Back to Multiple platform build/check report for BioC 3.16:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2023-04-12 11:05:52 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for sigsquared on palomino4


To the developers/maintainers of the sigsquared package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sigsquared.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1874/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sigsquared 1.30.0  (landing page)
UnJin Lee
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/sigsquared
git_branch: RELEASE_3_16
git_last_commit: 1694364
git_last_commit_date: 2022-11-01 11:11:09 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: sigsquared
Version: 1.30.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sigsquared.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings sigsquared_1.30.0.tar.gz
StartedAt: 2023-04-11 06:03:21 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 06:04:33 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 71.3 seconds
RetCode: 0
Status:   OK  
CheckDir: sigsquared.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sigsquared.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings sigsquared_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/sigsquared.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'sigsquared/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sigsquared' version '1.30.0'
* 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 'sigsquared' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL version 3
Standardizable: TRUE
Standardized license specification:
  GPL-3
* 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 ... NOTE
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
analysisPipeline,ExpressionSet-geneSignature: no visible binding for
  global variable 'nCores'
analysisPipeline,ExpressionSet-geneSignature: no visible global
  function definition for 'mcparallel'
analysisPipeline,ExpressionSet-geneSignature: no visible global
  function definition for 'mccollect'
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
  binding for global variable 'mc'
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
  binding for global variable 'nCores'
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
  global function definition for 'mcparallel'
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
  global function definition for 'mccollect'
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
  definition for 'new'
eJPDF,ExpressionSet-geneSignature-numeric: no visible binding for
  global variable 'mc'
eJPDF,ExpressionSet-geneSignature-numeric: no visible binding for
  global variable 'nCores'
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
  definition for 'rnorm'
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
  definition for 'mcparallel'
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
  definition for 'mccollect'
genGeneDirect,matrix: no visible global function definition for 'sd'
optCF,ExpressionSet-geneSignature: no visible global function
  definition for 'new'
optCF,ExpressionSet-geneSignature: no visible global function
  definition for 'rnorm'
optCF,ExpressionSet-geneSignature: no visible global function
  definition for 'optim'
summarizeSolnSpace,solnSpace: no visible global function definition for
  'sd'
Undefined global functions or variables:
  mc mccollect mcparallel nCores new optim rnorm sd
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "optim", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
analysisPipeline 11.2   0.19   11.39
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/sigsquared.Rcheck/00check.log'
for details.



Installation output

sigsquared.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL sigsquared
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'sigsquared' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'ensembleCostFcn' with signature 'dataSet="ExpressionSet",geneSig="geneSignature",jpdf="solnSpace"': no definition for class "solnSpace"
in method for 'getCVCuts' with signature 'cutoffResults="solnSpace"': no definition for class "solnSpace"
in method for 'summarizeCVCuts' with signature 'cutoffResults="solnSpace"': no definition for class "solnSpace"
** 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 (sigsquared)

Tests output

sigsquared.Rcheck/tests/runTests.Rout


R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
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("sigsquared")


RUNIT TEST PROTOCOL -- Tue Apr 11 06:04:22 2023 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
sigsquared RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.48    0.20    1.64 

Example timings

sigsquared.Rcheck/sigsquared-Ex.timings

nameusersystemelapsed
analysisPipeline11.20 0.1911.39
ensembleAdjustable0.080.000.08
geneSignature-class000
setGeneSignature000