Package: AnnotationHub

Version: 2.14.5

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:AnnotationHub.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings AnnotationHub_2.14.5.tar.gz

StartedAt: 2019-04-15 22:12:02 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:14:23 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 141.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: AnnotationHub.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:AnnotationHub.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings AnnotationHub_2.14.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/AnnotationHub.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘2.14.5’
* 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:
  ‘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 42.54  0.664  44.067
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/AnnotationHub.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL AnnotationHub
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, lengths, 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

snapshotDate(): 2018-10-24
snapshotDate(): 2018-10-24
snapshotDate(): 2018-10-24
snapshotDate(): 2018-10-24
snapshotDate(): 2018-10-24
snapshotDate(): 2018-10-24
require("xxx_foo")


RUNIT TEST PROTOCOL -- Mon Apr 15 22:14:21 2019 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHub RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: call dbDisconnect() when finished working with a connection 
2: 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 
 16.120   0.776  21.507 

name	user	system	elapsed
AnnotationHub-class	42.540	0.664	44.067
AnnotationHub-package	0	0	0
getAnnotationHubOption	0.000	0.000	0.001