Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:59 -0400 (Fri, 15 Oct 2021).

CHECK results for CancerSubtypes on tokay2

To the developers/maintainers of the CancerSubtypes package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CancerSubtypes.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 238/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerSubtypes 1.18.0  (landing page)
Taosheng Xu
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/CancerSubtypes
git_branch: RELEASE_3_13
git_last_commit: 66e771e
git_last_commit_date: 2021-05-19 12:22:25 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: CancerSubtypes
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CancerSubtypes.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CancerSubtypes_1.18.0.tar.gz
StartedAt: 2021-10-14 20:36:36 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 20:42:38 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 361.6 seconds
RetCode: 0
Status:   OK  
CheckDir: CancerSubtypes.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CancerSubtypes.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CancerSubtypes_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CancerSubtypes.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.18.0'
* 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 ... NOTE
displayClusters: no visible global function definition for 'grey'
Undefined global functions or variables:
  grey
Consider adding
  importFrom("grDevices", "grey")
to your NAMESPACE file.
* 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  29.30   0.08   29.38
ExecuteSNF.CC 13.56   0.08   13.66
survAnalysis  11.11   0.00   11.11
FSbyCox        7.48   0.02    7.50
ExecuteCC      6.40   0.47    6.91
drawHeatmap    5.59   0.09    5.69
ExecuteCNMF    2.59   0.57   17.71
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
sigclustTest  35.67   0.03   35.70
ExecuteSNF.CC 18.37   0.06   18.50
survAnalysis  13.68   0.05   13.71
FSbyCox        9.62   0.00    9.63
ExecuteCC      7.97   0.38    8.39
drawHeatmap    6.21   0.11    6.41
ExecuteCNMF    2.22   0.69   19.53
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/CancerSubtypes.Rcheck/00check.log'
for details.



Installation output

CancerSubtypes.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CancerSubtypes_1.18.0.tar.gz && rm -rf CancerSubtypes.buildbin-libdir && mkdir CancerSubtypes.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CancerSubtypes.buildbin-libdir CancerSubtypes_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CancerSubtypes_1.18.0.zip && rm CancerSubtypes_1.18.0.tar.gz CancerSubtypes_1.18.0.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
 14 2102k   14  309k    0     0   709k      0  0:00:02 --:--:--  0:00:02  708k
 82 2102k   82 1744k    0     0  1220k      0  0:00:01  0:00:01 --:--:-- 1220k
100 2102k  100 2102k    0     0  1305k      0  0:00:01  0:00:01 --:--:-- 1304k

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  
    affinityMatrix                          html  
    data.checkDistribution                  html  
    data.imputation                         html  
    data.normalization                      html  
    dist2                                   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_1.18.0.zip
* DONE (CancerSubtypes)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CancerSubtypes' successfully unpacked and MD5 sums checked

Tests output

CancerSubtypes.Rcheck/tests_i386/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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.

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


RUNIT TEST PROTOCOL -- Thu Oct 14 20:42:25 2021 
*********************************************** 
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 
   3.71    0.17    3.87 

CancerSubtypes.Rcheck/tests_x64/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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.

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


RUNIT TEST PROTOCOL -- Thu Oct 14 20:42:30 2021 
*********************************************** 
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 
   4.21    0.15    4.35 

Example timings

CancerSubtypes.Rcheck/examples_i386/CancerSubtypes-Ex.timings

nameusersystemelapsed
DiffExp.limma0.280.020.29
ExecuteCC6.400.476.91
ExecuteCNMF 2.59 0.5717.71
ExecuteSNF.CC13.56 0.0813.66
ExecuteSNF0.200.020.22
ExecuteWSNF1.470.031.50
ExecuteiCluster2.810.032.85
FSbyCox7.480.027.50
FSbyMAD0.160.010.17
FSbyPCA0.140.000.15
FSbyVar0.040.000.05
GeneExp0.020.000.01
Ranking0.020.010.03
affinityMatrix0.010.000.02
data.checkDistribution0.250.010.26
data.imputation0.020.000.02
data.normalization0.120.020.14
dist20.020.000.01
drawHeatmap5.590.095.69
miRNAExp0.000.020.02
saveFigure0.950.121.07
sigclustTest29.30 0.0829.38
silhouette_SimilarityMatrix0.280.000.28
spectralAlg000
status0.000.010.01
survAnalysis11.11 0.0011.11
time000

CancerSubtypes.Rcheck/examples_x64/CancerSubtypes-Ex.timings

nameusersystemelapsed
DiffExp.limma0.440.070.51
ExecuteCC7.970.388.39
ExecuteCNMF 2.22 0.6919.53
ExecuteSNF.CC18.37 0.0618.50
ExecuteSNF0.270.010.28
ExecuteWSNF2.470.042.56
ExecuteiCluster3.640.063.70
FSbyCox9.620.009.63
FSbyMAD0.350.000.34
FSbyPCA0.170.010.19
FSbyVar0.070.000.07
GeneExp0.000.020.01
Ranking0.040.000.05
affinityMatrix0.040.000.03
data.checkDistribution0.280.000.28
data.imputation000
data.normalization0.130.000.12
dist20.010.010.03
drawHeatmap6.210.116.41
miRNAExp000
saveFigure1.360.111.47
sigclustTest35.67 0.0335.70
silhouette_SimilarityMatrix0.670.020.69
spectralAlg000
status0.010.000.02
survAnalysis13.68 0.0513.71
time000