Back to Multiple platform build/check report for BioC 3.20:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-06-14 12:02 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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 421/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
consICA 2.3.0  (landing page)
Petr V. Nazarov
Snapshot Date: 2024-06-13 14:00 -0400 (Thu, 13 Jun 2024)
git_url: https://git.bioconductor.org/packages/consICA
git_branch: devel
git_last_commit: 6227be0
git_last_commit_date: 2024-04-30 11:44:34 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for consICA on nebbiolo2

To the developers/maintainers of the consICA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/consICA.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: consICA
Version: 2.3.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:consICA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings consICA_2.3.0.tar.gz
StartedAt: 2024-06-13 22:25:25 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 22:36:04 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 639.1 seconds
RetCode: 0
Status:   OK  
CheckDir: consICA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:consICA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings consICA_2.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/consICA.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘consICA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘consICA’ version ‘2.3.0’
* package encoding: UTF-8
* 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 ‘consICA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... 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
anovaIC: no visible binding for global variable ‘weight’
consICA: no visible global function definition for ‘GetAssayData’
getGO : par_getGO: no visible global function definition for ‘str’
get_X_num: no visible global function definition for ‘GetAssayData’
oneICA: no visible global function definition for ‘GetAssayData’
Undefined global functions or variables:
  GetAssayData str weight
Consider adding
  importFrom("utils", "str")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
getGO                     215.698  2.872 218.049
saveReport                 45.726  0.136  44.861
plotICVarianceExplained    10.368  0.148   9.753
consICA                     8.530  0.367   8.111
estimateVarianceExplained   8.477  0.352   8.021
anovaIC                     7.925  0.463   7.857
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/consICA.Rcheck/00check.log’
for details.


Installation output

consICA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL consICA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘consICA’ ...
** using staged installation
** R
** data
** 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 (consICA)

Tests output

consICA.Rcheck/tests/runTests.Rout


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> require("consICA") || stop("unable to load consICA")
Loading required package: consICA


[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
[1] TRUE
> test_check("consICA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 107 ]
> 
> proc.time()
   user  system elapsed 
 46.643   1.211  43.889 

Example timings

consICA.Rcheck/consICA-Ex.timings

nameusersystemelapsed
anovaIC7.9250.4637.857
consICA8.5300.3678.111
estimateVarianceExplained8.4770.3528.021
getFeatures2.8220.1482.411
getGO215.698 2.872218.049
is.consICA000
oneICA1.5950.0081.603
overlapGO000
plotICVarianceExplained10.368 0.148 9.753
saveReport45.726 0.13644.861
setOrientation000
sortDataFrame0.0010.0000.001
sortFeatures000
survivalAnalysis2.2760.0161.755