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CHECK report for TxRegInfra on malbec1

This page was generated on 2020-04-15 12:14:15 -0400 (Wed, 15 Apr 2020).

Package 1773/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TxRegInfra 1.6.0
VJ Carey
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/TxRegInfra
Branch: RELEASE_3_10
Last Commit: 0d523ea
Last Changed Date: 2019-10-29 13:11:10 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  TIMEOUT  skipped  skipped 

Summary

Package: TxRegInfra
Version: 1.6.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TxRegInfra.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TxRegInfra_1.6.0.tar.gz
StartedAt: 2020-04-15 05:44:52 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:48:45 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 233.1 seconds
RetCode: 0
Status:  OK 
CheckDir: TxRegInfra.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TxRegInfra.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TxRegInfra_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/TxRegInfra.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 ‘TxRegInfra/DESCRIPTION’ ... OK
* this is package ‘TxRegInfra’ version ‘1.6.0’
* 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 ‘TxRegInfra’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘rjson’
A package should be listed in only one of these fields.
* 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
'library' or 'require' call to 'shiny' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addsyms: no visible global function definition for ‘genes’
dnmetaApp: no visible global function definition for ‘fluidPage’
dnmetaApp: no visible global function definition for ‘sidebarLayout’
dnmetaApp: no visible global function definition for ‘sidebarPanel’
dnmetaApp: no visible global function definition for ‘helpText’
dnmetaApp: no visible global function definition for ‘radioButtons’
dnmetaApp: no visible global function definition for
  ‘checkboxGroupInput’
dnmetaApp: no visible global function definition for ‘uiOutput’
dnmetaApp: no visible global function definition for ‘mainPanel’
dnmetaApp: no visible global function definition for ‘dataTableOutput’
dnmetaApp : server: no visible global function definition for
  ‘renderUI’
dnmetaApp : server: no visible global function definition for
  ‘selectInput’
dnmetaApp : server: no visible global function definition for
  ‘renderDataTable’
dnmetaApp: no visible global function definition for ‘runApp’
Undefined global functions or variables:
  checkboxGroupInput dataTableOutput fluidPage genes helpText mainPanel
  radioButtons renderDataTable renderUI runApp selectInput
  sidebarLayout sidebarPanel uiOutput
* checking Rd files ... NOTE
prepare_Rd: addsyms.Rd:23-25: Dropping empty section \examples
* 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
  Note: found 14 marked UTF-8 strings
* 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
sbov_to_graphNEL 32.124  0.152  32.388
txmodels         19.208  0.684  22.198
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/TxRegInfra.Rcheck/00check.log’
for details.



Installation output

TxRegInfra.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL TxRegInfra
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘TxRegInfra’ ...
** 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 (TxRegInfra)

Tests output

TxRegInfra.Rcheck/tests/testthat.Rout


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(TxRegInfra)
Loading required package: RaggedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: mongolite
> 
> test_check("TxRegInfra")
Error in system2(cmd, args = "--help", stdout = TRUE, stderr = TRUE) : 
  error in running command
Error in system2(cmd, args = "--help", stdout = TRUE, stderr = TRUE) : 
  error in running command
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  8.320   0.408   8.767 

Example timings

TxRegInfra.Rcheck/TxRegInfra-Ex.timings

nameusersystemelapsed
URL_txregInAWS0.0000.0000.001
basicColData0.0440.0000.047
basicFormatter0.0160.0000.015
demo_eQTL_granges0.0040.0000.007
demo_fimo_granges0.0880.0000.089
dgf_meta0.0040.0000.004
dnmeta0.5040.0120.533
dnmetaApp000
getDocumentFields0.0040.0000.001
getFieldNames0.0520.0040.323
grConverter0.0400.0000.042
importBedToMongo0.0040.0240.047
listAllCollections0.0040.0000.001
makeAggregator0.0040.0240.034
makeColData0.0000.0200.026
oldbasicColData0.0080.0000.009
ragged41FP0.2000.0080.208
sbov0.0000.0280.044
sbov_output_FP0.0320.0040.037
sbov_output_HS0.0160.0040.019
sbov_output_eQTL0.0200.0000.027
sbov_to_graphNEL32.124 0.15232.388
txmodels19.208 0.68422.198
txregCollections0.0000.0400.044
verifyHasMongoCmd0.0000.0000.001
verifyRunningMongodb000