Back to Multiple platform build/check report for BioC 3.13 experimental data
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

CHECK report for RNAmodR.Data on riesling1

This page was generated on 2021-01-18 15:58:50 -0500 (Mon, 18 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE RNAmodR.Data PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 299/385HostnameOS / ArchINSTALLBUILDCHECK
RNAmodR.Data 1.5.0
Felix G.M. Ernst
Snapshot Date: 2021-01-18 09:00:15 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/RNAmodR.Data
Branch: master
Last Commit: f7833d3
Last Changed Date: 2020-10-27 10:30:16 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: RNAmodR.Data
Version: 1.5.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAmodR.Data.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RNAmodR.Data_1.5.0.tar.gz
StartedAt: 2021-01-18 11:41:49 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 11:49:06 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 437.3 seconds
RetCode: 0
Status:  OK  
CheckDir: RNAmodR.Data.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAmodR.Data.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RNAmodR.Data_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/RNAmodR.Data.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 'RNAmodR.Data/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RNAmodR.Data' version '1.5.0'
* package encoding: UTF-8
* 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 'RNAmodR.Data' 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
RNAmodR.Data.AAS     22.08   1.97   27.72
RNAmodR.Data.example 11.36   0.75   14.03
RNAmodR.Data.RMS      8.73   0.69   10.89
example.man.fasta     4.17   0.30    5.22
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
RNAmodR.Data.AAS     23.27   2.28   29.00
RNAmodR.Data.example 12.64   0.83   15.63
RNAmodR.Data.RMS      9.23   0.76   11.53
example.man.fasta     4.30   0.47    5.48
* 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

RNAmodR.Data.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/RNAmodR.Data_1.5.0.tar.gz && rm -rf RNAmodR.Data.buildbin-libdir && mkdir RNAmodR.Data.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RNAmodR.Data.buildbin-libdir RNAmodR.Data_1.5.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL RNAmodR.Data_1.5.0.zip && rm RNAmodR.Data_1.5.0.tar.gz RNAmodR.Data_1.5.0.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  7892  100  7892    0     0   550k      0 --:--:-- --:--:-- --:--:--  550k

install for i386

* installing *source* package 'RNAmodR.Data' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RNAmodR.Data'
    finding HTML links ... done
    RNAmodR.Data.AAS                        html  
REDIRECT:topic	 RNAmodR.Data.AAS -> RNAmodR.Data.AAS.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.AAS.fasta -> RNAmodR.Data.AAS.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.AAS.gff3 -> RNAmodR.Data.AAS.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.bud23.1 -> RNAmodR.Data.AAS.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.bud23.2 -> RNAmodR.Data.AAS.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.trm8.1 -> RNAmodR.Data.AAS.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.trm8.2 -> RNAmodR.Data.AAS.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.wt.1 -> RNAmodR.Data.AAS.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.wt.2 -> RNAmodR.Data.AAS.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.wt.3 -> RNAmodR.Data.AAS.html [ SUCCESS ]
    RNAmodR.Data.RMS                        html  
REDIRECT:topic	 RNAmodR.Data.RMS -> RNAmodR.Data.RMS.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.RMS.fasta -> RNAmodR.Data.RMS.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.RMS.gff3 -> RNAmodR.Data.RMS.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.RMS.1 -> RNAmodR.Data.RMS.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.RMS.2 -> RNAmodR.Data.RMS.html [ SUCCESS ]
    RNAmodR.Data                            html  
REDIRECT:topic	 RNAmodR.Data -> RNAmodR.Data.html [ SUCCESS ]
    RNAmodR.Data.example                    html  
REDIRECT:topic	 RNAmodR.Data.example -> RNAmodR.Data.example.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.fasta -> RNAmodR.Data.example.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.gff3 -> RNAmodR.Data.example.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.bam.1 -> RNAmodR.Data.example.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.bam.2 -> RNAmodR.Data.example.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.bam.3 -> RNAmodR.Data.example.html [ SUCCESS ]
    RNAmodR.Data.snoRNAdb                   html  
REDIRECT:topic	 RNAmodR.Data.snoRNAdb -> RNAmodR.Data.snoRNAdb.html [ SUCCESS ]
    example.man.fasta                       html  
REDIRECT:topic	 example.man.fasta -> example.man.fasta.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.man.fasta -> example.man.fasta.html [ SUCCESS ]
REDIRECT:topic	 RNAmodR.Data.example.man.gff3 -> example.man.fasta.html [ SUCCESS ]
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2021-01-15
** testing if installed package can be loaded from final location
snapshotDate(): 2021-01-15
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'RNAmodR.Data' ...
** testing if installed package can be loaded
snapshotDate(): 2021-01-15
* MD5 sums
packaged installation of 'RNAmodR.Data' as RNAmodR.Data_1.5.0.zip
* DONE (RNAmodR.Data)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'RNAmodR.Data' successfully unpacked and MD5 sums checked

Tests output

RNAmodR.Data.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(RNAmodR.Data)
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 required package: ExperimentHubData
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: AnnotationHubData
Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
snapshotDate(): 2021-01-15
> 
> test_check("RNAmodR.Data")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
   8.40    0.43   11.10 

RNAmodR.Data.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(RNAmodR.Data)
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 required package: ExperimentHubData
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: AnnotationHubData
Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
snapshotDate(): 2021-01-15
> 
> test_check("RNAmodR.Data")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
   9.39    0.59   12.03 

Example timings

RNAmodR.Data.Rcheck/examples_i386/RNAmodR.Data-Ex.timings

nameusersystemelapsed
RNAmodR.Data.AAS22.08 1.9727.72
RNAmodR.Data.RMS 8.73 0.6910.89
RNAmodR.Data.example11.36 0.7514.03
RNAmodR.Data.snoRNAdb1.750.152.21
example.man.fasta4.170.305.22

RNAmodR.Data.Rcheck/examples_x64/RNAmodR.Data-Ex.timings

nameusersystemelapsed
RNAmodR.Data.AAS23.27 2.2829.00
RNAmodR.Data.RMS 9.23 0.7611.53
RNAmodR.Data.example12.64 0.8315.63
RNAmodR.Data.snoRNAdb1.930.062.31
example.man.fasta4.300.475.48