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This page was generated on 2024-03-27 11:37:26 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 267/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerSubtypes 1.28.0  (landing page)
Taosheng Xu
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/CancerSubtypes
git_branch: RELEASE_3_18
git_last_commit: 03e787b
git_last_commit_date: 2023-10-24 10:52:09 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for CancerSubtypes on merida1


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: 1.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CancerSubtypes_1.28.0.tar.gz
StartedAt: 2024-03-26 00:08:00 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 00:14:16 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 375.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CancerSubtypes.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CancerSubtypes_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/CancerSubtypes.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CancerSubtypes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CancerSubtypes’ version ‘1.28.0’
* 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 for sufficient/correct file permissions ... 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
ExecuteCNMF     49.367  2.333  36.807
sigclustTest    40.810  2.509  44.746
ExecuteSNF.CC   33.675  1.062  35.382
survAnalysis    20.961  0.265  21.906
FSbyCox         13.779  0.295  16.346
ExecuteCC       11.817  1.753  14.438
drawHeatmap      7.728  0.325   8.962
ExecuteiCluster  5.373  0.160   6.853
* 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
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/CancerSubtypes.Rcheck/00check.log’
for details.



Installation output

CancerSubtypes.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CancerSubtypes
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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: synchronicity] | Cores 2/2
  To enable shared memory capabilities, try: install.extras('
NMF
')


RUNIT TEST PROTOCOL -- Tue Mar 26 00:14:02 2024 
*********************************************** 
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 
  6.193   0.458   6.644 

Example timings

CancerSubtypes.Rcheck/CancerSubtypes-Ex.timings

nameusersystemelapsed
DiffExp.limma0.5030.0530.563
ExecuteCC11.817 1.75314.438
ExecuteCNMF49.367 2.33336.807
ExecuteSNF.CC33.675 1.06235.382
ExecuteSNF0.3840.0380.517
ExecuteWSNF3.7040.1374.271
ExecuteiCluster5.3730.1606.853
FSbyCox13.779 0.29516.346
FSbyMAD0.4770.0260.573
FSbyPCA0.2110.0120.255
FSbyVar0.1080.0070.267
GeneExp0.0170.0050.022
Ranking0.0700.0090.081
affinityMatrix0.0400.0040.048
data.checkDistribution0.6190.0230.726
data.imputation0.0130.0010.016
data.normalization0.2620.0210.336
dist20.0170.0030.027
drawHeatmap7.7280.3258.962
miRNAExp0.0070.0040.010
saveFigure1.5590.0981.685
sigclustTest40.810 2.50944.746
silhouette_SimilarityMatrix0.4420.0420.568
spectralAlg0.0070.0040.011
status0.0010.0080.009
survAnalysis20.961 0.26521.906
time0.0020.0070.010