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CHECK report for PathwaySplice on veracruz1

This page was generated on 2018-04-12 13:45:51 -0400 (Thu, 12 Apr 2018).

Package 1010/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PathwaySplice 1.0.0
Aimin Yan
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/PathwaySplice
Branch: RELEASE_3_6
Last Commit: 3965ad3
Last Changed Date: 2017-10-30 12:41:59 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: PathwaySplice
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PathwaySplice_1.0.0.tar.gz
StartedAt: 2018-04-12 07:28:52 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 07:41:46 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 773.5 seconds
RetCode: 0
Status:  OK 
CheckDir: PathwaySplice.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PathwaySplice_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/PathwaySplice.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PathwaySplice/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PathwaySplice’ version ‘1.0.0’
* 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 ‘PathwaySplice’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
enrichmentMap    60.349  4.177  65.891
runPathwaySplice 50.995  4.031  56.333
compareResults   49.690  1.132  52.709
lrTestBias       20.916  0.109  21.536
makeGeneTable    19.355  0.061  19.728
gmtGene2Cat      17.701  0.232  18.542
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/PathwaySplice.Rcheck/00check.log’
for details.



Installation output

PathwaySplice.Rcheck/00install.out

* installing *source* package ‘PathwaySplice’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PathwaySplice)

Tests output

PathwaySplice.Rcheck/tests/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
> test_check("PathwaySplice")
Loading required package: PathwaySplice



[1] "P-value from logistic regression is 3.98e-205"
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 4 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
227.380  16.959 250.148 

Example timings

PathwaySplice.Rcheck/PathwaySplice-Ex.timings

nameusersystemelapsed
compareResults49.690 1.13252.709
enrichmentMap60.349 4.17765.891
gmtGene2Cat17.701 0.23218.542
lrTestBias20.916 0.10921.536
makeGeneTable19.355 0.06119.728
runPathwaySplice50.995 4.03156.333