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CHECK report for weitrix on tokay1

This page was generated on 2021-05-06 12:34:11 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the weitrix package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1953/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
weitrix 1.2.0  (landing page)
Paul Harrison
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/weitrix
Branch: RELEASE_3_12
Last Commit: 72b5965
Last Changed Date: 2020-10-27 11:57:06 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: weitrix
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:weitrix.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings weitrix_1.2.0.tar.gz
StartedAt: 2021-05-06 07:56:46 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 08:11:57 -0400 (Thu, 06 May 2021)
EllapsedTime: 911.4 seconds
RetCode: 0
Status:   OK   
CheckDir: weitrix.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:weitrix.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings weitrix_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/weitrix.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'weitrix/DESCRIPTION' ... OK
* this is package 'weitrix' version '1.2.0'
* 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 'weitrix' 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
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
components_seq_scree    8.33   1.41   27.86
weitrix_calplot         5.38   0.14   87.16
weitrix_calibrate_trend 3.21   0.19   34.33
weitrix_calibrate       2.64   0.25   20.61
weitrix_dispersions     2.33   0.17   31.63
weitrix_components      1.03   0.10   13.93
weitrix_sd_confects     1.08   0.00   24.83
weitrix_calibrate_all   0.80   0.03   14.44
weitrix_confects        0.64   0.01   10.18
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
components_seq_scree    5.75   1.00   20.97
weitrix_calplot         4.96   0.10   75.16
weitrix_calibrate_trend 3.02   0.26   27.32
weitrix_dispersions     2.33   0.13   25.57
weitrix_calibrate       1.84   0.21   14.53
weitrix_sd_confects     1.30   0.00   24.44
weitrix_components      0.93   0.09   11.95
weitrix_calibrate_all   0.75   0.03   12.57
weitrix_confects        0.68   0.00    8.82
* 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

weitrix.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/weitrix_1.2.0.tar.gz && rm -rf weitrix.buildbin-libdir && mkdir weitrix.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=weitrix.buildbin-libdir weitrix_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL weitrix_1.2.0.zip && rm weitrix_1.2.0.tar.gz weitrix_1.2.0.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 2280k  100 2280k    0     0  44.6M      0 --:--:-- --:--:-- --:--:-- 45.4M

install for i386

* installing *source* package 'weitrix' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'weitrix'
    finding HTML links ... done
    as_weitrix                              html  
    bless_weitrix                           html  
    components_seq_scree                    html  
    counts_proportions                      html  
    counts_shift                            html  
    matrix_long                             html  
    simwei                                  html  
    weitrix_calibrate                       html  
    weitrix_calibrate_all                   html  
    weitrix_calibrate_trend                 html  
    weitrix_calplot                         html  
    weitrix_components                      html  
    weitrix_confects                        html  
    weitrix_dispersions                     html  
    weitrix_elist                           html  
    weitrix_hill                            html  
    weitrix_randomize                       html  
    weitrix_sd_confects                     html  
    weitrix_weights                         html  
    weitrix_x                               html  
    well_knotted_spline                     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 'weitrix' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'weitrix' as weitrix_1.2.0.zip
* DONE (weitrix)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'weitrix' successfully unpacked and MD5 sums checked

Tests output

weitrix.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(weitrix)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

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: stats4
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: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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("weitrix")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
  11.14    0.73   86.87

weitrix.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(weitrix)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

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: stats4
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: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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("weitrix")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
  12.01    0.42   88.11

Example timings

weitrix.Rcheck/examples_i386/weitrix-Ex.timings

nameusersystemelapsed
as_weitrix0.090.000.09
bless_weitrix0.030.000.03
components_seq_scree 8.33 1.4127.86
counts_proportions0.070.000.07
counts_shift0.080.000.08
matrix_long0.030.000.03
weitrix_calibrate 2.64 0.2520.61
weitrix_calibrate_all 0.80 0.0314.44
weitrix_calibrate_trend 3.21 0.1934.33
weitrix_calplot 5.38 0.1487.16
weitrix_components 1.03 0.1013.93
weitrix_confects 0.64 0.0110.18
weitrix_dispersions 2.33 0.1731.63
weitrix_elist0.030.000.03
weitrix_hill0.030.000.03
weitrix_randomize0.010.000.01
weitrix_sd_confects 1.08 0.0024.83
weitrix_weights000
weitrix_x0.030.000.03
well_knotted_spline1.830.132.07

weitrix.Rcheck/examples_x64/weitrix-Ex.timings

nameusersystemelapsed
as_weitrix0.060.030.10
bless_weitrix0.030.000.03
components_seq_scree 5.75 1.0020.97
counts_proportions0.060.000.06
counts_shift0.040.000.05
matrix_long0.040.000.03
weitrix_calibrate 1.84 0.2114.53
weitrix_calibrate_all 0.75 0.0312.57
weitrix_calibrate_trend 3.02 0.2627.32
weitrix_calplot 4.96 0.1075.16
weitrix_components 0.93 0.0911.95
weitrix_confects0.680.008.82
weitrix_dispersions 2.33 0.1325.57
weitrix_elist0.030.000.04
weitrix_hill0.020.000.01
weitrix_randomize0.030.000.03
weitrix_sd_confects 1.30 0.0024.44
weitrix_weights000
weitrix_x0.030.000.03
well_knotted_spline1.260.041.33