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

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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

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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)

name	user	system	elapsed
gdsCoxSurv	0.090	0.136	15.875
impute2CoxSurv	1.040	0.207	16.470
michiganCoxSurv	0.870	0.180	17.407
plinkCoxSurv	1.061	0.278	16.662
sangerCoxSurv	0.801	0.150	16.134