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CHECK report for CancerSubtypes on tokay1

This page was generated on 2020-08-10 12:21:07 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CancerSubtypes PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 221/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerSubtypes 1.15.0
Taosheng Xu
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/CancerSubtypes
Branch: master
Last Commit: 6859df3
Last Changed Date: 2020-04-27 15:00:39 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CancerSubtypes
Version: 1.15.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CancerSubtypes.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CancerSubtypes_1.15.0.tar.gz
StartedAt: 2020-08-10 03:13:22 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 03:20:23 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 420.7 seconds
RetCode: 0
Status:  OK  
CheckDir: CancerSubtypes.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CancerSubtypes.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CancerSubtypes_1.15.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CancerSubtypes.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CancerSubtypes/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CancerSubtypes' version '1.15.0'
* 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 'CancerSubtypes' 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 installed files from 'inst/doc' ... 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
sigclustTest  38.93   0.39   39.33
ExecuteSNF.CC 19.67   0.10   19.78
survAnalysis  16.05   0.06   16.11
ExecuteCC     10.57   0.53   11.09
FSbyCox        9.42   0.01    9.44
drawHeatmap    6.43   0.05    6.48
ExecuteCNMF    3.34   0.65   23.71
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
sigclustTest  35.46   0.06   35.56
ExecuteSNF.CC 16.93   0.10   17.02
survAnalysis  12.49   0.00   12.49
FSbyCox       11.83   0.01   11.84
ExecuteCC      8.58   0.33    8.94
drawHeatmap    7.70   0.11    7.82
ExecuteCNMF    3.04   0.54   20.11
* 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

CancerSubtypes.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/CancerSubtypes_1.15.0.tar.gz && rm -rf CancerSubtypes.buildbin-libdir && mkdir CancerSubtypes.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CancerSubtypes.buildbin-libdir CancerSubtypes_1.15.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CancerSubtypes_1.15.0.zip && rm CancerSubtypes_1.15.0.tar.gz CancerSubtypes_1.15.0.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 2100k  100 2100k    0     0  28.2M      0 --:--:-- --:--:-- --:--:-- 29.7M

install for i386

* installing *source* package 'CancerSubtypes' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CancerSubtypes'
    finding HTML links ... done
    DiffExp.limma                           html  
    ExecuteCC                               html  
    ExecuteCNMF                             html  
    finding level-2 HTML links ... done

    ExecuteSNF.CC                           html  
    ExecuteSNF                              html  
    ExecuteWSNF                             html  
    ExecuteiCluster                         html  
    FSbyCox                                 html  
    FSbyMAD                                 html  
    FSbyPCA                                 html  
    FSbyVar                                 html  
    GeneExp                                 html  
    Ranking                                 html  
    data.checkDistribution                  html  
    data.imputation                         html  
    data.normalization                      html  
    drawHeatmap                             html  
    miRNAExp                                html  
    saveFigure                              html  
    sigclustTest                            html  
    silhouette_SimilarityMatrix             html  
    spectralAlg                             html  
    status                                  html  
    survAnalysis                            html  
    time                                    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 'CancerSubtypes' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CancerSubtypes' as CancerSubtypes_1.15.0.zip
* DONE (CancerSubtypes)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CancerSubtypes' successfully unpacked and MD5 sums checked

Tests output

CancerSubtypes.Rcheck/tests_i386/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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.

> BiocGenerics:::testPackage("CancerSubtypes")
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 39/40


RUNIT TEST PROTOCOL -- Mon Aug 10 03:20:10 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CancerSubtypes 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 
   4.01    0.26    4.28 

CancerSubtypes.Rcheck/tests_x64/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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.

> BiocGenerics:::testPackage("CancerSubtypes")
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 39/40


RUNIT TEST PROTOCOL -- Mon Aug 10 03:20:14 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CancerSubtypes 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 
   4.20    0.29    4.48 

Example timings

CancerSubtypes.Rcheck/examples_i386/CancerSubtypes-Ex.timings

nameusersystemelapsed
DiffExp.limma0.480.050.54
ExecuteCC10.57 0.5311.09
ExecuteCNMF 3.34 0.6523.71
ExecuteSNF.CC19.67 0.1019.78
ExecuteSNF0.250.000.25
ExecuteWSNF1.750.051.80
ExecuteiCluster3.610.083.68
FSbyCox9.420.019.44
FSbyMAD0.170.020.19
FSbyPCA0.110.000.10
FSbyVar0.060.000.07
GeneExp0.010.000.01
Ranking0.040.000.03
data.checkDistribution0.260.010.29
data.imputation0.020.000.01
data.normalization0.110.000.11
drawHeatmap6.430.056.48
miRNAExp000
saveFigure1.570.141.71
sigclustTest38.93 0.3939.33
silhouette_SimilarityMatrix0.720.000.71
spectralAlg0.050.020.07
status000
survAnalysis16.05 0.0616.11
time000

CancerSubtypes.Rcheck/examples_x64/CancerSubtypes-Ex.timings

nameusersystemelapsed
DiffExp.limma0.510.030.55
ExecuteCC8.580.338.94
ExecuteCNMF 3.04 0.5420.11
ExecuteSNF.CC16.93 0.1017.02
ExecuteSNF0.230.000.23
ExecuteWSNF2.230.052.28
ExecuteiCluster3.170.063.24
FSbyCox11.83 0.0111.84
FSbyMAD0.370.020.39
FSbyPCA0.220.000.22
FSbyVar0.080.030.11
GeneExp0.020.000.01
Ranking0.030.020.05
data.checkDistribution0.420.000.42
data.imputation0.020.000.02
data.normalization0.120.000.12
drawHeatmap7.700.117.82
miRNAExp0.020.000.01
saveFigure1.720.141.86
sigclustTest35.46 0.0635.56
silhouette_SimilarityMatrix0.500.010.51
spectralAlg0.040.000.05
status000
survAnalysis12.49 0.0012.49
time000