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) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:55:59 -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 1853/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TxRegInfra 1.8.0 VJ Carey
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: TxRegInfra |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:TxRegInfra.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings TxRegInfra_1.8.0.tar.gz |
| StartedAt: 2020-10-17 06:19:24 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:23:38 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 254.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TxRegInfra.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:TxRegInfra.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings TxRegInfra_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/TxRegInfra.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.8.0’
* 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 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 (user + system) or elapsed time > 5s
user system elapsed
sbov_to_graphNEL 33.180 0.031 33.211
txmodels 21.841 0.959 28.477
* 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-3.11-bioc/meat/TxRegInfra.Rcheck/00check.log’
for details.
TxRegInfra.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL TxRegInfra ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-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)
TxRegInfra.Rcheck/tests/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-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
7.829 0.318 8.132
TxRegInfra.Rcheck/TxRegInfra-Ex.timings
| name | user | system | elapsed | |
| URL_txregInAWS | 0.000 | 0.000 | 0.001 | |
| basicColData | 0.045 | 0.003 | 0.049 | |
| basicFormatter | 0.012 | 0.004 | 0.016 | |
| demo_eQTL_granges | 0.007 | 0.000 | 0.007 | |
| demo_fimo_granges | 0.017 | 0.001 | 0.017 | |
| dgf_meta | 0.000 | 0.003 | 0.004 | |
| dnmeta | 0.032 | 0.008 | 0.040 | |
| dnmetaApp | 0 | 0 | 0 | |
| getDocumentFields | 0 | 0 | 0 | |
| getFieldNames | 0.052 | 0.000 | 0.309 | |
| grConverter | 0.063 | 0.000 | 0.077 | |
| importBedToMongo | 0.000 | 0.036 | 0.036 | |
| listAllCollections | 0.002 | 0.001 | 0.002 | |
| makeAggregator | 0.002 | 0.031 | 0.035 | |
| makeColData | 0.004 | 0.026 | 0.030 | |
| oldbasicColData | 0.01 | 0.00 | 0.01 | |
| ragged41FP | 0.218 | 0.004 | 0.222 | |
| sbov | 0.000 | 0.035 | 0.034 | |
| sbov_output_FP | 0.04 | 0.00 | 0.04 | |
| sbov_output_HS | 0.02 | 0.00 | 0.02 | |
| sbov_output_eQTL | 0.024 | 0.000 | 0.024 | |
| sbov_to_graphNEL | 33.180 | 0.031 | 33.211 | |
| txmodels | 21.841 | 0.959 | 28.477 | |
| txregCollections | 0.005 | 0.064 | 0.069 | |
| verifyHasMongoCmd | 0 | 0 | 0 | |
| verifyRunningMongodb | 0 | 0 | 0 | |