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CHECK report for bioassayR on riesling1

This page was generated on 2020-10-21 12:13:48 -0400 (Wed, 21 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE bioassayR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 146/1939HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioassayR 1.27.0
Tyler Backman
Snapshot Date: 2020-10-20 14:40:34 -0400 (Tue, 20 Oct 2020)
URL: https://git.bioconductor.org/packages/bioassayR
Branch: master
Last Commit: 288a60a
Last Changed Date: 2020-04-27 14:36:43 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: bioassayR
Version: 1.27.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bioassayR.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings bioassayR_1.27.0.tar.gz
StartedAt: 2020-10-20 20:14:54 -0400 (Tue, 20 Oct 2020)
EndedAt: 2020-10-20 20:16:28 -0400 (Tue, 20 Oct 2020)
EllapsedTime: 94.3 seconds
RetCode: 0
Status:  OK  
CheckDir: bioassayR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bioassayR.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings bioassayR_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/bioassayR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bioassayR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bioassayR' version '1.27.0'
* 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 'bioassayR' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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

bioassayR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/bioassayR_1.27.0.tar.gz && rm -rf bioassayR.buildbin-libdir && mkdir bioassayR.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bioassayR.buildbin-libdir bioassayR_1.27.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL bioassayR_1.27.0.zip && rm bioassayR_1.27.0.tar.gz bioassayR_1.27.0.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  305k  100  305k    0     0  74.4M      0 --:--:-- --:--:-- --:--:-- 74.4M

install for i386

* installing *source* package 'bioassayR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'organism' in package 'bioassayR'
Creating a new generic function for 'organism<-' in package 'bioassayR'
** help
*** installing help indices
  converting help for package 'bioassayR'
    finding HTML links ... done
    BioAssayDB-class                        html  
    activeAgainst                           html  
    activeTargets                           html  
    addBioassayIndex                        html  
    addDataSource                           html  
    allCids                                 html  
    allTargets                              html  
    assaySetTargets                         html  
    bioactivityFingerprint                  html  
    bioassay-class                          html  
    bioassaySet-class                       html  
    connectBioassayDB                       html  
    crossReactivityProbability              html  
    disconnectBioassayDB                    html  
    dropBioassay                            html  
    dropBioassayIndex                       html  
    getAssay                                html  
    getAssays                               html  
    getBioassaySetByCids                    html  
    inactiveTargets                         html  
    loadBioassay                            html  
    loadIdMapping                           html  
    newBioassayDB                           html  
    parsePubChemBioassay                    html  
    perTargetMatrix                         html  
    queryBioassayDB                         html  
    samplebioassay                          html  
    scaleBioassaySet                        html  
    screenedAtLeast                         html  
    selectiveAgainst                        html  
    targetSelectivity                       html  
    translateTargetId                       html  
    trinarySimilarity                       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 'bioassayR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bioassayR' as bioassayR_1.27.0.zip
* DONE (bioassayR)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'bioassayR' successfully unpacked and MD5 sums checked

Tests output

bioassayR.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(bioassayR)
Loading required package: DBI
Loading required package: RSQLite
Loading required package: Matrix
Loading required package: rjson
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


Attaching package: 'bioassayR'

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

    organism, organism<-

> 
> test_check("bioassayR")
== testthat results  ===========================================================
[ OK: 22 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   4.01    0.21    4.21 

bioassayR.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(bioassayR)
Loading required package: DBI
Loading required package: RSQLite
Loading required package: Matrix
Loading required package: rjson
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


Attaching package: 'bioassayR'

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

    organism, organism<-

> 
> test_check("bioassayR")
== testthat results  ===========================================================
[ OK: 22 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   3.31    0.23    3.54 

Example timings

bioassayR.Rcheck/examples_i386/bioassayR-Ex.timings

nameusersystemelapsed
BioAssayDB-class0.020.000.01
activeAgainst0.020.000.02
activeTargets0.010.000.01
addBioassayIndex0.000.010.11
addDataSource0.020.020.06
allCids0.010.000.02
allTargets000
assaySetTargets0.030.000.03
bioactivityFingerprint0.180.000.17
bioassay-class0.000.010.02
bioassaySet-class000
connectBioassayDB0.000.000.05
crossReactivityProbability0.170.000.18
disconnectBioassayDB0.020.000.06
dropBioassay0.010.000.25
dropBioassayIndex0.040.000.41
getAssay000
getAssays000
getBioassaySetByCids0.090.000.09
inactiveTargets0.020.000.02
loadBioassay0.030.000.11
loadIdMapping0.000.000.05
newBioassayDB0.020.000.03
parsePubChemBioassay000
perTargetMatrix0.110.000.11
queryBioassayDB0.000.020.01
samplebioassay000
scaleBioassaySet0.010.000.02
screenedAtLeast0.020.000.01
selectiveAgainst0.060.000.06
targetSelectivity0.020.000.02
translateTargetId0.030.000.06
trinarySimilarity0.110.000.11

bioassayR.Rcheck/examples_x64/bioassayR-Ex.timings

nameusersystemelapsed
BioAssayDB-class000
activeAgainst0.020.000.02
activeTargets0.010.000.02
addBioassayIndex0.030.000.09
addDataSource0.020.000.08
allCids000
allTargets000
assaySetTargets0.010.020.04
bioactivityFingerprint0.080.000.08
bioassay-class0.020.000.01
bioassaySet-class000
connectBioassayDB0.000.020.04
crossReactivityProbability0.080.000.08
disconnectBioassayDB0.000.000.08
dropBioassay0.030.010.16
dropBioassayIndex0.000.000.22
getAssay000
getAssays0.020.000.02
getBioassaySetByCids0.080.000.08
inactiveTargets0.010.000.01
loadBioassay0.020.020.22
loadIdMapping0.010.000.13
newBioassayDB0.020.000.06
parsePubChemBioassay000
perTargetMatrix0.090.000.09
queryBioassayDB0.020.000.02
samplebioassay000
scaleBioassaySet0.010.000.01
screenedAtLeast0.020.000.02
selectiveAgainst0.030.010.04
targetSelectivity0.020.000.02
translateTargetId0.000.000.06
trinarySimilarity0.090.000.09