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CHECK report for sesameData on riesling1

This page was generated on 2021-01-11 15:59:33 -0500 (Mon, 11 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE sesameData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 329/385HostnameOS / ArchINSTALLBUILDCHECK
sesameData 1.9.1
Wanding Zhou
Snapshot Date: 2021-01-11 09:00:09 -0500 (Mon, 11 Jan 2021)
URL: https://git.bioconductor.org/packages/sesameData
Branch: master
Last Commit: 59f185e
Last Changed Date: 2021-01-09 09:59:59 -0500 (Sat, 09 Jan 2021)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK YES, new version is higher than in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: sesameData
Version: 1.9.1
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sesameData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings sesameData_1.9.1.tar.gz
StartedAt: 2021-01-11 11:46:25 -0500 (Mon, 11 Jan 2021)
EndedAt: 2021-01-11 11:56:02 -0500 (Mon, 11 Jan 2021)
EllapsedTime: 577.1 seconds
RetCode: 0
Status:  OK  
CheckDir: sesameData.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sesameData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings sesameData_1.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/sesameData.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sesameData/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sesameData' version '1.9.1'
* 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 'sesameData' 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 ... 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
sesameDataCacheAll 8.67   0.85   11.67
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
sesameDataCacheAll 9.53   0.86   12.72
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: OK


Installation output

sesameData.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/sesameData_1.9.1.tar.gz && rm -rf sesameData.buildbin-libdir && mkdir sesameData.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sesameData.buildbin-libdir sesameData_1.9.1.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL sesameData_1.9.1.zip && rm sesameData_1.9.1.tar.gz sesameData_1.9.1.zip
###
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##############################################################################


  % 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 1491k  100 1491k    0     0  45.5M      0 --:--:-- --:--:-- --:--:-- 45.5M

install for i386

* installing *source* package 'sesameData' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sesameData'
    finding HTML links ... done
    sesameDataCacheAll                      html  
REDIRECT:topic	 sesameDataCacheAll -> sesameDataCacheAll.html [ SUCCESS ]
    sesameDataGet                           html  
REDIRECT:topic	 sesameDataGet -> sesameDataGet.html [ SUCCESS ]
    sesameDataList                          html  
REDIRECT:topic	 sesameDataList -> sesameDataList.html [ SUCCESS ]
    sesameDataListDates                     html  
REDIRECT:topic	 sesameDataListDates -> sesameDataListDates.html [ SUCCESS ]
    sesameDataPullManifest                  html  
REDIRECT:topic	 sesameDataPullManifest -> sesameDataPullManifest.html [ SUCCESS ]
    sesameDataPullVariantAnno_InfiniumI     html  
REDIRECT:topic	 sesameDataPullVariantAnno_InfiniumI -> sesameDataPullVariantAnno_InfiniumI.html [ SUCCESS ]
    sesameDataPullVariantAnno_SNP           html  
REDIRECT:topic	 sesameDataPullVariantAnno_SNP -> sesameDataPullVariantAnno_SNP.html [ SUCCESS ]
** 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 'sesameData' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sesameData' as sesameData_1.9.1.zip
* DONE (sesameData)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'sesameData' successfully unpacked and MD5 sums checked

Tests output

sesameData.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 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.

> library(testthat)
> library(sesame)
Loading required package: sesameData
Loading required package: ExperimentHub
Loading required package: BiocGenerics
Loading required package: parallel

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, 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

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading sesameData.
> 
> test_check("sesameData")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 112 ]
> 
> proc.time()
   user  system elapsed 
 103.64    3.82  119.03 

sesameData.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 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.

> library(testthat)
> library(sesame)
Loading required package: sesameData
Loading required package: ExperimentHub
Loading required package: BiocGenerics
Loading required package: parallel

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, 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

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading sesameData.
> 
> test_check("sesameData")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 112 ]
> 
> proc.time()
   user  system elapsed 
 101.59    3.85  110.84 

Example timings

sesameData.Rcheck/examples_i386/sesameData-Ex.timings

nameusersystemelapsed
sesameDataCacheAll 8.67 0.8511.67
sesameDataGet2.720.603.53
sesameDataList1.000.051.20
sesameDataListDates0.990.061.24
sesameDataPullManifest0.180.000.50
sesameDataPullVariantAnno_InfiniumI0.000.000.04
sesameDataPullVariantAnno_SNP0.000.000.05

sesameData.Rcheck/examples_x64/sesameData-Ex.timings

nameusersystemelapsed
sesameDataCacheAll 9.53 0.8612.72
sesameDataGet2.640.703.45
sesameDataList1.080.051.29
sesameDataListDates0.990.061.20
sesameDataPullManifest0.190.000.46
sesameDataPullVariantAnno_InfiniumI0.000.000.03
sesameDataPullVariantAnno_SNP0.000.000.04