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CHECK report for TFARM on malbec1

This page was generated on 2019-04-16 11:53:00 -0400 (Tue, 16 Apr 2019).

Package 1554/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFARM 1.4.0
Liuba Nausicaa Martino
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/TFARM
Branch: RELEASE_3_8
Last Commit: ac05e23
Last Changed Date: 2018-10-30 11:42:06 -0400 (Tue, 30 Oct 2018)
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: TFARM
Version: 1.4.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TFARM.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TFARM_1.4.0.tar.gz
StartedAt: 2019-04-16 03:23:06 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:24:59 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 112.6 seconds
RetCode: 0
Status:  OK 
CheckDir: TFARM.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:TFARM.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TFARM_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/TFARM.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 ‘TFARM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TFARM’ version ‘1.4.0’
* 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 ‘TFARM’ 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
rulesTF0 5.228  0.004   5.233
* 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

TFARM.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL TFARM
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘TFARM’ ...
** R
** data
*** moving datasets to lazyload DB
** 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 (TFARM)

Tests output


Example timings

TFARM.Rcheck/TFARM-Ex.timings

nameusersystemelapsed
DELTA0.0040.0040.010
IComp0.0360.0040.041
IMP0.0000.0000.002
IMP_Z0.0000.0040.001
IPCA0.0160.0000.017
I_c_20.0040.0000.001
MCF7_chr10.0720.0000.072
TF_Imp0.0040.0000.003
distribViz0.0200.0000.019
heatI0.0520.0000.052
imp_FOSL20.0000.0000.002
items000
itemset0.0000.0000.001
p_TFs0.0040.0000.001
presAbs0.1520.0000.153
r_FOSL20.0040.0000.002
r_TEAD40.0040.0000.003
r_noFOSL20.0000.0000.002
rulesGen0.7480.0000.750
rulesTF0.1320.0000.132
rulesTF05.2280.0045.233