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This page was generated on 2022-08-12 13:23:30 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4364
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4117
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4182
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 qsea on merida1


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? 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 1542/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qsea 1.22.0  (landing page)
Matthias Lienhard
Snapshot Date: 2022-08-11 13:55:06 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/qsea
git_branch: RELEASE_3_15
git_last_commit: 3fff61a
git_last_commit_date: 2022-04-26 11:33:15 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: qsea
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qsea.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qsea_1.22.0.tar.gz
StartedAt: 2022-08-12 06:32:36 -0400 (Fri, 12 Aug 2022)
EndedAt: 2022-08-12 06:40:22 -0400 (Fri, 12 Aug 2022)
EllapsedTime: 466.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: qsea.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qsea.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qsea_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/qsea.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.22.0’
* 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 ... WARNING
Codoc mismatches from documentation object 'getPCA':
getPCA
  Code: function(qs, chr = getChrNames(qs), ROIs, minRowSum = 20, keep,
                 norm_method = normMethod(logRPM = c("log",
                 "library_size", "cnv", "preference", "psC10")), topVar
                 = 1000, samples = getSampleNames(qs), minEnrichment =
                 0)
  Docs: function(qs, chr = getChrNames(qs), ROIs, minRowSum = 20, keep,
                 norm_method = normMethod(logRPM = c("log",
                 "library_size", "cnv", "preference", "psC10")), topVar
                 = 1000, samples = getSampleNames(qs))
  Argument names in code not in docs:
    minEnrichment

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'getPCA':
  ‘minEnrichment’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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     26.675  1.261  28.007
addCNV             8.451  0.385   8.865
addPatternDensity  6.593  0.557   7.161
* 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 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/qsea.Rcheck/00check.log’
for details.



Installation output

qsea.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘qsea’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c lm.c -o lm.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o qsea.so lm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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(qsea)
> 
> test_check("qsea")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
 21.369   0.776  22.161 

Example timings

qsea.Rcheck/qsea-Ex.timings

nameusersystemelapsed
addCNV8.4510.3858.865
addContrast3.2660.0363.314
addCoverage4.6040.1154.729
addEnrichmentParameters0.7480.0280.777
addLibraryFactors1.4040.0691.477
addNewSamples26.675 1.26128.007
addOffset0.5510.0210.572
addPatternDensity6.5930.5577.161
createQseaSet0.3440.0180.363
example0.4150.0050.421
fitNBglm1.9130.0912.008
getPCA1.0430.0161.059
isSignificant2.4520.0362.491
makeTable2.9760.0593.041
normMethod0.0020.0000.003
plotCNV0.4750.0040.479
plotCoverage1.3180.0351.356
plotEnrichmentProfile0.6210.0750.697
plotPCA0.9620.0080.972
qseaGLM-class0.0010.0000.001
qseaPCA-class0.0010.0000.001
qseaSet-class0.0000.0010.002
regionStats1.0900.0051.096