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CHECK report for derfinder on malbec2

This page was generated on 2018-10-17 08:26:44 -0400 (Wed, 17 Oct 2018).

Package 370/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
derfinder 1.14.0
Leonardo Collado-Torres
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/derfinder
Branch: RELEASE_3_7
Last Commit: 7be868d
Last Changed Date: 2018-04-30 10:35:34 -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  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: derfinder
Version: 1.14.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:derfinder.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings derfinder_1.14.0.tar.gz
StartedAt: 2018-10-15 23:45:54 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 23:53:14 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 439.3 seconds
RetCode: 0
Status:  OK 
CheckDir: derfinder.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:derfinder.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings derfinder_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/derfinder.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 ‘derfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘derfinder’ version ‘1.14.0’
* 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 ‘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 9.772  0.204  10.122
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/derfinder.Rcheck/00check.log’
for details.



Installation output

derfinder.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL derfinder
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘derfinder’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘IRanges’ for request: ‘subset’ when loading ‘derfinder’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package ‘IRanges’ for request: ‘subset’ when loading ‘derfinder’
* DONE (derfinder)

Tests output

derfinder.Rcheck/tests/test-all.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.

> ## 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
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
class: SerialParam
  bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bptimeout: 2592000; bpprogressbar: FALSE
  bplogdir: NA
Error in x$.self$finalize() : attempt to apply non-function
class: SerialParam
  bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bptimeout: 2592000; bpprogressbar: FALSE
  bplogdir: NA
class: SerialParam
  bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bptimeout: 2592000; bpprogressbar: FALSE
  bplogdir: NA
class: SerialParam
  bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bptimeout: 2592000; bpprogressbar: FALSE
  bplogdir: NA
class: SerialParam
  bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bptimeout: 2592000; bpprogressbar: FALSE
  bplogdir: NA
class: SerialParam
  bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bptimeout: 2592000; bpprogressbar: FALSE
  bplogdir: NA
class: SerialParam
  bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bptimeout: 2592000; bpprogressbar: FALSE
  bplogdir: NA
class: SerialParam
  bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bptimeout: 2592000; bpprogressbar: FALSE
  bplogdir: NA
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 137 SKIPPED: 0 FAILED: 0
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
215.208   3.260 218.737 

Example timings

derfinder.Rcheck/derfinder-Ex.timings

nameusersystemelapsed
analyzeChr1.5960.0201.618
annotateRegions0.3040.0000.301
calculatePvalues0.5960.0240.622
calculateStats0.2240.0000.224
coerceGR0.0520.0040.058
collapseFullCoverage0.0080.0000.007
coverageToExon3.6840.2403.924
createBw0.1320.0000.133
createBwSample0.040.000.04
define_cluster0.0000.0040.005
derfinder-deprecated0.0040.0000.002
extendedMapSeqlevels0.0720.0000.074
filterData0.1280.0000.129
findRegions0.3640.0000.366
fullCoverage0.2920.0040.313
getRegionCoverage0.1960.0000.214
getTotalMapped0.0080.0000.010
loadCoverage0.1360.0040.140
makeGenomicState3.4120.0123.428
makeModels0.020.000.02
mergeResults0.3160.0000.317
preprocessCoverage0.2360.0000.234
railMatrix 9.772 0.20410.122
rawFiles0.0040.0000.003
regionMatrix0.8600.0120.872
sampleDepth0.0160.0000.020