Leonardo Collado-Torres
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/derfinder |
| Branch: RELEASE_3_9 |
| Last Commit: c5d1065 |
| Last Changed Date: 2019-09-20 10:19:12 -0400 (Fri, 20 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:54:09 -0400 (Wed, 16 Oct 2019).
| Package 419/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| derfinder 1.18.9 Leonardo Collado-Torres
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: derfinder |
| Version: 1.18.9 |
| 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_1.18.9.tar.gz |
| StartedAt: 2019-10-16 02:08:08 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:22:34 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 866.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: derfinder.Rcheck |
| Warnings: 0 |
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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_1.18.9.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/derfinder.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.18.9’
* 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 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 13.659 2.228 15.945
coverageToExon 5.288 0.962 6.250
makeGenomicState 5.874 0.074 5.957
* 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.
derfinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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’ ... ** 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)
derfinder.Rcheck/tests/test-all.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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: 136 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
392.278 21.162 430.661
derfinder.Rcheck/derfinder-Ex.timings
| name | user | system | elapsed | |
| analyzeChr | 2.231 | 0.126 | 2.358 | |
| annotateRegions | 0.454 | 0.038 | 0.492 | |
| calculatePvalues | 1.698 | 0.076 | 1.774 | |
| calculateStats | 1.246 | 0.083 | 1.329 | |
| coerceGR | 0.098 | 0.003 | 0.102 | |
| collapseFullCoverage | 0.015 | 0.005 | 0.020 | |
| coverageToExon | 5.288 | 0.962 | 6.250 | |
| createBw | 0.277 | 0.005 | 0.282 | |
| createBwSample | 0.084 | 0.002 | 0.088 | |
| define_cluster | 0.012 | 0.001 | 0.013 | |
| derfinder-deprecated | 0.005 | 0.001 | 0.005 | |
| extendedMapSeqlevels | 0.143 | 0.016 | 0.159 | |
| filterData | 0.226 | 0.009 | 0.236 | |
| findRegions | 1.053 | 0.057 | 1.111 | |
| fullCoverage | 0.524 | 0.080 | 0.606 | |
| getRegionCoverage | 0.452 | 0.032 | 0.485 | |
| getTotalMapped | 0.024 | 0.002 | 0.026 | |
| loadCoverage | 0.260 | 0.007 | 0.266 | |
| makeGenomicState | 5.874 | 0.074 | 5.957 | |
| makeModels | 0.040 | 0.004 | 0.044 | |
| mergeResults | 0.639 | 0.029 | 0.670 | |
| preprocessCoverage | 0.752 | 0.004 | 0.757 | |
| railMatrix | 13.659 | 2.228 | 15.945 | |
| rawFiles | 0.007 | 0.001 | 0.009 | |
| regionMatrix | 1.530 | 0.184 | 1.716 | |
| sampleDepth | 0.033 | 0.001 | 0.034 | |