Leonardo Collado-Torres
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/derfinder |
| Branch: RELEASE_3_7 |
| Last Commit: 7be868d |
| Last Changed Date: 2018-04-30 10:35:34 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:26:44 -0400 (Wed, 17 Oct 2018).
| Package 370/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| derfinder 1.14.0 Leonardo Collado-Torres
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: derfinder |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:derfinder.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings derfinder_1.14.0.tar.gz |
| StartedAt: 2018-10-15 23:45:54 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 23:53:14 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 439.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: derfinder.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:derfinder.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings derfinder_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/derfinder.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.14.0’
* 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 9.772 0.204 10.122
* 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-3.7-bioc/meat/derfinder.Rcheck/00check.log’
for details.
derfinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL derfinder ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘derfinder’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘IRanges’ for request: ‘subset’ when loading ‘derfinder’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded No methods found in package ‘IRanges’ for request: ‘subset’ when loading ‘derfinder’ * DONE (derfinder)
derfinder.Rcheck/tests/test-all.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
class: SerialParam
bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bptimeout: 2592000; bpprogressbar: FALSE
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
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
215.208 3.260 218.737
derfinder.Rcheck/derfinder-Ex.timings
| name | user | system | elapsed | |
| analyzeChr | 1.596 | 0.020 | 1.618 | |
| annotateRegions | 0.304 | 0.000 | 0.301 | |
| calculatePvalues | 0.596 | 0.024 | 0.622 | |
| calculateStats | 0.224 | 0.000 | 0.224 | |
| coerceGR | 0.052 | 0.004 | 0.058 | |
| collapseFullCoverage | 0.008 | 0.000 | 0.007 | |
| coverageToExon | 3.684 | 0.240 | 3.924 | |
| createBw | 0.132 | 0.000 | 0.133 | |
| createBwSample | 0.04 | 0.00 | 0.04 | |
| define_cluster | 0.000 | 0.004 | 0.005 | |
| derfinder-deprecated | 0.004 | 0.000 | 0.002 | |
| extendedMapSeqlevels | 0.072 | 0.000 | 0.074 | |
| filterData | 0.128 | 0.000 | 0.129 | |
| findRegions | 0.364 | 0.000 | 0.366 | |
| fullCoverage | 0.292 | 0.004 | 0.313 | |
| getRegionCoverage | 0.196 | 0.000 | 0.214 | |
| getTotalMapped | 0.008 | 0.000 | 0.010 | |
| loadCoverage | 0.136 | 0.004 | 0.140 | |
| makeGenomicState | 3.412 | 0.012 | 3.428 | |
| makeModels | 0.02 | 0.00 | 0.02 | |
| mergeResults | 0.316 | 0.000 | 0.317 | |
| preprocessCoverage | 0.236 | 0.000 | 0.234 | |
| railMatrix | 9.772 | 0.204 | 10.122 | |
| rawFiles | 0.004 | 0.000 | 0.003 | |
| regionMatrix | 0.860 | 0.012 | 0.872 | |
| sampleDepth | 0.016 | 0.000 | 0.020 | |