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This page was generated on 2022-06-24 11:08:16 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 NanoTube on lconway


To the developers/maintainers of the NanoTube package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NanoTube.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 1289/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoTube 1.3.6  (landing page)
Caleb Class
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/NanoTube
git_branch: master
git_last_commit: 84db14f
git_last_commit_date: 2022-06-17 15:40:18 -0400 (Fri, 17 Jun 2022)
nebbiolo2Linux (Ubuntu 20.04.4 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 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NanoTube
Version: 1.3.6
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NanoTube.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NanoTube_1.3.6.tar.gz
StartedAt: 2022-06-23 21:29:05 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 21:30:43 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 98.5 seconds
RetCode: 0
Status:   OK  
CheckDir: NanoTube.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NanoTube.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NanoTube_1.3.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/NanoTube.Rcheck’
* using R version 4.2.0 Patched (2022-05-29 r82424)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NanoTube/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NanoTube’ version ‘1.3.6’
* 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 ‘NanoTube’ 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
untar_dirs: no visible global function definition for ‘untar’
Undefined global functions or variables:
  untar
Consider adding
  importFrom("utils", "untar")
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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/NanoTube.Rcheck/00check.log’
for details.



Installation output

NanoTube.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘NanoTube’ ...
** 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 (NanoTube)

Tests output

NanoTube.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> library(testthat)
> library(NanoTube)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

> 
> test_check("NanoTube")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  3.318   0.235   3.555 

Example timings

NanoTube.Rcheck/NanoTube-Ex.timings

nameusersystemelapsed
deVolcano0.1760.0230.199
fgseaPostprocessing1.0530.5841.079
fgseaPostprocessingXLSX0.5560.5800.509
fgseaToLEdge0.4990.4620.490
gm_mean0.0000.0000.001
groupFGSEA0.5020.5320.471
groupedGSEAtoStackedReport0.6370.6440.617
limmaToFGSEA1.0230.9690.998
makeDiffExprFile0.0350.0070.043
makeNanoStringSetFromEset0.4370.0690.520
nanostringPCA0.7520.1110.868
negativeQC0.2590.0170.284
normalize_housekeeping0.2530.0130.268
normalize_pos_controls0.0910.0070.097
nsdiffToFGSEA0.0000.0010.000
positiveQC2.6150.0302.650
processNanostringData0.5530.0300.584
read_merge_rcc0.1220.0090.131
read_rcc0.0030.0000.003
read_sampleData0.1220.0080.131
remove_background0.5180.0320.552
runLimmaAnalysis0.1770.0130.190