Back to Multiple platform build/check report for BioC 3.15
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-10-19 13:20:11 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for derfinder on nebbiolo1


To the developers/maintainers of the derfinder package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/derfinder.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 510/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
derfinder 1.30.0  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/derfinder
git_branch: RELEASE_3_15
git_last_commit: 7dbc750
git_last_commit_date: 2022-04-26 11:21:49 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: derfinder
Version: 1.30.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:derfinder.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings derfinder_1.30.0.tar.gz
StartedAt: 2022-10-18 19:24:05 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 19:33:00 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 535.2 seconds
RetCode: 0
Status:   OK  
CheckDir: derfinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:derfinder.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings derfinder_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/derfinder.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.30.0’
* package encoding: UTF-8
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
railMatrix     8.602  0.328   8.957
coverageToExon 5.016  0.592   5.608
* 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-3.15-bioc/meat/derfinder.Rcheck/00check.log’
for details.



Installation output

derfinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL derfinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘derfinder’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (derfinder)

Tests output

derfinder.Rcheck/tests/test-all.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE
  bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE; bpfallback: FALSE
  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: NA; bpprogressbar: FALSE
  bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE; bpfallback: FALSE
  bplogdir: NA
  bpresultdir: NA
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE
  bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE; bpfallback: FALSE
  bplogdir: NA
  bpresultdir: NA
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE
  bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE; bpfallback: FALSE
  bplogdir: NA
  bpresultdir: NA
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE
  bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE; bpfallback: FALSE
  bplogdir: NA
  bpresultdir: NA
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE
  bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE; bpfallback: FALSE
  bplogdir: NA
  bpresultdir: NA
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE
  bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE; bpfallback: FALSE
  bplogdir: NA
  bpresultdir: NA
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE
  bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE; bpfallback: FALSE
  bplogdir: NA
  bpresultdir: NA
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 137 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
224.941   6.490 231.583 

Example timings

derfinder.Rcheck/derfinder-Ex.timings

nameusersystemelapsed
analyzeChr1.4470.0881.535
annotateRegions0.3090.0040.313
calculatePvalues2.0410.0482.089
calculateStats0.5770.0080.585
coerceGR0.0650.0080.073
collapseFullCoverage0.0040.0040.007
coverageToExon5.0160.5925.608
createBw0.1790.0000.178
createBwSample0.0650.0000.065
define_cluster0.0060.0000.006
derfinder-deprecated0.0020.0000.003
extendedMapSeqlevels0.0630.0040.067
filterData0.1420.0080.150
findRegions0.6840.0080.692
fullCoverage0.2820.0080.290
getRegionCoverage0.3680.0240.679
getTotalMapped0.0100.0000.011
loadCoverage0.1480.0000.149
makeGenomicState4.0580.0724.131
makeModels0.0130.0030.016
mergeResults0.3470.0370.383
preprocessCoverage0.5480.0000.548
railMatrix8.6020.3288.957
rawFiles0.0000.0030.003
regionMatrix1.9780.1702.149
sampleDepth0.0130.0000.014