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CHECK report for gwasurvivr on malbec2

This page was generated on 2019-04-09 11:51:10 -0400 (Tue, 09 Apr 2019).

Package 727/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gwasurvivr 1.1.0
Abbas Rizvi
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/gwasurvivr
Branch: master
Last Commit: b9ac9a9
Last Changed Date: 2018-10-30 11:54:39 -0400 (Tue, 30 Oct 2018)
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  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: gwasurvivr
Version: 1.1.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:gwasurvivr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings gwasurvivr_1.1.0.tar.gz
StartedAt: 2019-04-09 01:08:21 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:14:57 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 396.1 seconds
RetCode: 0
Status:  OK 
CheckDir: gwasurvivr.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:gwasurvivr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings gwasurvivr_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/gwasurvivr.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gwasurvivr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gwasurvivr’ version ‘1.1.0’
* 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 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 or elapsed time > 5s
                 user system elapsed
plinkCoxSurv    1.061  0.278  16.662
impute2CoxSurv  1.040  0.207  16.470
michiganCoxSurv 0.870  0.180  17.407
sangerCoxSurv   0.801  0.150  16.134
gdsCoxSurv      0.090  0.136  15.875
* 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: OK


Installation output

gwasurvivr.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL gwasurvivr
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 0.090 0.13615.875
impute2CoxSurv 1.040 0.20716.470
michiganCoxSurv 0.870 0.18017.407
plinkCoxSurv 1.061 0.27816.662
sangerCoxSurv 0.801 0.15016.134