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This page was generated on 2023-04-12 11:05:47 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 palomino4


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 1567/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qsea 1.24.0  (landing page)
Matthias Lienhard
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/qsea
git_branch: RELEASE_3_16
git_last_commit: 662ea99
git_last_commit_date: 2022-11-01 11:13:58 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: qsea
Version: 1.24.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:qsea.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings qsea_1.24.0.tar.gz
StartedAt: 2023-04-11 04:51:16 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 04:55:41 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 264.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: qsea.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:qsea.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings qsea_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/qsea.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.24.0'
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/qsea/libs/x64/qsea.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
addNewSamples     16.79   0.58   18.02
addPatternDensity  8.06   0.22    8.28
addCNV             8.06   0.17    8.43
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/qsea.Rcheck/00check.log'
for details.



Installation output

qsea.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL qsea
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'qsea' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c lm.c -o lm.o
gcc -shared -s -static-libgcc -o qsea.dll tmp.def lm.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-qsea/00new/qsea/libs/x64
** 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
** 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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 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(qsea)
> 
> test_check("qsea")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
  11.00    0.76   12.96 

Example timings

qsea.Rcheck/qsea-Ex.timings

nameusersystemelapsed
addCNV8.060.178.43
addContrast1.250.091.34
addCoverage2.060.082.14
addEnrichmentParameters0.310.000.31
addLibraryFactors0.750.140.91
addNewSamples16.79 0.5818.02
addOffset0.510.110.62
addPatternDensity8.060.228.28
createQseaSet0.190.000.19
example0.200.010.22
fitNBglm0.660.080.74
getPCA0.640.050.69
isSignificant0.860.161.01
makeTable1.110.061.17
normMethod000
plotCNV0.210.010.24
plotCoverage0.750.070.81
plotEnrichmentProfile0.320.010.33
plotPCA0.700.020.72
qseaGLM-class000
qseaPCA-class000
qseaSet-class000
regionStats0.480.040.53