Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:04:59 -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 BioQC on nebbiolo2


To the developers/maintainers of the BioQC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioQC.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 199/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioQC 1.26.0  (landing page)
Jitao David Zhang
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/BioQC
git_branch: RELEASE_3_16
git_last_commit: c4cfa15
git_last_commit_date: 2022-11-01 11:12:35 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BioQC
Version: 1.26.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:BioQC.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings BioQC_1.26.0.tar.gz
StartedAt: 2023-04-10 19:20:36 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:23:06 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 150.0 seconds
RetCode: 0
Status:   OK  
CheckDir: BioQC.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:BioQC.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings BioQC_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/BioQC.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘BioQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioQC’ version ‘1.26.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BioQC’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
* 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 loading without being on the library search path ... 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 ...
  ‘BioQC.Rmd’ using ‘UTF-8’... OK
  ‘bioqc-efficiency.Rmd’ using ‘UTF-8’... OK
  ‘bioqc-introduction.Rmd’ using ‘UTF-8’... OK
  ‘bioqc-signedGenesets.Rmd’ using ‘UTF-8’... OK
  ‘bioqc-simulation.Rmd’ using ‘UTF-8’... OK
  ‘bioqc-wmw-test-performance.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/BioQC.Rcheck/00check.log’
for details.



Installation output

BioQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL BioQC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘BioQC’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.16-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c gini.c -o gini.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.16-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.16-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c read_gmt.cpp -o read_gmt.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.16-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c stat_rank.c -o stat_rank.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.16-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c wmw_test.c -o wmw_test.o
wmw_test.c: In function ‘wmw_test_list’:
wmw_test.c:118: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  118 | #pragma omp parallel for
      | 
wmw_test.c: In function ‘wmw_test’:
wmw_test.c:168: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  168 | #pragma omp parallel for
      | 
wmw_test.c: In function ‘signed_wmw_test_list’:
wmw_test.c:201: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  201 | #pragma omp parallel for
      | 
wmw_test.c: In function ‘signed_wmw_test’:
wmw_test.c:270: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  270 | #pragma omp parallel for
      | 
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o BioQC.so gini.o init.o read_gmt.o stat_rank.o wmw_test.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-BioQC/00new/BioQC/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (BioQC)

Tests output

BioQC.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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(BioQC)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> 
> test_check("BioQC")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 125 ]
> 
> proc.time()
   user  system elapsed 
  6.963   0.138   7.084 

Example timings

BioQC.Rcheck/BioQC-Ex.timings

nameusersystemelapsed
GmtList0.0020.0000.002
IndexList0.010.000.01
SignedGenesets0.0010.0000.001
SignedIndexList0.0020.0000.002
absLog10p000
appendGmtList0.0000.0030.003
as.GmtList000
entropy0.0010.0000.001
entropyDiversity0.0040.0000.003
entropySpecificity0.0040.0000.004
filterPmat0.0000.0000.001
getLeadingEdgeIndexFromVector0.0020.0000.002
gini000
gmtlist2signedGenesets0.0040.0000.005
matchGenes0.0770.0000.077
offset-set0.0010.0000.001
offset0.0010.0000.001
prettySigNames0.0380.0000.039
readCurrentSignatures0.0420.0000.042
readGmt0.0550.0000.055
readSignedGmt0.0060.0000.005
sampleSpecialization0.0050.0000.005
setNamespace0.0050.0000.006
simplifyMatrix0.0000.0000.001
sub-.GmtList0.0090.0000.008
sub-sub-.GmtList0.0010.0000.001
uniqGenesetsByNamespace0.0070.0000.006
wmwLeadingEdge0.0070.0000.006
wmwTest0.1830.0000.183
wmwTestInR0.0030.0000.004