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CHECK report for gCrisprTools on malbec2

This page was generated on 2018-10-17 08:29:23 -0400 (Wed, 17 Oct 2018).

Package 550/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 1.8.0
Peter Haverty
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/gCrisprTools
Branch: RELEASE_3_7
Last Commit: cc624bb
Last Changed Date: 2018-04-30 10:35:43 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gCrisprTools
Version: 1.8.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings gCrisprTools_1.8.0.tar.gz
StartedAt: 2018-10-16 00:35:06 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 00:39:39 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 272.6 seconds
RetCode: 0
Status:  OK 
CheckDir: gCrisprTools.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings gCrisprTools_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/gCrisprTools.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘1.8.0’
* 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 ‘gCrisprTools’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
* 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
ct.PantherPathwayEnrichment 77.348  1.540  80.629
ct.makeReport               20.284  0.576  20.899
ct.makeContrastReport        8.968  0.668   9.672
ct.guideCDF                  7.428  0.300   7.735
ct.makeQCReport              5.956  0.288   6.266
ct.GCbias                    5.776  0.068   5.854
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘unit.tests.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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.



Installation output

gCrisprTools.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL gCrisprTools
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘gCrisprTools’ ...
** R
** data
** 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 (gCrisprTools)

Tests output

gCrisprTools.Rcheck/tests/unit.tests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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.

> #require("BiocGenerics", quietly = TRUE)
> BiocGenerics:::testPackage("gCrisprTools")
PANTHER.db version 1.0.4


RUNIT TEST PROTOCOL -- Tue Oct 16 00:39:36 2018 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
gCrisprTools RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  3.008   0.128   3.132 

Example timings

gCrisprTools.Rcheck/gCrisprTools-Ex.timings

nameusersystemelapsed
aln0.0040.0000.020
ann0.1360.0000.146
ct.DirectionalTests0.3400.0560.406
ct.GCbias5.7760.0685.854
ct.PRC0.9520.0160.986
ct.PantherPathwayEnrichment77.348 1.54080.629
ct.ROC0.1520.0040.157
ct.RRAaPvals1.6320.0681.705
ct.RRAalpha0.2400.0000.242
ct.alignmentChart0.0000.0040.005
ct.alphaBeta0.0080.0000.007
ct.ecdf0.0040.0000.001
ct.filterReads0.2200.0000.221
ct.gRNARankByReplicate0.4080.0080.415
ct.generateResults0.4640.0000.465
ct.guideCDF7.4280.3007.735
ct.inputCheck0.0760.0000.077
ct.makeContrastReport8.9680.6689.672
ct.makeQCReport5.9560.2886.266
ct.makeReport20.284 0.57620.899
ct.normalizeBySlope1.0280.0561.085
ct.normalizeGuides3.2920.1083.406
ct.normalizeMedians0.7120.0360.751
ct.normalizeNTC0.8760.0280.904
ct.normalizeSpline1.0160.0321.048
ct.prepareAnnotation0.5280.0240.554
ct.preprocessFit1.7840.1241.908
ct.rawCountDensities0.1240.0040.132
ct.resultCheck0.1040.0040.110
ct.stackGuides4.0880.1644.256
ct.targetSetEnrichment0.1080.0040.114
ct.topTargets0.3760.0040.380
ct.viewControls0.2400.0040.243
ct.viewGuides0.3080.0160.323
es0.0520.0000.051
essential.genes0.0040.0000.002
fit0.1680.0040.171
resultsDF0.1160.0000.115