Build/check report for BioC 3.10 experimental data - CHECK report for SomaticCancerAlterations on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SomaticCancerAlterations.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SomaticCancerAlterations_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-data-experiment/meat/SomaticCancerAlterations.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SomaticCancerAlterations/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SomaticCancerAlterations’ version ‘1.22.0’
* 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 ‘SomaticCancerAlterations’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
.load_dataset: no visible global function definition for ‘data’
.maf2gr: no visible binding for global variable ‘Chromosome’
.maf2gr: no visible binding for global variable ‘Start_position’
.maf2gr: no visible binding for global variable ‘End_position’
.read_maf: no visible global function definition for ‘read.delim’
hg2ncbi: no visible global function definition for ‘seqnameStyle<-’
hg2ncbi: no visible global function definition for ‘genome<-’
mutationDensity: no visible global function definition for
  ‘keepSeqlevels’
mutationDensity: no visible global function definition for ‘as’
ncbi2hg: no visible global function definition for ‘seqnameStyle<-’
ncbi2hg: no visible global function definition for ‘genome<-’
scaListDatasets: no visible global function definition for ‘data’
Undefined global functions or variables:
  Chromosome End_position Start_position as data genome<- keepSeqlevels
  read.delim seqnameStyle<-
Consider adding
  importFrom("methods", "as")
  importFrom("utils", "data", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... WARNING
Found the following significant warnings:

  Warning: 'GenomicRangesList' is deprecated.
  Warning: 'GenomicRangesList' is deprecated.
  Warning: 'GenomicRangesList' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-data-experiment/meat/SomaticCancerAlterations.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL SomaticCancerAlterations
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘SomaticCancerAlterations’ ...
** 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 (SomaticCancerAlterations)

Tests output


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(SomaticCancerAlterations)
> test_package("SomaticCancerAlterations")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 41 | SKIPPED: 0 | WARNINGS: 17 | FAILED: 0 ]
Warning message:
Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
> 
> proc.time()
   user  system elapsed 
 12.736   0.332  13.083

name	user	system	elapsed
all-data	0.056	0.000	0.071
all-functions	0.160	0.000	0.159

CHECK report for SomaticCancerAlterations on malbec1

Summary

Command output

Installation output

Tests output

Example timings