Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

CHECK report for TxRegInfra on tokay2

This page was generated on 2020-10-17 11:57:58 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE TxRegInfra PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1853/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TxRegInfra 1.8.0
VJ Carey
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/TxRegInfra
Branch: RELEASE_3_11
Last Commit: c33350e
Last Changed Date: 2020-04-27 15:16:35 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TxRegInfra
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TxRegInfra.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TxRegInfra_1.8.0.tar.gz
StartedAt: 2020-10-17 09:06:56 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 09:16:13 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 557.0 seconds
RetCode: 0
Status:  OK  
CheckDir: TxRegInfra.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TxRegInfra.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TxRegInfra_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/TxRegInfra.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TxRegInfra/DESCRIPTION' ... OK
* this is package 'TxRegInfra' version '1.8.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
sbov_to_graphNEL 27.06   0.33   27.55
txmodels         20.25   3.80  203.59
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
sbov_to_graphNEL 31.39   0.09   31.50
txmodels         21.00   1.39   25.65
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/TxRegInfra.Rcheck/00check.log'
for details.



Installation output

TxRegInfra.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/TxRegInfra_1.8.0.tar.gz && rm -rf TxRegInfra.buildbin-libdir && mkdir TxRegInfra.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TxRegInfra.buildbin-libdir TxRegInfra_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL TxRegInfra_1.8.0.zip && rm TxRegInfra_1.8.0.tar.gz TxRegInfra_1.8.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  342k  100  342k    0     0  5331k      0 --:--:-- --:--:-- --:--:-- 5908k

install for i386

* 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
  converting help for package 'TxRegInfra'
    finding HTML links ... done
    RaggedMongoExpt                         html  
    URL_txregInAWS                          html  
    URL_txregLocal                          html  
    addsyms                                 html  
    basicColData                            html  
    basicFormatter                          html  
    demo_eQTL_granges                       html  
    demo_fimo_granges                       html  
    dgf_meta                                html  
    dnmeta                                  html  
    dnmetaApp                               html  
    getDocumentFields                       html  
    getFieldNames                           html  
    grConverter                             html  
    importBedToMongo                        html  
    listAllCollections                      html  
    makeAggregator                          html  
    makeColData                             html  
    makeGRConverterList                     html  
    oldbasicColData                         html  
    ragged41FP                              html  
    sbov                                    html  
    sbov_output_FP                          html  
    sbov_output_HS                          html  
    sbov_output_eQTL                        html  
    sbov_to_graphNEL                        html  
    txmodels                                html  
    txregCollections                        html  
    verifyHasMongoCmd                       html  
    verifyRunningMongodb                    html  
** 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

install for x64

* installing *source* package 'TxRegInfra' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TxRegInfra' as TxRegInfra_1.8.0.zip
* DONE (TxRegInfra)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'TxRegInfra' successfully unpacked and MD5 sums checked

Tests output

TxRegInfra.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: mongolite
> 
> test_check("TxRegInfra")
Error in system2(cmd, args = "--help", stdout = TRUE, stderr = TRUE) : 
  '"mongo"' not found
Error in system2(cmd, args = "--help", stdout = TRUE, stderr = TRUE) : 
  '"mongo"' not found
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   7.89    0.90    8.82 

TxRegInfra.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: mongolite
> 
> test_check("TxRegInfra")
Error in system2(cmd, args = "--help", stdout = TRUE, stderr = TRUE) : 
  '"mongo"' not found
Error in system2(cmd, args = "--help", stdout = TRUE, stderr = TRUE) : 
  '"mongo"' not found
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   8.84    0.45    9.31 

Example timings

TxRegInfra.Rcheck/examples_i386/TxRegInfra-Ex.timings

nameusersystemelapsed
URL_txregInAWS000
basicColData0.070.000.08
basicFormatter0.020.000.02
demo_eQTL_granges0.010.000.01
demo_fimo_granges0.030.000.03
dgf_meta000
dnmeta0.060.000.06
dnmetaApp0.020.000.02
getDocumentFields000
getFieldNames0.140.010.53
grConverter0.060.000.06
importBedToMongo0.020.000.02
listAllCollections0.000.001.01
makeAggregator000
makeColData000
oldbasicColData0.000.020.02
ragged41FP0.190.060.25
sbov000
sbov_output_FP0.040.000.05
sbov_output_HS0.020.000.01
sbov_output_eQTL0.030.000.03
sbov_to_graphNEL27.06 0.3327.55
txmodels 20.25 3.80203.59
txregCollections000
verifyHasMongoCmd000
verifyRunningMongodb000

TxRegInfra.Rcheck/examples_x64/TxRegInfra-Ex.timings

nameusersystemelapsed
URL_txregInAWS000
basicColData0.730.000.73
basicFormatter0.020.000.01
demo_eQTL_granges0.000.010.02
demo_fimo_granges0.030.000.03
dgf_meta0.010.000.01
dnmeta0.070.000.07
dnmetaApp000
getDocumentFields000
getFieldNames0.040.060.50
grConverter0.050.000.23
importBedToMongo000
listAllCollections0.010.001.03
makeAggregator000
makeColData000
oldbasicColData0.000.020.02
ragged41FP0.210.020.22
sbov000
sbov_output_FP0.030.000.03
sbov_output_HS0.010.000.01
sbov_output_eQTL0.020.000.02
sbov_to_graphNEL31.39 0.0931.50
txmodels21.00 1.3925.65
txregCollections000
verifyHasMongoCmd000
verifyRunningMongodb000