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CHECK report for AnnotationHub on tokay1

This page was generated on 2018-04-12 13:22:42 -0400 (Thu, 12 Apr 2018).

Package 54/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationHub 2.10.1
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/AnnotationHub
Branch: RELEASE_3_6
Last Commit: b7cb668
Last Changed Date: 2017-11-07 01:04:40 -0400 (Tue, 07 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AnnotationHub
Version: 2.10.1
Command: rm -rf AnnotationHub.buildbin-libdir AnnotationHub.Rcheck && mkdir AnnotationHub.buildbin-libdir AnnotationHub.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationHub.buildbin-libdir AnnotationHub_2.10.1.tar.gz >AnnotationHub.Rcheck\00install.out 2>&1 && cp AnnotationHub.Rcheck\00install.out AnnotationHub-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=AnnotationHub.buildbin-libdir --install="check:AnnotationHub-install.out" --force-multiarch --no-vignettes --timings AnnotationHub_2.10.1.tar.gz
StartedAt: 2018-04-11 22:12:50 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:17:05 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 254.5 seconds
RetCode: 0
Status:  OK  
CheckDir: AnnotationHub.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf AnnotationHub.buildbin-libdir AnnotationHub.Rcheck && mkdir AnnotationHub.buildbin-libdir AnnotationHub.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationHub.buildbin-libdir AnnotationHub_2.10.1.tar.gz >AnnotationHub.Rcheck\00install.out 2>&1 && cp AnnotationHub.Rcheck\00install.out AnnotationHub-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=AnnotationHub.buildbin-libdir --install="check:AnnotationHub-install.out" --force-multiarch --no-vignettes --timings AnnotationHub_2.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/AnnotationHub.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnnotationHub/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AnnotationHub' version '2.10.1'
* 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 '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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.get1,EnsDbResource: no visible global function definition for 'EnsDb'
Undefined global functions or variables:
  EnsDb
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
AnnotationHub-class 42.45   0.97   48.84
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
AnnotationHub-class 41.47   0.88   42.62
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/AnnotationHub.Rcheck/00check.log'
for details.



Installation output

AnnotationHub.Rcheck/00install.out


install for i386

* installing *source* package 'AnnotationHub' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'AnnotationHub'
    finding HTML links ... done
    AnnotationHub-class                     html  
    AnnotationHub-package                   html  
    AnnotationHubResource-class             html  
    getAnnotationHubOption                  html  
    listResources                           html  
    readMetadataFromCsv                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'AnnotationHub' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationHub' as AnnotationHub_2.10.1.zip
* DONE (AnnotationHub)
In R CMD INSTALL
In R CMD INSTALL

Tests output

AnnotationHub.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, cbind, colMeans, colSums, colnames, 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(): 2017-10-27
snapshotDate(): 2017-10-27
snapshotDate(): 2017-10-27
snapshotDate(): 2017-10-27
snapshotDate(): 2017-10-27
snapshotDate(): 2017-10-27
using guess work to populate seqinfo
require("xxx_foo")


RUNIT TEST PROTOCOL -- Wed Apr 11 22:16:40 2018 
*********************************************** 
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHub RUnit Tests - 7 test functions, 0 errors, 0 failures
Number of test functions: 7 
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 
  13.57    1.14   24.93 

AnnotationHub.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("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, cbind, colMeans, colSums, colnames, 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(): 2017-10-27
snapshotDate(): 2017-10-27
snapshotDate(): 2017-10-27
snapshotDate(): 2017-10-27
snapshotDate(): 2017-10-27
snapshotDate(): 2017-10-27
using guess work to populate seqinfo
require("xxx_foo")


RUNIT TEST PROTOCOL -- Wed Apr 11 22:16:57 2018 
*********************************************** 
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHub RUnit Tests - 7 test functions, 0 errors, 0 failures
Number of test functions: 7 
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 
  14.56    1.01   17.64 

Example timings

AnnotationHub.Rcheck/examples_i386/AnnotationHub-Ex.timings

nameusersystemelapsed
AnnotationHub-class42.45 0.9748.84
AnnotationHub-package000
getAnnotationHubOption000
readMetadataFromCsv000

AnnotationHub.Rcheck/examples_x64/AnnotationHub-Ex.timings

nameusersystemelapsed
AnnotationHub-class41.47 0.8842.62
AnnotationHub-package000
getAnnotationHubOption000
readMetadataFromCsv000