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CHECK report for COSMIC.67 on malbec2

This page was generated on 2021-01-14 15:58:58 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE COSMIC.67 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 77/385HostnameOS / ArchINSTALLBUILDCHECK
COSMIC.67 1.27.0
Julian Gehring
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/COSMIC.67
Branch: master
Last Commit: db73308
Last Changed Date: 2020-10-27 10:06:45 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK 

Summary

Package: COSMIC.67
Version: 1.27.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:COSMIC.67.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings COSMIC.67_1.27.0.tar.gz
StartedAt: 2021-01-14 11:54:27 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:58:54 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 266.4 seconds
RetCode: 0
Status:  OK 
CheckDir: COSMIC.67.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:COSMIC.67.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings COSMIC.67_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/COSMIC.67.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* 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 ‘1.27.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
COSMIC.67-package 11.178   0.13  11.727
* 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-3.13-data-experiment/meat/COSMIC.67.Rcheck/00check.log’
for details.



Installation output

COSMIC.67.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL COSMIC.67
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘COSMIC.67’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (COSMIC.67)

Tests output

COSMIC.67.Rcheck/tests/test_all.Rout


R Under development (unstable) (2021-01-05 r79797) -- "Unsuffered Consequences"
Copyright (C) 2021 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")
No installed testthat tests found for COSMIC.67
> 
> proc.time()
   user  system elapsed 
 10.159   0.273  11.092 

Example timings

COSMIC.67.Rcheck/COSMIC.67-Ex.timings

nameusersystemelapsed
COSMIC.67-package11.178 0.13011.727