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This page was generated on 2023-04-12 11:05:06 -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 gwasurvivr on nebbiolo2


To the developers/maintainers of the gwasurvivr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gwasurvivr.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 885/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gwasurvivr 1.16.0  (landing page)
Abbas Rizvi
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/gwasurvivr
git_branch: RELEASE_3_16
git_last_commit: 727e03f
git_last_commit_date: 2022-11-01 11:18:00 -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: gwasurvivr
Version: 1.16.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:gwasurvivr.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings gwasurvivr_1.16.0.tar.gz
StartedAt: 2023-04-10 21:11:51 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:20:21 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 509.7 seconds
RetCode: 0
Status:   OK  
CheckDir: gwasurvivr.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:gwasurvivr.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings gwasurvivr_1.16.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/gwasurvivr.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 ‘gwasurvivr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gwasurvivr’ version ‘1.16.0’
* 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 ‘gwasurvivr’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
impute2CoxSurv  1.128  0.052  16.679
plinkCoxSurv    1.091  0.048  15.382
michiganCoxSurv 0.919  0.168  16.336
sangerCoxSurv   0.646  0.006  15.396
gdsCoxSurv      0.078  0.006  15.895
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘gwasurvivr_Introduction.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

gwasurvivr.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘gwasurvivr’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gwasurvivr)

Tests output


Example timings

gwasurvivr.Rcheck/gwasurvivr-Ex.timings

nameusersystemelapsed
gdsCoxSurv 0.078 0.00615.895
impute2CoxSurv 1.128 0.05216.679
michiganCoxSurv 0.919 0.16816.336
plinkCoxSurv 1.091 0.04815.382
sangerCoxSurv 0.646 0.00615.396