Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:06:09 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 palomino3


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: 2022-06-23 13:55:15 -0400 (Thu, 23 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
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: icetea
Version: 1.14.0
Command: set _R_CHECK_FORCE_SUGGESTS_=0&& F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:icetea.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings icetea_1.14.0.tar.gz
StartedAt: 2022-06-24 01:52:42 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 02:00:00 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 437.5 seconds
RetCode: 0
Status:   OK  
CheckDir: icetea.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   set _R_CHECK_FORCE_SUGGESTS_=0&& F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:icetea.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings icetea_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/icetea.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (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 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      15.04   0.55   28.82
annotateTSS     8.99   0.36    9.46
getNormFactors  2.12   0.06   24.28
* 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
  'F:/biocbuild/bbs-3.15-bioc/meat/icetea.Rcheck/00check.log'
for details.



Installation output

icetea.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL icetea
###
##############################################################################
##############################################################################


* installing to library 'F:/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 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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.

> library(testthat)
> library(icetea)
> 
> test_check("icetea")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  41.54    1.67   72.06 

Example timings

icetea.Rcheck/icetea-Ex.timings

nameusersystemelapsed
annotateTSS8.990.369.46
demultiplexFASTQ3.050.083.50
detectDiffTSS000
detectTSS15.04 0.5528.82
exampleCSobject0.090.010.11
exportTSS0.170.000.18
filterDuplicates1.890.132.06
fitDiffTSS000
getGeneCounts1.910.031.94
getNormFactors 2.12 0.0624.28
mapCaps000
newCapSet0.100.000.09
plotReadStats0.450.020.47
plotTSSprecision2.190.152.36
sampleInfo0.080.030.11
splitBAM_byIndex0.310.030.37
splitBAM_byRepindex0.260.050.32