Package: COSMIC.67

Version: 1.16.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:COSMIC.67.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings COSMIC.67_1.16.0.tar.gz

StartedAt: 2018-10-16 10:46:58 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 10:50:14 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 195.7 seconds

RetCode: 0

Status:  OK

CheckDir: COSMIC.67.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:COSMIC.67.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings COSMIC.67_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-data-experiment/meat/COSMIC.67.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COSMIC.67/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COSMIC.67’ 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 ‘COSMIC.67’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 39.2Mb
  sub-directories of 1Mb or more:
    data  16.6Mb
    vcf   22.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
  Failed with error:  'package 'DelayedArray' could not be loaded'
  Error in .requirePackage(package) : 
    unable to find required package 'VariantAnnotation'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
COSMIC.67-package 11.996    0.2  12.955
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_all.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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-data-experiment/meat/COSMIC.67.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL COSMIC.67
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘COSMIC.67’ ...
** 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
* DONE (COSMIC.67)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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(COSMIC.67)
> test_package("COSMIC.67")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 1 SKIPPED: 0 FAILED: 0
Warning message:
Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
> 
> proc.time()
   user  system elapsed 
  8.808   0.284  10.149 

name	user	system	elapsed
COSMIC.67-package	11.996	0.200	12.955