Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:10 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 AnnotationHub on tokay2


To the developers/maintainers of the AnnotationHub package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AnnotationHub.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 63/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationHub 3.2.2  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/AnnotationHub
git_branch: RELEASE_3_14
git_last_commit: 8e761e1
git_last_commit_date: 2022-02-28 12:33:25 -0400 (Mon, 28 Feb 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: AnnotationHub
Version: 3.2.2
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationHub.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings AnnotationHub_3.2.2.tar.gz
StartedAt: 2022-04-12 15:36:07 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 15:47:52 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 705.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: AnnotationHub.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationHub.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings AnnotationHub_3.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/AnnotationHub.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '3.2.2'
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
AnnotationHub-class 57.78   2.86   71.02
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
AnnotationHub-class 45.17    1.5   50.09
* 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 WARNING
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/AnnotationHub.Rcheck/00check.log'
for details.



Installation output

AnnotationHub.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/AnnotationHub_3.2.2.tar.gz && rm -rf AnnotationHub.buildbin-libdir && mkdir AnnotationHub.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AnnotationHub.buildbin-libdir AnnotationHub_3.2.2.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL AnnotationHub_3.2.2.zip && rm AnnotationHub_3.2.2.tar.gz AnnotationHub_3.2.2.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  209k  100  209k    0     0   780k      0 --:--:-- --:--:-- --:--:--  783k

install for i386

* installing *source* package 'AnnotationHub' ...
** using staged installation
** R
** inst
** byte-compile and prepare 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  
    Hub-utils                               html  
    convertHub                              html  
    getAnnotationHubOption                  html  
    listResources                           html  
    utils                                   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

install for x64

* installing *source* package 'AnnotationHub' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationHub' as AnnotationHub_3.2.2.zip
* DONE (AnnotationHub)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'AnnotationHub' successfully unpacked and MD5 sums checked

Tests output

AnnotationHub.Rcheck/tests_i386/runTests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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: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

snapshotDate(): 2021-10-20
snapshotDate(): 2022-04-12
snapshotDate(): 2021-10-20
snapshotDate(): 2021-10-20
snapshotDate(): 2021-10-20
snapshotDate(): 2021-10-20
snapshotDate(): 2021-10-20
snapshotDate(): 2021-10-20
snapshotDate(): 2021-10-20
snapshotDate(): 2021-10-20
snapshotDate(): 2021-10-20
Loading required package: S4Vectors
Loading required package: stats4

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

require("xxx_foo")


RUNIT TEST PROTOCOL -- Tue Apr 12 15:42:21 2022 
*********************************************** 
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 
> 
> proc.time()
   user  system elapsed 
  71.45    7.64   97.32 

AnnotationHub.Rcheck/tests_x64/runTests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
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("AnnotationHub")

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

snapshotDate(): 2021-10-20
snapshotDate(): 2022-04-12
snapshotDate(): 2021-10-20
snapshotDate(): 2021-10-20
snapshotDate(): 2021-10-20
snapshotDate(): 2021-10-20
snapshotDate(): 2021-10-20
snapshotDate(): 2021-10-20
snapshotDate(): 2021-10-20
snapshotDate(): 2021-10-20
snapshotDate(): 2021-10-20
Loading required package: S4Vectors
Loading required package: stats4

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

require("xxx_foo")


RUNIT TEST PROTOCOL -- Tue Apr 12 15:47:45 2022 
*********************************************** 
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 
> 
> proc.time()
   user  system elapsed 
  72.34    7.95  323.34 

Example timings

AnnotationHub.Rcheck/examples_i386/AnnotationHub-Ex.timings

nameusersystemelapsed
AnnotationHub-class57.78 2.8671.02
AnnotationHub-package000
Hub-utils000
convertHub000
getAnnotationHubOption000
utils000

AnnotationHub.Rcheck/examples_x64/AnnotationHub-Ex.timings

nameusersystemelapsed
AnnotationHub-class45.17 1.5050.09
AnnotationHub-package000
Hub-utils000
convertHub000
getAnnotationHubOption000
utils000