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CHECK report for TxRegInfra on malbec1

This page was generated on 2019-04-16 11:53:31 -0400 (Tue, 16 Apr 2019).

Package 1606/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TxRegInfra 1.2.1
VJ Carey
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/TxRegInfra
Branch: RELEASE_3_8
Last Commit: 2028a2f
Last Changed Date: 2019-03-08 09:07:00 -0400 (Fri, 08 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TxRegInfra
Version: 1.2.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TxRegInfra.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TxRegInfra_1.2.1.tar.gz
StartedAt: 2019-04-16 03:35:17 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:38:04 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 167.2 seconds
RetCode: 0
Status:  OK 
CheckDir: TxRegInfra.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TxRegInfra.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TxRegInfra_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/TxRegInfra.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.2.1’
* 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 ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* 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 ... OK
* 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
txmodels 16.236  0.868   27.42
* 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: OK


Installation output

TxRegInfra.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL TxRegInfra
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘TxRegInfra’ ...
** 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
* DONE (TxRegInfra)

Tests output


Example timings

TxRegInfra.Rcheck/TxRegInfra-Ex.timings

nameusersystemelapsed
URL_txregInAWS000
basicColData0.0480.0000.050
basicFormatter0.0120.0000.012
dgf_meta0.0040.0000.004
getDocumentFields000
getFieldNames0.0440.0040.539
grConverter0.0360.0000.035
importBedToMongo0.0040.0200.039
listAllCollections0.0000.0200.023
makeAggregator0.0040.0200.024
makeColData0.0000.0200.024
ragged41FP0.1840.0000.186
sbov0.0040.0240.026
txmodels16.236 0.86827.420
txregCollections0.0040.0360.039
verifyHasMongoCmd000
verifyRunningMongodb000