Leonardo Collado-Torres
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/derfinder |
| Branch: RELEASE_3_6 |
| Last Commit: 265e982 |
| Last Changed Date: 2018-01-19 19:50:27 -0400 (Fri, 19 Jan 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:39:29 -0400 (Thu, 12 Apr 2018).
| Package 353/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| derfinder 1.12.6 Leonardo Collado-Torres
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: derfinder |
| Version: 1.12.6 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings derfinder_1.12.6.tar.gz |
| StartedAt: 2018-04-12 02:42:51 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:52:18 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 566.9 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 --no-vignettes --timings derfinder_1.12.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/derfinder.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.12.6’
* 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 ... NOTE
installed size is 6.6Mb
sub-directories of 1Mb or more:
doc 5.4Mb
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
railMatrix 8.217 1.199 9.567
* 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-3.6-bioc/meat/derfinder.Rcheck/00check.log’
for details.
derfinder.Rcheck/00install.out
* installing *source* package ‘derfinder’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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
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
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
275.878 8.210 288.457
derfinder.Rcheck/derfinder-Ex.timings
| name | user | system | elapsed | |
| analyzeChr | 1.866 | 0.019 | 1.909 | |
| annotateRegions | 0.775 | 0.010 | 0.789 | |
| calculatePvalues | 1.288 | 0.008 | 1.323 | |
| calculateStats | 0.204 | 0.001 | 0.205 | |
| coerceGR | 0.098 | 0.001 | 0.099 | |
| collapseFullCoverage | 0.008 | 0.002 | 0.010 | |
| coverageToExon | 2.651 | 0.388 | 3.078 | |
| createBw | 0.227 | 0.002 | 0.230 | |
| createBwSample | 0.061 | 0.003 | 0.069 | |
| define_cluster | 0.008 | 0.001 | 0.010 | |
| derfinder-deprecated | 0.003 | 0.000 | 0.003 | |
| extendedMapSeqlevels | 0.121 | 0.020 | 0.140 | |
| filterData | 0.323 | 0.034 | 0.358 | |
| findRegions | 0.267 | 0.004 | 0.276 | |
| fullCoverage | 0.732 | 0.011 | 0.755 | |
| getRegionCoverage | 0.335 | 0.010 | 0.355 | |
| getTotalMapped | 0.178 | 0.001 | 0.179 | |
| loadCoverage | 0.148 | 0.003 | 0.152 | |
| makeGenomicState | 4.349 | 0.042 | 4.459 | |
| makeModels | 0.027 | 0.001 | 0.028 | |
| mergeResults | 0.370 | 0.012 | 0.390 | |
| preprocessCoverage | 0.156 | 0.002 | 0.162 | |
| railMatrix | 8.217 | 1.199 | 9.567 | |
| rawFiles | 0.004 | 0.001 | 0.005 | |
| regionMatrix | 1.134 | 0.026 | 1.180 | |
| sampleDepth | 0.026 | 0.001 | 0.026 | |