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CHECK report for CVE on machv2

This page was generated on 2020-10-17 11:58:20 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CVE PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 408/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CVE 1.14.0
Andreas Mock
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CVE
Branch: RELEASE_3_11
Last Commit: 31cf4ab
Last Changed Date: 2020-04-27 15:00:18 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: CVE
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CVE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CVE_1.14.0.tar.gz
StartedAt: 2020-10-17 00:12:28 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 00:15:42 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 194.3 seconds
RetCode: 1
Status:  ERROR 
CheckDir: CVE.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CVE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CVE_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CVE.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CVE/DESCRIPTION’ ... OK
* this is package ‘CVE’ version ‘1.14.0’
* 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 ‘CVE’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'CVE' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/CVE.Rcheck/00install.out’ for details.
* 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 ... NOTE
Namespace in Imports field not imported from: ‘RTCGAToolbox’
  All declared Imports should be used.
Package in Depends field not imported from: ‘tidyverse’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                old_size new_size compress
  WGCNAmelanoma_extension.RData    2.4Mb    2.1Mb       xz
  crcCase.RData                    1.1Mb    677Kb       xz
  melanomaCase.RData               654Kb    473Kb       xz
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘CVE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get.oncotator.anno
> ### Title: Open Cancer Variant Explorer (CVE) Shiny app
> ### Aliases: get.oncotator.anno
> 
> ### ** Examples
> 
> exCase <- data.frame(chr = rep(10, 3),
+     start = c("100894110", "100985376", "101137905"),
+     end = c("100894110", "100985376", "101137905"),
+     ref_allele = c("T", "C", "G"),
+     obs_allele = c("G", "A", "A"))
> get.oncotator.anno(exCase)
Error in open.connection(con, "rb") : HTTP error 502.
Calls: get.oncotator.anno ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
* 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 ERROR, 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/CVE.Rcheck/00check.log’
for details.


Installation output

CVE.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CVE
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CVE’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
Warning: Package 'CVE' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'CVE' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (CVE)

Tests output


Example timings

CVE.Rcheck/CVE-Ex.timings

nameusersystemelapsed