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CHECK report for BioQC on nebbiolo1

This page was generated on 2020-11-26 12:16:01 -0500 (Thu, 26 Nov 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BioQC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 184/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioQC 1.18.0
Jitao David Zhang
Snapshot Date: 2020-11-25 14:42:33 -0500 (Wed, 25 Nov 2020)
URL: https://git.bioconductor.org/packages/BioQC
Branch: RELEASE_3_12
Last Commit: 93ea3cd
Last Changed Date: 2020-10-27 11:09:46 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BioQC
Version: 1.18.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BioQC.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BioQC_1.18.0.tar.gz
StartedAt: 2020-11-25 20:12:11 -0500 (Wed, 25 Nov 2020)
EndedAt: 2020-11-25 20:21:39 -0500 (Wed, 25 Nov 2020)
EllapsedTime: 567.5 seconds
RetCode: 0
Status:  OK 
CheckDir: BioQC.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BioQC.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BioQC_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BioQC.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioQC’ version ‘1.18.0’
* 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 ... 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 ... 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/BioQC.Rcheck/00check.log’
for details.



Installation output

BioQC.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BioQC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BioQC’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.12-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c gini.c -o gini.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.12-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.12-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c read_gmt.cpp -o read_gmt.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.12-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c stat_rank.c -o stat_rank.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.12-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.12-bioc/R/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:105: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  105 | #pragma omp parallel for
      | 
wmw_test.c: In function ‘wmw_test’:
wmw_test.c:155: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  155 | #pragma omp parallel for
      | 
wmw_test.c: In function ‘signed_wmw_test_list’:
wmw_test.c:188: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  188 | #pragma omp parallel for
      | 
wmw_test.c: In function ‘signed_wmw_test’:
wmw_test.c:257: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  257 | #pragma omp parallel for
      | 
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-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-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-BioQC/00new/BioQC/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 (BioQC)

Tests output

BioQC.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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")
> 
> proc.time()
   user  system elapsed 
  5.039   0.115   5.138 

Example timings

BioQC.Rcheck/BioQC-Ex.timings

nameusersystemelapsed
GmtList0.0010.0000.002
IndexList0.0000.0020.003
SignedGenesets0.0010.0000.001
SignedIndexList0.0000.0020.002
absLog10p0.0000.0010.001
appendGmtList0.0020.0000.004
as.GmtList0.0000.0000.001
entropy0.0010.0000.001
entropyDiversity0.0010.0020.003
entropySpecificity0.0020.0020.004
filterPmat0.0020.0000.002
gini000
gmtlist2signedGenesets0.0010.0020.003
matchGenes0.060.000.06
offset-set0.0010.0000.001
offset000
readGmt0.0500.0050.055
readSignedGmt0.0050.0000.005
sampleSpecialization0.0040.0000.004
setNamespace0.0050.0000.004
simplifyMatrix000
sub-.GmtList0.0010.0000.002
sub-sub-.GmtList0.0000.0000.001
uniqGenesetsByNamespace0.0030.0020.005
wmwTest0.1510.0080.159
wmwTestInR0.0030.0000.003