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CHECK report for CATALYST on tokay1

This page was generated on 2020-04-15 12:28:18 -0400 (Wed, 15 Apr 2020).

Package 228/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CATALYST 1.10.3
Helena L. Crowell
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/CATALYST
Branch: RELEASE_3_10
Last Commit: d2e724c
Last Changed Date: 2020-04-02 07:29:58 -0400 (Thu, 02 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CATALYST
Version: 1.10.3
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CATALYST.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CATALYST_1.10.3.tar.gz
StartedAt: 2020-04-15 01:49:36 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:08:55 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 1159.1 seconds
RetCode: 0
Status:  OK  
CheckDir: CATALYST.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CATALYST.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CATALYST_1.10.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/CATALYST.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CATALYST/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CATALYST' version '1.10.3'
* 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 'CATALYST' 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 or elapsed time > 5s
                    user system elapsed
plotDR             34.49   0.20   33.63
plotClusterExprs   24.10   0.47   24.57
plotClusterHeatmap 15.52   0.21   15.69
plotMedExprs       13.21   0.42   13.64
estCutoffs         11.80   0.06   12.03
applyCutoffs       11.58   0.03   11.71
assignPrelim       11.20   0.00   11.25
plotMahal          10.61   0.00   10.61
outFrames          10.11   0.03   10.14
outFCS              9.95   0.03    9.99
normCytof           9.97   0.00    9.96
plotYields          9.44   0.23    9.59
SCE-utils           8.77   0.69    9.46
plotAbundances      9.10   0.07    9.16
plotEvents          9.13   0.00    9.13
mergeClusters       8.67   0.06    8.72
dbFrame-methods     8.53   0.00    8.53
cluster             8.19   0.08    8.26
adaptSpillmat       7.72   0.04    7.78
plotDiffHeatmap     7.12   0.13    7.18
compCytof           6.97   0.05    7.01
filterSCE           6.89   0.00    6.89
runDR               6.42   0.02    6.44
computeSpillmat     6.29   0.00    6.30
extractClusters     6.09   0.02    6.11
plotCodes           5.73   0.13    5.86
plotSpillmat        5.19   0.02    5.21
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plotDR             29.80   0.03   28.64
plotClusterExprs   26.53   0.30   26.85
plotClusterHeatmap 18.27   0.23   18.37
plotMedExprs       15.12   0.07   15.13
plotMahal          14.96   0.01   14.96
estCutoffs         12.47   0.01   12.49
assignPrelim       11.99   0.01   12.00
dbFrame-methods    11.46   0.00   11.46
plotDiffHeatmap    11.25   0.12   11.56
plotAbundances     11.19   0.03   11.22
plotYields         10.42   0.09   10.47
outFrames          10.20   0.00   10.20
plotEvents         10.04   0.00   10.05
mergeClusters       9.53   0.05    9.51
outFCS              9.38   0.02    9.39
applyCutoffs        9.16   0.00    9.17
SCE-utils           8.58   0.18    8.76
compCytof           8.58   0.03    8.61
normCytof           8.27   0.09    8.39
filterSCE           7.57   0.00    7.58
plotCodes           7.15   0.10    7.25
computeSpillmat     7.19   0.04    7.23
extractClusters     6.96   0.02    6.97
adaptSpillmat       6.90   0.05    6.95
runDR               6.55   0.00    6.40
plotExprs           6.25   0.00    6.25
cluster             5.60   0.02    5.63
plotSpillmat        5.30   0.03    5.32
* 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

CATALYST.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/CATALYST_1.10.3.tar.gz && rm -rf CATALYST.buildbin-libdir && mkdir CATALYST.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CATALYST.buildbin-libdir CATALYST_1.10.3.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL CATALYST_1.10.3.zip && rm CATALYST_1.10.3.tar.gz CATALYST_1.10.3.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 3584k  100 3584k    0     0  38.5M      0 --:--:-- --:--:-- --:--:-- 40.2M

install for i386

* installing *source* package 'CATALYST' ...
** 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 'CATALYST'
    finding HTML links ... done
    SCE-utils                               html  
    finding level-2 HTML links ... done

