Back to Multiple platform build/check report for BioC 3.7 |
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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 | |