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CHECK report for gCrisprTools on malbec1

This page was generated on 2019-04-16 11:52:19 -0400 (Tue, 16 Apr 2019).

Package 580/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 1.10.1
Peter Haverty
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/gCrisprTools
Branch: RELEASE_3_8
Last Commit: fe836ed
Last Changed Date: 2019-01-04 13:33:50 -0400 (Fri, 04 Jan 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: gCrisprTools
Version: 1.10.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings gCrisprTools_1.10.1.tar.gz
StartedAt: 2019-04-16 00:04:06 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:10:40 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 394.2 seconds
RetCode: 0
Status:  OK 
CheckDir: gCrisprTools.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings gCrisprTools_1.10.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/gCrisprTools.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 ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘1.10.1’
* 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 112.436  2.012 116.076
ct.makeReport                32.216  1.400  33.714
ct.guideCDF                  33.340  0.088  33.535
ct.makeContrastReport        14.644  0.736  15.448
ct.makeQCReport               8.480  0.484   9.016
ct.GCbias                     6.984  0.064   7.064
ct.stackGuides                6.088  0.108   6.208
* 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-3.8-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.



Installation output

gCrisprTools.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL gCrisprTools
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.8-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 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 Apr 16 00:10:36 2019 
*********************************************** 
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 
  3.888   0.124   4.020 

Example timings

gCrisprTools.Rcheck/gCrisprTools-Ex.timings

nameusersystemelapsed
aln0.0040.0000.021
ann0.1480.0000.149
ct.DirectionalTests0.4440.0840.588
ct.GCbias6.9840.0647.064
ct.PRC1.1480.0161.185
ct.PantherPathwayEnrichment112.436 2.012116.076
ct.ROC0.1720.0040.175
ct.RRAaPvals0.4800.0360.516
ct.RRAalpha0.4560.0080.467
ct.alignmentChart0.0080.0000.007
ct.alphaBeta0.0160.0000.015
ct.ecdf0.0040.0000.001
ct.filterReads0.4320.0400.473
ct.gRNARankByReplicate0.6360.0280.663
ct.generateResults0.7560.0720.828
ct.guideCDF33.340 0.08833.535
ct.inputCheck0.0960.0000.098
ct.makeContrastReport14.644 0.73615.448
ct.makeQCReport8.4800.4849.016
ct.makeReport32.216 1.40033.714
ct.normalizeBySlope1.1720.0521.227
ct.normalizeGuides4.5160.2244.755
ct.normalizeMedians0.7920.0040.795
ct.normalizeNTC0.9640.0280.994
ct.normalizeSpline1.1800.0201.201
ct.prepareAnnotation0.6680.0240.691
ct.preprocessFit1.9440.0922.039
ct.rawCountDensities0.1200.0120.132
ct.resultCheck0.1040.0000.105
ct.stackGuides6.0880.1086.208
ct.targetSetEnrichment0.1200.0000.121
ct.topTargets0.4320.0000.432
ct.viewControls0.3840.0040.387
ct.viewGuides0.5080.0040.513
es0.0840.0000.084
essential.genes0.0000.0000.003
fit0.2240.0000.225
resultsDF0.120.000.12