    adaptSpillmat                           html  
    applyCutoffs                            html  
    assignPrelim                            html  
    cluster                                 html  
    compCytof                               html  
    computeSpillmat                         html  
    concatFCS                               html  
    data                                    html  
    dbFrame-class                           html  
    dbFrame-methods                         html  
    estCutoffs                              html  
    extractClusters                         html  
    filterSCE                               html  
    guessPanel                              html  
    launchGUI                               html  
    mergeClusters                           html  
    normCytof                               html  
    outFCS                                  html  
    outFrames                               html  
    plotAbundances                          html  
    plotClusterExprs                        html  
    plotClusterHeatmap                      html  
    plotCodes                               html  
    plotCounts                              html  
    plotDR                                  html  
    plotDiffHeatmap                         html  
    plotEvents                              html  
    plotExprHeatmap                         html  
    plotExprs                               html  
    plotMDS                                 html  
    plotMahal                               html  
    plotMedExprs                            html  
    plotNRS                                 html  
    plotSpillmat                            html  
    plotYields                              html  
    prepData                                html  
    runDR                                   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 'CATALYST' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CATALYST' as CATALYST_1.10.3.zip
* DONE (CATALYST)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'CATALYST' successfully unpacked and MD5 sums checked

Tests output

CATALYST.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(CATALYST)
> 
> test_check("CATALYST")
== testthat results  ===========================================================
[ OK: 228 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  42.29    2.60   44.64 

CATALYST.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(CATALYST)
> 
> test_check("CATALYST")
== testthat results  ===========================================================
[ OK: 228 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  54.96    1.12   55.85 

Example timings

CATALYST.Rcheck/examples_i386/CATALYST-Ex.timings

nameusersystemelapsed
SCE-utils8.770.699.46
adaptSpillmat7.720.047.78
applyCutoffs11.58 0.0311.71
assignPrelim11.20 0.0011.25
cluster8.190.088.26
compCytof6.970.057.01
computeSpillmat6.290.006.30
concatFCS0.050.000.05
data0.000.030.03
dbFrame-methods8.530.008.53
estCutoffs11.80 0.0612.03
extractClusters6.090.026.11
filterSCE6.890.006.89
guessPanel0.050.000.05
launchGUI000
mergeClusters8.670.068.72
normCytof9.970.009.96
outFCS9.950.039.99
outFrames10.11 0.0310.14
plotAbundances9.100.079.16
plotClusterExprs24.10 0.4724.57
plotClusterHeatmap15.52 0.2115.69
plotCodes5.730.135.86
plotCounts0.50.00.5
plotDR34.49 0.2033.63
plotDiffHeatmap7.120.137.18
plotEvents9.130.009.13
plotExprHeatmap1.110.001.11
plotExprs4.830.014.84
plotMDS0.790.000.80
plotMahal10.61 0.0010.61
plotMedExprs13.21 0.4213.64
plotNRS1.650.001.65
plotSpillmat5.190.025.21
plotYields9.440.239.59
prepData0.310.020.33
runDR6.420.026.44

CATALYST.Rcheck/examples_x64/CATALYST-Ex.timings

nameusersystemelapsed
SCE-utils8.580.188.76
adaptSpillmat6.900.056.95
applyCutoffs9.160.009.17
assignPrelim11.99 0.0112.00
cluster5.600.025.63
compCytof8.580.038.61
computeSpillmat7.190.047.23
concatFCS0.110.000.11
data0.020.040.05
dbFrame-methods11.46 0.0011.46
estCutoffs12.47 0.0112.49
extractClusters6.960.026.97
filterSCE7.570.007.58
guessPanel0.040.000.03
launchGUI000
mergeClusters9.530.059.51
normCytof8.270.098.39
outFCS9.380.029.39
outFrames10.2 0.010.2
plotAbundances11.19 0.0311.22
plotClusterExprs26.53 0.3026.85
plotClusterHeatmap18.27 0.2318.37
plotCodes7.150.107.25
plotCounts0.780.000.78
plotDR29.80 0.0328.64
plotDiffHeatmap11.25 0.1211.56
plotEvents10.04 0.0010.05
plotExprHeatmap1.750.001.75
plotExprs6.250.006.25
plotMDS0.920.020.94
plotMahal14.96 0.0114.96
plotMedExprs15.12 0.0715.13
plotNRS1.280.001.28
plotSpillmat5.300.035.32
plotYields10.42 0.0910.47
prepData0.360.000.36
runDR6.550.006.40