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This page was generated on 2022-01-14 13:07:01 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 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 RegEnrich on tokay2


To the developers/maintainers of the RegEnrich package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RegEnrich.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1572/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RegEnrich 1.4.0  (landing page)
Weiyang Tao
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/RegEnrich
git_branch: RELEASE_3_14
git_last_commit: 1dcf069
git_last_commit_date: 2021-10-26 13:00:23 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RegEnrich
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RegEnrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RegEnrich_1.4.0.tar.gz
StartedAt: 2022-01-14 00:55:38 -0500 (Fri, 14 Jan 2022)
EndedAt: 2022-01-14 01:04:10 -0500 (Fri, 14 Jan 2022)
EllapsedTime: 511.9 seconds
RetCode: 0
Status:   OK  
CheckDir: RegEnrich.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RegEnrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RegEnrich_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RegEnrich.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RegEnrich/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RegEnrich' version '1.4.0'
* 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 'RegEnrich' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plot_Enrich    15.09   0.39   23.68
plotRegTarExpr 12.75   0.70   13.46
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plot_Enrich    16.94   0.46   25.78
plotRegTarExpr 13.42   0.17   13.60
* 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

RegEnrich.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RegEnrich_1.4.0.tar.gz && rm -rf RegEnrich.buildbin-libdir && mkdir RegEnrich.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RegEnrich.buildbin-libdir RegEnrich_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RegEnrich_1.4.0.zip && rm RegEnrich_1.4.0.tar.gz RegEnrich_1.4.0.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
 35  950k   35  340k    0     0  1879k      0 --:--:-- --:--:-- --:--:-- 1878k
100  950k  100  950k    0     0  4099k      0 --:--:-- --:--:-- --:--:-- 4098k

install for i386

* installing *source* package 'RegEnrich' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RegEnrich'
    finding HTML links ... done
    DeaSet-class                            html  
    Enrich-class                            html  
    Lyme_GSE63085                           html  
    RegenrichSet-class                      html  
    RegenrichSet                            html  
    finding level-2 HTML links ... done

    Score                                   html  
    TFs                                     html  
    TopNetwork-class                        html  
    dim-TopNetwork-method                   html  
    getResultsNames                         html  
    headTailScore                           html  
    methodsOfShow                           html  
    newDeaSet                               html  
    newTopNetwork                           html  
    plotOrders                              html  
    plotRegTarExpr                          html  
    plotSoftPower                           html  
    plot_Enrich                             html  
    print.Score                             html  
    reexports                               html  
    regenrich_diffExpr                      html  
    regenrich_enrich                        html  
    regenrich_network                       html  
    regenrich_rankScore                     html  
    results_expr                            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 'RegEnrich' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RegEnrich' as RegEnrich_1.4.0.zip
* DONE (RegEnrich)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'RegEnrich' successfully unpacked and MD5 sums checked

Tests output

RegEnrich.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(RegEnrich)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

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


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:S4Vectors':

    first, intersect, rename, setdiff, setequal, union

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

    combine, intersect, setdiff, union

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: tibble
Loading required package: BiocSet
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    count


Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: IRanges

Attaching package: 'IRanges'

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

    collapse, desc, slice

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

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians


> 
> test_check("RegEnrich")




[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
  25.76    2.06   71.71 

RegEnrich.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(RegEnrich)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

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


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:S4Vectors':

    first, intersect, rename, setdiff, setequal, union

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

    combine, intersect, setdiff, union

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: tibble
Loading required package: BiocSet
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    count


Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: IRanges

Attaching package: 'IRanges'

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

    collapse, desc, slice

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

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians


> 
> test_check("RegEnrich")




[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
  27.67    1.00   71.37 

Example timings

RegEnrich.Rcheck/examples_i386/RegEnrich-Ex.timings

nameusersystemelapsed
DeaSet-class0.110.000.11
RegenrichSet1.510.051.57
Score0.140.000.14
dim-TopNetwork-method0.020.000.02
getResultsNames000
headTailScore0.060.000.06
methodsOfShow0.010.010.03
newDeaSet0.110.030.14
newTopNetwork0.040.030.06
plotOrders0.170.050.22
plotRegTarExpr12.75 0.7013.46
plotSoftPower0.170.020.18
plot_Enrich15.09 0.3923.68
print.Score0.030.000.03
reexports000
regenrich_diffExpr0.390.020.40
regenrich_enrich0.210.040.25
regenrich_network0.20.10.3
regenrich_rankScore0.220.060.28
results_expr0.230.030.27

RegEnrich.Rcheck/examples_x64/RegEnrich-Ex.timings

nameusersystemelapsed
DeaSet-class0.140.000.14
RegenrichSet1.080.001.08
Score0.160.000.16
dim-TopNetwork-method000
getResultsNames0.000.000.01
headTailScore0.030.000.07
methodsOfShow0.030.000.03
newDeaSet0.200.000.22
newTopNetwork0.050.000.04
plotOrders0.250.000.25
plotRegTarExpr13.42 0.1713.60
plotSoftPower0.110.000.11
plot_Enrich16.94 0.4625.78
print.Score0.030.000.03
reexports000
regenrich_diffExpr0.560.000.56
regenrich_enrich0.240.010.25
regenrich_network0.200.030.24
regenrich_rankScore0.200.020.21
results_expr0.220.020.24