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) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:30:29 -0400 (Wed, 15 Apr 2020).
| Package 1773/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TxRegInfra 1.6.0 VJ Carey
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | TIMEOUT | skipped | skipped |
| Package: TxRegInfra |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TxRegInfra.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings TxRegInfra_1.6.0.tar.gz |
| StartedAt: 2020-04-15 07:18:02 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 07:25:40 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 458.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TxRegInfra.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TxRegInfra.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings TxRegInfra_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/TxRegInfra.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.6.0'
* 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 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 or elapsed time > 5s
user system elapsed
sbov_to_graphNEL 24.29 0.08 24.39
txmodels 18.29 3.50 123.69
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sbov_to_graphNEL 37.36 0.03 37.39
txmodels 25.03 1.39 27.86
* 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-3.10-bioc/meat/TxRegInfra.Rcheck/00check.log'
for details.
TxRegInfra.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/TxRegInfra_1.6.0.tar.gz && rm -rf TxRegInfra.buildbin-libdir && mkdir TxRegInfra.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TxRegInfra.buildbin-libdir TxRegInfra_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL TxRegInfra_1.6.0.zip && rm TxRegInfra_1.6.0.tar.gz TxRegInfra_1.6.0.zip
###
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% 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 344k 100 344k 0 0 2490k 0 --:--:-- --:--:-- --:--:-- 2569k
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_1.6.0.zip
* DONE (TxRegInfra)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'TxRegInfra' successfully unpacked and MD5 sums checked
|
TxRegInfra.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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
5.87 0.39 6.28
|
TxRegInfra.Rcheck/tests_x64/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-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
8.81 0.31 9.12
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TxRegInfra.Rcheck/examples_i386/TxRegInfra-Ex.timings
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TxRegInfra.Rcheck/examples_x64/TxRegInfra-Ex.timings
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