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This page was generated on 2022-01-20 11:10:52 -0500 (Thu, 20 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4162
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4057
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3999
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4116
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 merida1


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? here 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 492/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
derfinder 1.29.0  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2022-01-19 13:55:26 -0500 (Wed, 19 Jan 2022)
git_url: https://git.bioconductor.org/packages/derfinder
git_branch: master
git_last_commit: 5c1cbd4
git_last_commit_date: 2021-10-26 12:16:21 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'BiocGenerics' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: derfinder
Version: 1.29.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:derfinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings derfinder_1.29.0.tar.gz
StartedAt: 2022-01-20 00:06:20 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 00:22:02 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 941.2 seconds
RetCode: 0
Status:   OK  
CheckDir: derfinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:derfinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings derfinder_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/derfinder.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.29.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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       14.547  0.888  15.842
makeGenomicState  8.236  0.064   8.831
coverageToExon    5.645  0.323   5.973
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/derfinder.Rcheck/00check.log’
for details.



Installation output

derfinder.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: NA; bpprogressbar: FALSE
  bpexportglobals: FALSE; bpforceGC: 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; bpforceGC: 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; bpforceGC: 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; bpforceGC: 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; bpforceGC: 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; bpforceGC: 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; bpforceGC: 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; bpforceGC: FALSE
  bplogdir: NA
  bpresultdir: NA
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 137 ]
> 
> proc.time()
   user  system elapsed 
419.480   7.055 438.948 

Example timings

derfinder.Rcheck/derfinder-Ex.timings

nameusersystemelapsed
analyzeChr2.8470.1112.963
annotateRegions0.6920.0130.705
calculatePvalues2.2600.0152.279
calculateStats1.2800.0131.294
coerceGR0.1480.0010.150
collapseFullCoverage0.0110.0020.013
coverageToExon5.6450.3235.973
createBw0.3260.0030.330
createBwSample0.1180.0020.120
define_cluster0.010.000.01
derfinder-deprecated0.0030.0000.004
extendedMapSeqlevels0.1390.0130.152
filterData0.2520.0060.258
findRegions1.3780.0861.465
fullCoverage0.5260.0650.592
getRegionCoverage0.6270.0391.030
getTotalMapped0.0150.0010.016
loadCoverage0.3000.0060.305
makeGenomicState8.2360.0648.831
makeModels0.0360.0010.037
mergeResults0.8260.0220.904
preprocessCoverage1.1530.0061.234
railMatrix14.547 0.88815.842
rawFiles0.0030.0010.004
regionMatrix1.7800.0691.852
sampleDepth0.0250.0010.026