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This page was generated on 2022-06-27 11:09:57 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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 icetea on nebbiolo1


To the developers/maintainers of the icetea package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/icetea.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 929/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
icetea 1.14.0  (landing page)
Vivek Bhardwaj
Snapshot Date: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/icetea
git_branch: RELEASE_3_15
git_last_commit: 5220193
git_last_commit_date: 2022-04-26 11:49:42 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: icetea
Version: 1.14.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:icetea.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings icetea_1.14.0.tar.gz
StartedAt: 2022-06-26 20:18:02 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 20:24:06 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 363.5 seconds
RetCode: 0
Status:   OK  
CheckDir: icetea.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:icetea.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings icetea_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/icetea.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘icetea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘icetea’ version ‘1.14.0’
* 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 ‘icetea’ 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
detectTSS,CapSet : <anonymous>: no visible binding for global variable
  ‘logFC’
fitDiffTSS,CapSet: no visible binding for global variable ‘ResizeReads’
Undefined global functions or variables:
  ResizeReads logFC
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
detectTSS   16.779  1.292  17.428
annotateTSS  9.649  0.392  10.065
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/icetea.Rcheck/00check.log’
for details.



Installation output

icetea.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL icetea
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘icetea’ ...
** using staged installation
** R
** 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 (icetea)

Tests output

icetea.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(icetea)
> 
> test_check("icetea")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
 39.922   2.227  41.476 

Example timings

icetea.Rcheck/icetea-Ex.timings

nameusersystemelapsed
annotateTSS 9.649 0.39210.065
demultiplexFASTQ1.9600.0402.004
detectDiffTSS0.0000.0000.001
detectTSS16.779 1.29217.428
exampleCSobject0.0950.0080.103
exportTSS0.1620.0160.178
filterDuplicates1.7340.1521.886
fitDiffTSS0.0010.0000.000
getGeneCounts1.4970.0641.560
getNormFactors1.0800.4341.232
mapCaps000
newCapSet0.2260.1210.066
plotReadStats0.3350.0280.363
plotTSSprecision2.0340.1082.142
sampleInfo0.0830.0120.095
splitBAM_byIndex0.2500.1120.361
splitBAM_byRepindex0.1960.1080.304