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CHECK report for derfinder on merida2

This page was generated on 2019-04-09 13:30:31 -0400 (Tue, 09 Apr 2019).

Package 412/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
derfinder 1.17.1
Leonardo Collado-Torres
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/derfinder
Branch: master
Last Commit: efb0859
Last Changed Date: 2018-12-03 16:40:56 -0400 (Mon, 03 Dec 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: derfinder
Version: 1.17.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:derfinder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings derfinder_1.17.1.tar.gz
StartedAt: 2019-04-09 00:25:00 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:35:37 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 637.5 seconds
RetCode: 0
Status:  OK 
CheckDir: derfinder.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:derfinder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings derfinder_1.17.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/derfinder.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘derfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘derfinder’ version ‘1.17.1’
* 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 ‘derfinder’ 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘GenomeInfoDb:::.guessSpeciesStyle’
  ‘GenomeInfoDb:::.supportedSeqnameMappings’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.smootherFstats’
* 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
railMatrix 12.034  1.192  13.373
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.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-3.9-bioc/meat/derfinder.Rcheck/00check.log’
for details.



Installation output

derfinder.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL derfinder
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘derfinder’ ...
** R
** data
*** moving datasets to lazyload DB
** 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 (derfinder)

Tests output

derfinder.Rcheck/tests/test-all.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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.

> ## Disable the tests if the system variable 'R_DISABLE_TESTS' is set to TRUE
> 
> flag <- as.logical(Sys.getenv('R_DISABLE_TESTS'))
> if(is.na(flag) | flag == FALSE) {
+     library('testthat')
+     test_check('derfinder')
+ }
Loading required package: derfinder
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
  bpexportglobals: TRUE
  bplogdir: NA
  bpresultdir: NA
Error in x$.self$finalize() : attempt to apply non-function
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
  bpexportglobals: TRUE
  bplogdir: NA
  bpresultdir: NA
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
  bpexportglobals: TRUE
  bplogdir: NA
  bpresultdir: NA
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
  bpexportglobals: TRUE
  bplogdir: NA
  bpresultdir: NA
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
  bpexportglobals: TRUE
  bplogdir: NA
  bpresultdir: NA
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
  bpexportglobals: TRUE
  bplogdir: NA
  bpresultdir: NA
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
  bpexportglobals: TRUE
  bplogdir: NA
  bpresultdir: NA
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
  bpexportglobals: TRUE
  bplogdir: NA
  bpresultdir: NA
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 137 SKIPPED: 0 FAILED: 0
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
292.998  10.810 313.927 

Example timings

derfinder.Rcheck/derfinder-Ex.timings

nameusersystemelapsed
analyzeChr1.6010.1151.732
annotateRegions0.4160.0110.433
calculatePvalues1.2450.0111.267
calculateStats0.8320.0030.842
coerceGR0.0870.0020.088
collapseFullCoverage0.0080.0020.009
coverageToExon4.1700.4754.679
createBw0.2010.0030.205
createBwSample0.0520.0010.053
define_cluster0.0070.0010.008
derfinder-deprecated0.0030.0000.003
extendedMapSeqlevels0.0890.0070.095
filterData0.1160.0040.120
findRegions0.9060.0310.946
fullCoverage0.2910.0110.307
getRegionCoverage0.2270.0090.238
getTotalMapped0.0150.0010.016
loadCoverage0.2120.0050.217
makeGenomicState4.5500.0554.649
makeModels0.0210.0020.023
mergeResults0.3670.0080.377
preprocessCoverage0.6600.0030.665
railMatrix12.034 1.19213.373
rawFiles0.0040.0010.004
regionMatrix1.0150.0261.054
sampleDepth0.0190.0010.020