BiocFileCache
require("xxx_foo")


RUNIT TEST PROTOCOL -- Mon Apr  8 23:17:58 2019 
*********************************************** 
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHub RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: call dbDisconnect() when finished working with a connection 
2: download failed
  hub path: 'bogus/url'
  cache resource: 'AHInvalid : 5012'
  reason: all(rtype == "web" | file.exists(fpath)) is not TRUE 
3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'xxx_foo'
> 
> proc.time()
   user  system elapsed 
 53.134   5.494  71.061 

Example timings

AnnotationHub.Rcheck/AnnotationHub-Ex.timings

nameusersystemelapsed
AnnotationHub-class58.470 2.80568.088
AnnotationHub-package000
Hub-utils0.0010.0000.000
convertHub0.0010.0000.000
getAnnotationHubOption000
utils0.0020.0010.003