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This page was generated on 2021-12-06 13:05:08 -0500 (Mon, 06 Dec 2021).

CHECK results for qsea on nebbiolo2

To the developers/maintainers of the qsea package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qsea.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1502/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qsea 1.20.0  (landing page)
Matthias Lienhard
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/qsea
git_branch: RELEASE_3_14
git_last_commit: ef9f9f7
git_last_commit_date: 2021-10-26 12:28:44 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: qsea
Version: 1.20.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:qsea.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings qsea_1.20.0.tar.gz
StartedAt: 2021-12-05 09:17:49 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 09:21:45 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 235.6 seconds
RetCode: 0
Status:   OK  
CheckDir: qsea.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:qsea.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings qsea_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/qsea.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qsea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qsea’ version ‘1.20.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘qsea’ 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
subdivideRegions: no visible global function definition for ‘metadata’
Undefined global functions or variables:
  metadata
* 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
addNewSamples     19.067  0.840  19.916
addPatternDensity  6.273  0.372   6.645
addCNV             5.842  0.288   6.134
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/qsea.Rcheck/00check.log’
for details.



Installation output

qsea.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL qsea
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘qsea’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c lm.c -o lm.o
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o qsea.so lm.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-qsea/00new/qsea/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (qsea)

Tests output

qsea.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(qsea)
> 
> test_check("qsea")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
 10.548   0.494  11.026 

Example timings

qsea.Rcheck/qsea-Ex.timings

nameusersystemelapsed
addCNV5.8420.2886.134
addContrast1.4290.0961.525
addCoverage3.1550.5923.746
addEnrichmentParameters0.4320.1600.592
addLibraryFactors0.9410.0761.017
addNewSamples19.067 0.84019.916
addOffset0.3790.0000.379
addPatternDensity6.2730.3726.645
createQseaSet0.1720.0000.171
example0.2530.0000.254
fitNBglm0.8050.0000.806
getPCA0.6000.0080.607
isSignificant1.0180.0001.019
makeTable1.2160.0071.223
normMethod0.0000.0000.001
plotCNV0.3120.0000.312
plotCoverage0.7160.0240.740
plotEnrichmentProfile0.3400.0040.344
plotPCA0.5440.0000.544
qseaGLM-class0.0010.0000.001
qseaPCA-class0.0010.0000.001
qseaSet-class000
regionStats0.6290.0080.637