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CHECK report for GOfuncR on malbec2

This page was generated on 2019-10-16 12:12:51 -0400 (Wed, 16 Oct 2019).

Package 693/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOfuncR 1.4.0
Steffi Grote
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GOfuncR
Branch: RELEASE_3_9
Last Commit: 2f633dc
Last Changed Date: 2019-05-02 11:54:10 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GOfuncR
Version: 1.4.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GOfuncR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GOfuncR_1.4.0.tar.gz
StartedAt: 2019-10-16 02:04:22 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:10:53 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 391.5 seconds
RetCode: 0
Status:  OK 
CheckDir: GOfuncR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GOfuncR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GOfuncR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GOfuncR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOfuncR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GOfuncR’ version ‘1.4.0’
* 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 ‘GOfuncR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   8.3Mb
* 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 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 or elapsed time > 5s
                      user system elapsed
plot_anno_scores    17.478  0.711  20.722
get_anno_categories 10.410  0.804  12.691
go_enrich            9.689  0.276  10.610
* 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-3.9-bioc/meat/GOfuncR.Rcheck/00check.log’
for details.

Installation output

GOfuncR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GOfuncR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘GOfuncR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c binom_categorytest.cc -o binom_categorytest.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c binom_randset.cc -o binom_randset.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c blocks.cpp -o blocks.o
blocks.cpp: In function ‘std::set rannum_blocks(std::vector, std::vector, const std::map, int>&, std::vector)’:
blocks.cpp:30:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int j=0; j < candidate_bed.size(); j++){
                 ~~^~~~~~~~~~~~~~~~~~~~~~
blocks.cpp:34:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int k=0; k < background.size(); k++){
                  ~~^~~~~~~~~~~~~~~~~~~
blocks.cpp:68:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int g=0; g rannum_genelen(int, const std::map, int>&, std::vector, long int)’:
ran_genelen.cpp:19:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  while (random_numbers.size() < n_candidate) {
         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c read_bed.cpp -o read_bed.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c roll.cpp -o roll.o
roll.cpp: In function ‘std::set rannum_roll(std::vector, std::vector, const std::map, int>&, std::vector)’:
roll.cpp:30:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int j=0; j < candidate_bed.size(); j++){
                ~~^~~~~~~~~~~~~~~~~~~~~~
roll.cpp:36:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i < background_bed.size(); i++){
                 ~~^~~~~~~~~~~~~~~~~~~~~~~
roll.cpp:92:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int g=0; g

Tests output

GOfuncR.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(GOfuncR)
Loading required package: vioplot
Loading required package: sm
Package 'sm', version 2.2-5.6: type help(sm) for summary information
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

> 
> test_check("GOfuncR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 60 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
189.417   5.220 205.726

Example timings

GOfuncR.Rcheck/GOfuncR-Ex.timings

nameusersystemelapsed
get_anno_categories10.410 0.80412.691
get_anno_genes2.4490.1093.152
get_child_nodes0.1090.0000.191
get_ids1.0190.0181.096
get_names0.0180.0000.019
get_parent_nodes0.0850.0000.085
go_enrich 9.689 0.27610.610
plot_anno_scores17.478 0.71120.722