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This page was generated on 2022-01-24 13:06:41 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 OMICsPCA on tokay2


To the developers/maintainers of the OMICsPCA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OMICsPCA.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 1327/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OMICsPCA 1.12.0  (landing page)
Subhadeep Das
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/OMICsPCA
git_branch: RELEASE_3_14
git_last_commit: 5161764
git_last_commit_date: 2021-10-26 12:47:05 -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: 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: 2022-01-23 23:34:19 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 23:42:30 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 491.3 seconds
RetCode: 0
Status:   OK  
CheckDir: OMICsPCA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/OMICsPCA.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 '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 7.44   1.06     9.5
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
analyse_individuals  6.4    0.4     6.8
* 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


Installation output

OMICsPCA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


  % 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   285k      0 --:--:-- --:--:-- --:--:--  286k

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

Tests output

OMICsPCA.Rcheck/tests_i386/runTests.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(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: 0.578127861022949"
[1] "time taken to run intersect() is: 0.562501907348633"
[1] "time taken to run merge_cells() is: 0.0156259536743164"


RUNIT TEST PROTOCOL -- Sun Jan 23 23:42:06 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 
  14.75    1.29   16.01 

OMICsPCA.Rcheck/tests_x64/runTests.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(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: 0.562503099441528"
[1] "time taken to run intersect() is: 0.546877145767212"
[1] "time taken to run merge_cells() is: 0.0156259536743164"


RUNIT TEST PROTOCOL -- Sun Jan 23 23:42:23 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 
  15.26    0.60   15.85 

Example timings

OMICsPCA.Rcheck/examples_i386/OMICsPCA-Ex.timings

nameusersystemelapsed
analyse_individuals7.441.069.50
analyse_integrated_individuals0.980.311.30
analyse_integrated_variables2.030.192.21
analyse_variables0.360.090.45
chart_correlation0.020.000.02
cluster0.950.171.20
cluster_boxplot0.560.000.56
cluster_parameters1.360.411.77
create_group0.480.080.56
descriptor0.830.140.97
extract0.780.170.95
extract_assay1.100.331.42
integrate_pca0.710.281.00
integrate_variables0.160.060.22
intersect0.50.00.5
merge_cells0.190.020.20
plot_density0.340.120.47
plot_density_3D0.350.030.38
plot_integrated_density2.090.192.28
plot_integrated_density_3D1.670.281.95
prepare_dataset0.200.000.21

OMICsPCA.Rcheck/examples_x64/OMICsPCA-Ex.timings

nameusersystemelapsed
analyse_individuals6.40.46.8
analyse_integrated_individuals1.970.292.27
analyse_integrated_variables1.070.221.29
analyse_variables0.370.020.39
chart_correlation0.020.000.01
cluster0.670.280.96
cluster_boxplot0.370.000.37
cluster_parameters1.100.261.36
create_group0.450.080.53
descriptor0.770.050.81
extract0.760.170.94
extract_assay0.880.301.17
integrate_pca1.720.201.92
integrate_variables0.100.050.16
intersect0.580.000.58
merge_cells0.220.010.23
plot_density0.420.070.49
plot_density_3D0.380.030.50
plot_integrated_density1.340.281.62
plot_integrated_density_3D1.840.232.08
prepare_dataset0.220.000.22