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This page was generated on 2022-01-14 13:05:14 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for GenVisR on nebbiolo2


To the developers/maintainers of the GenVisR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenVisR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 762/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenVisR 1.26.0  (landing page)
Zachary Skidmore
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/GenVisR
git_branch: RELEASE_3_14
git_last_commit: 9bd43fb
git_last_commit_date: 2021-10-26 12:24:58 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: GenVisR
Version: 1.26.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GenVisR_1.26.0.tar.gz
StartedAt: 2022-01-13 07:44:43 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 07:56:03 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 679.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GenVisR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GenVisR_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/GenVisR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenVisR/DESCRIPTION’ ... OK
* this is package ‘GenVisR’ version ‘1.26.0’
* 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 ‘GenVisR’ 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 ... NOTE
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
setTierTwo,data.table : a: no visible binding for global variable ‘tmp’
toLolliplot,GMS: no visible binding for global variable ‘missingINdex’
Undefined global functions or variables:
  missingINdex tmp
* 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 LazyData ... 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
Lolliplot-class 31.825  2.025  85.339
genCov          10.880  0.384  11.264
lolliplot        7.779  0.580  20.835
geneViz          8.057  0.168   8.225
cnFreq           7.509  0.164   7.672
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    4.   ├─GenVisR:::retrieveMart(object = species, host = host, verbose = verbose)
    5.   └─GenVisR:::retrieveMart(object = species, host = host, verbose = verbose)
    6.     └─GenVisR:::.local(object, ...)
    7.       └─biomaRt::listDatasets(ensembl_mart)
    8.         └─biomaRt:::.listDatasets(mart = mart, verbose = verbose, sort = TRUE)
    9.           └─biomaRt:::bmRequest(...)
   10.             └─httr::GET(request2, config = httr_config, content_type("text/plain"))
   11.               └─httr:::request_perform(req, hu$handle$handle)
   12.                 ├─httr:::request_fetch(req$output, req$url, handle)
   13.                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   14.                   └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 3 | WARN 18 | SKIP 44 | PASS 628 ]
  Error: Test failures
  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 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/GenVisR.Rcheck/00check.log’
for details.


Installation output

GenVisR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL GenVisR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘GenVisR’ ...
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenVisR)

Tests output

GenVisR.Rcheck/tests/testthat.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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(GenVisR)
> 
> test_check("GenVisR")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (44)

══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-Lolliplot-class.R:80:5): retreiveMart works in verbose mode ─────
Error in `curl::curl_fetch_memory(url, handle = handle)`: SSL certificate problem: unable to get local issuer certificate
Backtrace:
     █
  1. ├─testthat::expect_message(...) test-Lolliplot-class.R:80:4
  2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
  3. │   ├─testthat:::.capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─GenVisR:::retrieveMart(...)
  7. └─GenVisR:::retrieveMart(...)
  8.   └─GenVisR:::.local(object, ...)
  9.     └─biomaRt::useMart("ENSEMBL_MART_ENSEMBL", host = host)
 10.       └─biomaRt:::.useMart(...)
 11.         └─biomaRt:::bmVersion(mart, verbose = verbose)
 12.           └─biomaRt:::bmRequest(...)
 13.             └─httr::GET(request2, config = httr_config, content_type("text/plain"))
 14.               └─httr:::request_perform(req, hu$handle$handle)
 15.                 ├─httr:::request_fetch(req$output, req$url, handle)
 16.                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 17.                   └─curl::curl_fetch_memory(url, handle = handle)
── Failure (test-Lolliplot-class.R:526:5): setDomainHeights domains are nested correctly ──
`expected` not equivalent to `actual`.
1/1 mismatches
[1] 7 - 9 == -2
── Error (test-Lolliplot-class.R:559:5): (code run outside of `test_that()`) ───
Error in `curl::curl_fetch_memory(url, handle = handle)`: SSL certificate problem: unable to get local issuer certificate
Backtrace:
     █
  1. ├─base::suppressWarnings(...) test-Lolliplot-class.R:559:4
  2. │ └─base::withCallingHandlers(...)
  3. └─GenVisR:::LolliplotData(...)
  4.   ├─GenVisR:::retrieveMart(object = species, host = host, verbose = verbose)
  5.   └─GenVisR:::retrieveMart(object = species, host = host, verbose = verbose)
  6.     └─GenVisR:::.local(object, ...)
  7.       └─biomaRt::listDatasets(ensembl_mart)
  8.         └─biomaRt:::.listDatasets(mart = mart, verbose = verbose, sort = TRUE)
  9.           └─biomaRt:::bmRequest(...)
 10.             └─httr::GET(request2, config = httr_config, content_type("text/plain"))
 11.               └─httr:::request_perform(req, hu$handle$handle)
 12.                 ├─httr:::request_fetch(req$output, req$url, handle)
 13.                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 14.                   └─curl::curl_fetch_memory(url, handle = handle)

[ FAIL 3 | WARN 18 | SKIP 44 | PASS 628 ]
Error: Test failures
Execution halted

Example timings

GenVisR.Rcheck/GenVisR-Ex.timings

nameusersystemelapsed
Lolliplot-class31.825 2.02585.339
TvTi1.5910.1041.695
Waterfall-class0.5260.0120.539
cnFreq7.5090.1647.672
cnSpec4.2660.1244.390
cnView1.7380.0561.793
compIdent2.2780.0682.346
covBars1.0260.0201.046
genCov10.880 0.38411.264
geneViz8.0570.1688.225
ideoView1.2750.0201.294
lohSpec2.6010.0082.609
lohView1.6410.0241.665
lolliplot 7.779 0.58020.835
waterfall0.7920.0120.804