Leonardo Collado-Torres
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/derfinder |
| Branch: RELEASE_3_8 |
| Last Commit: fbc7300 |
| Last Changed Date: 2018-12-03 16:40:56 -0400 (Mon, 03 Dec 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:58:00 -0400 (Tue, 16 Apr 2019).
| Package 394/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| derfinder 1.16.1 Leonardo Collado-Torres
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: derfinder |
| Version: 1.16.1 |
| 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_1.16.1.tar.gz |
| StartedAt: 2019-04-15 23:27:02 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:38:12 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 669.1 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_1.16.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/derfinder.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.16.1’
* 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 12.766 1.241 14.187
makeGenomicState 5.170 0.034 5.249
* 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-3.8-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/3.5/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)
derfinder.Rcheck/tests/test-all.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE; bpexportglobals: TRUE
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; bpexportglobals: TRUE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE; bpexportglobals: TRUE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE; bpexportglobals: TRUE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE; bpexportglobals: TRUE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE; bpexportglobals: TRUE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE; bpexportglobals: TRUE
bplogdir: NA
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE; bpexportglobals: TRUE
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
333.751 11.263 349.078
derfinder.Rcheck/derfinder-Ex.timings
| name | user | system | elapsed | |
| analyzeChr | 1.977 | 0.028 | 2.031 | |
| annotateRegions | 0.441 | 0.029 | 0.473 | |
| calculatePvalues | 0.841 | 0.026 | 0.872 | |
| calculateStats | 0.347 | 0.004 | 0.356 | |
| coerceGR | 0.068 | 0.001 | 0.069 | |
| collapseFullCoverage | 0.007 | 0.001 | 0.009 | |
| coverageToExon | 4.281 | 0.495 | 4.829 | |
| createBw | 0.217 | 0.002 | 0.221 | |
| createBwSample | 0.073 | 0.001 | 0.074 | |
| define_cluster | 0.008 | 0.000 | 0.009 | |
| derfinder-deprecated | 0.003 | 0.001 | 0.004 | |
| extendedMapSeqlevels | 0.142 | 0.008 | 0.150 | |
| filterData | 0.165 | 0.005 | 0.171 | |
| findRegions | 0.617 | 0.028 | 0.651 | |
| fullCoverage | 0.331 | 0.009 | 0.342 | |
| getRegionCoverage | 0.312 | 0.010 | 0.324 | |
| getTotalMapped | 0.017 | 0.001 | 0.017 | |
| loadCoverage | 0.205 | 0.003 | 0.210 | |
| makeGenomicState | 5.170 | 0.034 | 5.249 | |
| makeModels | 0.031 | 0.001 | 0.033 | |
| mergeResults | 0.456 | 0.011 | 0.475 | |
| preprocessCoverage | 0.379 | 0.003 | 0.384 | |
| railMatrix | 12.766 | 1.241 | 14.187 | |
| rawFiles | 0.005 | 0.001 | 0.007 | |
| regionMatrix | 1.189 | 0.028 | 1.221 | |
| sampleDepth | 0.034 | 0.001 | 0.034 | |