Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-10-16 11:35:59 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 265/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerSubtypes 1.26.0  (landing page)
Taosheng Xu
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/CancerSubtypes
git_branch: RELEASE_3_17
git_last_commit: 1cfcdda
git_last_commit_date: 2023-04-25 10:48:56 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for CancerSubtypes on palomino3


To the developers/maintainers of the CancerSubtypes package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: CancerSubtypes
Version: 1.26.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CancerSubtypes.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings CancerSubtypes_1.26.0.tar.gz
StartedAt: 2023-10-16 00:14:54 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 00:17:46 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 171.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CancerSubtypes.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CancerSubtypes.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings CancerSubtypes_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/CancerSubtypes.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CancerSubtypes/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CancerSubtypes' version '1.26.0'
* 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
* 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'
plotiCluster: no visible global function definition for 'gray'
Undefined global functions or variables:
  gray grey
Consider adding
  importFrom("grDevices", "gray", "grey")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'ExecuteiCluster.Rd':
  'iCluster2'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
sigclustTest  22.40   0.18   22.60
ExecuteSNF.CC 13.46   0.26   13.72
survAnalysis   8.62   0.19    8.84
ExecuteCC      6.73   1.29    8.12
FSbyCox        5.32   0.16    5.48
ExecuteCNMF    1.36   0.02   14.53
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc/meat/CancerSubtypes.Rcheck/00check.log'
for details.



Installation output

CancerSubtypes.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL CancerSubtypes
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'CancerSubtypes' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (CancerSubtypes)

Tests output

CancerSubtypes.Rcheck/tests/runTests.Rout


R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 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 2/2


RUNIT TEST PROTOCOL -- Mon Oct 16 00:17:37 2023 
*********************************************** 
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 
   2.92    0.23    3.15 

Example timings

CancerSubtypes.Rcheck/CancerSubtypes-Ex.timings

nameusersystemelapsed
DiffExp.limma0.250.030.28
ExecuteCC6.731.298.12
ExecuteCNMF 1.36 0.0214.53
ExecuteSNF.CC13.46 0.2613.72
ExecuteSNF0.220.000.22
ExecuteWSNF1.460.041.50
ExecuteiCluster2.890.042.94
FSbyCox5.320.165.48
FSbyMAD0.140.010.16
FSbyPCA0.090.040.12
FSbyVar0.050.000.05
GeneExp0.010.000.01
Ranking0.040.000.04
affinityMatrix0.030.000.03
data.checkDistribution0.360.010.37
data.imputation000
data.normalization0.110.020.13
dist20.010.000.01
drawHeatmap3.640.063.71
miRNAExp0.000.020.01
saveFigure1.10.11.2
sigclustTest22.40 0.1822.60
silhouette_SimilarityMatrix0.220.000.22
spectralAlg0.020.000.01
status0.000.010.02
survAnalysis8.620.198.84
time000