Package: TxRegInfra

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TxRegInfra.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TxRegInfra_1.6.0.tar.gz

StartedAt: 2020-03-18 06:40:54 -0400 (Wed, 18 Mar 2020)

EndedAt: 2020-03-18 06:54:12 -0400 (Wed, 18 Mar 2020)

EllapsedTime: 797.7 seconds

RetCode: 1

Status:  ERROR

CheckDir: TxRegInfra.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TxRegInfra.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TxRegInfra_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/TxRegInfra.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ...sh: line 1: 26498 Abort trap: 6           LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --encoding=UTF-8 > 'TxRegInfra-Ex.Rout' 2>&1 < TxRegInfra-Ex.R
 ERROR
Running examples in ‘TxRegInfra-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getFieldNames
> ### Title: get names of fields in a collection in remote txregnet
> ### Aliases: getFieldNames
> 
> ### ** Examples
> 
> getFieldNames('CD34_DS12274_hg19_FP', check=FALSE) # we know this collection is there
mongoc/mongoc-async.c:124 mongoc_async_run(): precondition failed: poll_timeout_msec < INT32_MAX
* 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: 1 ERROR, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/TxRegInfra.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TxRegInfra
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 
  8.070   0.462   8.595 

name	user	system	elapsed
URL_txregInAWS	0.001	0.000	0.000
basicColData	0.058	0.005	0.065
basicFormatter	0.019	0.002	0.022
demo_eQTL_granges	0.007	0.000	0.008
demo_fimo_granges	0.099	0.002	0.101
dgf_meta	0.005	0.001	0.006
dnmeta	0.450	0.008	0.461
dnmetaApp	0.001	0.000	0.001
getDocumentFields	0.000	0.001	0.001