Multiple platform build/check report for BioC 3.14 - CHECK results for OMICsPCA on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	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*

Package: OMICsPCA

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OMICsPCA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings OMICsPCA_1.12.0.tar.gz

StartedAt: 2022-04-12 23:58:31 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-13 00:06:52 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 501.3 seconds

RetCode: 0

Status: OK

CheckDir: OMICsPCA.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OMICsPCA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings OMICsPCA_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/OMICsPCA.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OMICsPCA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OMICsPCA' version '1.12.0'
* 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 'OMICsPCA' 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
analyse_individuals 7.63    0.9    9.18
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
analyse_individuals 7.26   0.36    7.62
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/OMICsPCA_1.12.0.tar.gz && rm -rf OMICsPCA.buildbin-libdir && mkdir OMICsPCA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OMICsPCA.buildbin-libdir OMICsPCA_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL OMICsPCA_1.12.0.zip && rm OMICsPCA_1.12.0.tar.gz OMICsPCA_1.12.0.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 33786  100 33786    0     0  74588      0 --:--:-- --:--:-- --:--:-- 74747

install for i386

* installing *source* package 'OMICsPCA' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'OMICsPCA'
    finding HTML links ... done
    analyse_individuals                     html  
    analyse_integrated_individuals          html  
    analyse_integrated_variables            html  
    analyse_variables                       html  
    chart_correlation                       html  
    cluster                                 html  
    cluster_boxplot                         html  
    cluster_parameters                      html  
    create_group                            html  
    descriptor                              html  
    extract                                 html  
    extract_assay                           html  
    integrate_pca                           html  
    integrate_variables                     html  
    intersect                               html  
    merge_cells                             html  
    plot_density                            html  
    plot_density_3D                         html  
    plot_integrated_density                 html  
    plot_integrated_density_3D              html  
    prepare_dataset                         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 'OMICsPCA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OMICsPCA' as OMICsPCA_1.12.0.zip
* DONE (OMICsPCA)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'OMICsPCA' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(OMICsPCAdata)
> BiocGenerics:::testPackage("OMICsPCA")

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


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


Attaching package: 'IRanges'

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

    windows

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


Attaching package: 'OMICsPCA'

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

    intersect

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

    intersect

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

    intersect

The following object is masked from 'package:S4Vectors':

    intersect

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

    intersect

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

    intersect

[1] "Running intersect... This may take some time"
[1] "Merging cell lines... This may take some time"
[1] "Total time taken is: 0.765592098236084"
[1] "time taken to run intersect() is: 0.718717098236084"
[1] "time taken to run merge_cells() is: 0.046875"


RUNIT TEST PROTOCOL -- Wed Apr 13 00:06:26 2022 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
OMICsPCA RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  15.10    1.73   16.82


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(OMICsPCAdata)
> BiocGenerics:::testPackage("OMICsPCA")

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


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


Attaching package: 'IRanges'

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

    windows

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


Attaching package: 'OMICsPCA'

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

    intersect

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

    intersect

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

    intersect

The following object is masked from 'package:S4Vectors':

    intersect

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

    intersect

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

    intersect

[1] "Running intersect... This may take some time"
[1] "Merging cell lines... This may take some time"
[1] "Total time taken is: 0.562503814697266"
[1] "time taken to run intersect() is: 0.546878814697266"
[1] "time taken to run merge_cells() is: 0.015625"


RUNIT TEST PROTOCOL -- Wed Apr 13 00:06:44 2022 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
OMICsPCA RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  16.95    0.73   17.68

name	user	system	elapsed
analyse_individuals	7.63	0.90	9.18
analyse_integrated_individuals	1.08	0.19	1.26
analyse_integrated_variables	1.94	0.19	2.12
analyse_variables	0.39	0.05	0.44
chart_correlation	0.02	0.00	0.01
cluster	0.81	0.20	1.15
cluster_boxplot	0.58	0.00	0.60
cluster_parameters	1.36	0.30	1.66
create_group	0.54	0.01	0.56
descriptor	0.88	0.08	0.96
extract	0.73	0.25	0.98
extract_assay	1.14	0.33	1.47
integrate_pca	0.80	0.26	1.06
integrate_variables	0.16	0.07	0.22
intersect	0.73	0.00	0.83
merge_cells	0.23	0.00	0.23
plot_density	0.47	0.07	0.55
plot_density_3D	0.41	0.02	0.42
plot_integrated_density	2.03	0.23	2.27
plot_integrated_density_3D	1.62	0.32	1.94
prepare_dataset	0.2	0.0	0.2

name	user	system	elapsed
analyse_individuals	7.26	0.36	7.62
analyse_integrated_individuals	2.14	0.39	2.53
analyse_integrated_variables	0.95	0.29	1.25
analyse_variables	0.35	0.02	0.36
chart_correlation	0.01	0.00	0.02
cluster	0.85	0.23	1.08
cluster_boxplot	0.4	0.0	0.4
cluster_parameters	2.10	0.27	2.36
create_group	0.45	0.05	0.50
descriptor	0.81	0.06	0.88
extract	1.75	0.20	1.95
extract_assay	0.83	0.22	1.05
integrate_pca	0.63	0.23	0.86
integrate_variables	0.09	0.05	0.14
intersect	0.52	0.02	0.53
merge_cells	0.18	0.01	0.20
plot_density	0.35	0.02	0.36
plot_density_3D	0.39	0.03	0.52
plot_integrated_density	1.48	0.36	1.84
plot_integrated_density_3D	1.71	0.26	1.97
prepare_dataset	0.2	0.0	0.2

CHECK results for OMICsPCA on tokay2

Summary

Command output

Installation output

Tests output

Example timings