Back to Multiple platform build/check report for BioC 3.15
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-10-19 13:19:57 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 alevinQC on nebbiolo1


To the developers/maintainers of the alevinQC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/alevinQC.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 40/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alevinQC 1.12.1  (landing page)
Charlotte Soneson
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/alevinQC
git_branch: RELEASE_3_15
git_last_commit: e556ff5
git_last_commit_date: 2022-05-21 09:18:14 -0400 (Sat, 21 May 2022)
nebbiolo1Linux (Ubuntu 20.04.5 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: alevinQC
Version: 1.12.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:alevinQC.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings alevinQC_1.12.1.tar.gz
StartedAt: 2022-10-18 18:31:22 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 18:33:17 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 115.3 seconds
RetCode: 0
Status:   OK  
CheckDir: alevinQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:alevinQC.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings alevinQC_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/alevinQC.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alevinQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘alevinQC’ version ‘1.12.1’
* 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 ‘alevinQC’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.0Mb
  sub-directories of 1Mb or more:
    extdata  11.3Mb
* 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 ... OK
* 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 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
qcReport 11.417  0.293  11.724
* 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-3.15-bioc/meat/alevinQC.Rcheck/00check.log’
for details.



Installation output

alevinQC.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘alevinQC’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c convert_permit_freq.cpp -o convert_permit_freq.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o alevinQC.so RcppExports.o convert_permit_freq.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-alevinQC/00new/alevinQC/libs
** 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
** 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 (alevinQC)

Tests output

alevinQC.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-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(alevinQC)
> 
> test_check("alevinQC")
Reading Alevin-fry output files...
Generating summary tables...
Generating knee plot...
Generating barcode collapsing plot...
Generating quantification summary plot...
Generating knee plot for nbr genes...
Generating summary distribution plots...
Reading Alevin-fry output files...
Generating summary tables...
Generating knee plot...
Generating barcode collapsing plot...
Generating quantification summary plot...
Generating knee plot for nbr genes...
Generating summary distribution plots...
Reading Alevin-fry output files...
Generating summary tables...
Generating knee plot...
Generating barcode collapsing plot...
Generating quantification summary plot...
Generating knee plot for nbr genes...
Generating summary distribution plots...
Reading Alevin-fry output files...
Generating summary tables...
Generating knee plot...
Generating barcode collapsing plot...
Generating quantification summary plot...
Generating knee plot for nbr genes...
Generating summary distribution plots...
Reading Alevin-fry output files...
Generating summary tables...
Generating knee plot...
Generating barcode collapsing plot...
Generating quantification summary plot...
Generating knee plot for nbr genes...
Generating summary distribution plots...
Reading Alevin-fry output files...
Generating summary tables...
Generating knee plot...
Generating barcode collapsing plot...
Generating quantification summary plot...
Generating knee plot for nbr genes...
Generating summary distribution plots...
100% of barcodes in custom barcode set set2 were found in the data set (100% were quantified)
100% of barcodes in custom barcode set set2 were found in the data set (100% were quantified)
Reading Alevin output files...
100% of barcodes in custom barcode set set1 were found in the data set (100% were quantified)
100% of barcodes in custom barcode set set2 were found in the data set (100% were quantified)
Generating summary tables...
Generating knee plot...
Generating barcode collapsing plot...
Generating quantification summary plot...
Generating knee plot for nbr genes...
Generating summary distribution plots...
Reading Alevin output files...
Generating summary tables...
Generating knee plot...
Generating barcode collapsing plot...
Generating quantification summary plot...
Generating knee plot for nbr genes...
Generating summary distribution plots...
100% of barcodes in custom barcode set set1 were found in the data set (100% were quantified)
100% of barcodes in custom barcode set set2 were found in the data set (100% were quantified)
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 221 ]
> 
> proc.time()
   user  system elapsed 
 54.661   1.328  56.015 

Example timings

alevinQC.Rcheck/alevinQC-Ex.timings

nameusersystemelapsed
checkAlevinFryInputFiles0.0000.0040.004
checkAlevinInputFiles0.0020.0000.002
plotAlevinBarcodeCollapse1.1330.0651.201
plotAlevinHistogram0.5770.0160.593
plotAlevinKneeNbrGenes0.5680.0080.575
plotAlevinKneeRaw2.7710.1162.888
plotAlevinQuant0.9170.0160.932
plotAlevinQuantPairs1.6180.0161.634
qcReport11.417 0.29311.724
qcShiny0.6770.0340.711
readAlevinFryQC0.2320.0070.239
readAlevinQC0.3600.0080.368