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BioC 3.5: CHECK report for gCrisprTools on oaxaca

This page was generated on 2017-03-04 16:53:11 -0500 (Sat, 04 Mar 2017).

Package 480/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 1.2.70
Russell Bainer
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gCrisprTools
Last Changed Rev: 124896 / Revision: 127142
Last Changed Date: 2016-12-07 14:12:20 -0500 (Wed, 07 Dec 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: gCrisprTools
Version: 1.2.70
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCrisprTools_1.2.70.tar.gz
StartedAt: 2017-03-04 03:11:10 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 03:16:29 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 319.3 seconds
RetCode: 0
Status:  OK 
CheckDir: gCrisprTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCrisprTools_1.2.70.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/gCrisprTools.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.2.70’
* 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  9.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    1.4Mb
* 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 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
ct.PantherPathwayEnrichment 58.022  1.169  60.963
ct.makeReport               37.689  3.149  41.200
ct.makeContrastReport       19.875  1.844  21.750
ct.guideCDF                 14.243  5.876  20.127
ct.makeQCReport              9.925  0.543  12.590
ct.RRAaPvals                 5.573  1.337   4.358
ct.GCbias                    5.373  0.228   5.631
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.


gCrisprTools.Rcheck/00install.out:

* installing *source* package ‘gCrisprTools’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gCrisprTools)

gCrisprTools.Rcheck/gCrisprTools-Ex.timings:

nameusersystemelapsed
aln0.0030.0010.004
ann0.0930.0100.102
ct.DirectionalTests0.4020.1170.518
ct.GCbias5.3730.2285.631
ct.PRC1.2620.0331.326
ct.PantherPathwayEnrichment58.022 1.16960.963
ct.ROC0.2670.0130.280
ct.RRAaPvals5.5731.3374.358
ct.RRAalpha0.3480.0240.374
ct.RRAalphaBatch1.5300.1381.670
ct.alignmentChart0.0040.0010.005
ct.alphaBeta0.0100.0010.037
ct.ecdf0.0010.0000.001
ct.filterReads0.5070.0420.550
ct.gRNARankByReplicate0.5510.0580.611
ct.generateResults1.8820.8441.079
ct.guideCDF14.243 5.87620.127
ct.inputCheck0.1230.0090.133
ct.makeContrastReport19.875 1.84421.750
ct.makeQCReport 9.925 0.54312.590
ct.makeReport37.689 3.14941.200
ct.normalizeBySlope0.8490.0631.002
ct.normalizeGuides2.5700.2772.992
ct.normalizeMedians0.5290.0480.598
ct.normalizeNTC0.6760.0530.750
ct.normalizeSpline0.8690.0970.985
ct.prepareAnnotation0.5300.0360.584
ct.preprocessFit2.3810.0512.430
ct.rawCountDensities0.1090.0080.587
ct.resultCheck0.0960.0060.101
ct.stackGuides3.9670.8644.960
ct.targetSetEnrichment0.1060.0070.114
ct.topTargets0.3420.0200.362
ct.viewControls0.2460.0350.282
ct.viewGuides0.3300.0440.373
es0.0710.0050.076
essential.genes0.0010.0010.002
fit0.1840.0070.191
resultsDF0.0950.0060.101