Back to Multiple platform build/check report for BioC 3.14
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-12-03 13:04:47 -0500 (Fri, 03 Dec 2021).

CHECK results for discordant on nebbiolo2

To the developers/maintainers of the discordant package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/discordant.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 517/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
discordant 1.18.0  (landing page)
Charlotte Siska
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/discordant
git_branch: RELEASE_3_14
git_last_commit: 7872d84
git_last_commit_date: 2021-10-26 12:32:49 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: discordant
Version: 1.18.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:discordant.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings discordant_1.18.0.tar.gz
StartedAt: 2021-12-02 06:57:59 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 06:58:28 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 29.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: discordant.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:discordant.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings discordant_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/discordant.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘discordant/DESCRIPTION’ ... OK
* this is package ‘discordant’ version ‘1.18.0’
* package encoding: latin1
* 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 ‘discordant’ can be installed ... WARNING
Found the following significant warnings:
  discordant.c:21:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  discordant.c:147:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/biocbuild/bbs-3.14-bioc/meat/discordant.Rcheck/00install.out’ for details.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
* 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/discordant.Rcheck/00check.log’
for details.



Installation output

discordant.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL discordant
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘discordant’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c discordant.c -o discordant.o
discordant.c: In function ‘em_normal_partial_concordant’:
discordant.c:21:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
   21 |   while(flag>0 & iter<(*iteration)){
      |         ~~~~^~
discordant.c:147:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  147 |   while(flag>0 & iter<(*iteration)){
      |         ~~~~^~
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o discordant.so discordant.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-discordant/00new/discordant/libs
** R
** data
** 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 (discordant)

Tests output


Example timings

discordant.Rcheck/discordant-Ex.timings

nameusersystemelapsed
createVectors0.0130.0040.018
discordantRun0.3750.0040.380
fishersTrans0.010.000.01
split.MADOutlier0.0290.0000.030