Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:39 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the derfinder package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/derfinder.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 510/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
derfinder 1.33.0 (landing page) Leonardo Collado-Torres
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: derfinder |
Version: 1.33.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:derfinder.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings derfinder_1.33.0.tar.gz |
StartedAt: 2023-02-28 01:41:49 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 01:58:39 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 1010.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: derfinder.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:derfinder.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings derfinder_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/derfinder.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘derfinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘derfinder’ version ‘1.33.0’ * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed railMatrix 11.999 0.303 12.365 coverageToExon 6.109 0.432 6.541 makeGenomicState 5.340 0.032 5.374 * 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 ... ‘derfinder-quickstart.Rmd’ using ‘UTF-8’... OK ‘derfinder-users-guide.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/derfinder.Rcheck/00check.log’ for details.
derfinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL derfinder ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 class: SerialParam bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE bpfallback: FALSE 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: NA; bpprogressbar: FALSE bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE bpfallback: FALSE bplogdir: NA bpresultdir: NA class: SerialParam bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE bpfallback: FALSE bplogdir: NA bpresultdir: NA class: SerialParam bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE bpfallback: FALSE bplogdir: NA bpresultdir: NA class: SerialParam bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE bpfallback: FALSE bplogdir: NA bpresultdir: NA class: SerialParam bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE bpfallback: FALSE bplogdir: NA bpresultdir: NA class: SerialParam bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE bpfallback: FALSE bplogdir: NA bpresultdir: NA class: SerialParam bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE bpfallback: FALSE bplogdir: NA bpresultdir: NA [ FAIL 0 | WARN 0 | SKIP 0 | PASS 137 ] Warning message: call dbDisconnect() when finished working with a connection > > proc.time() user system elapsed 319.942 7.481 327.859
derfinder.Rcheck/derfinder-Ex.timings
name | user | system | elapsed | |
analyzeChr | 1.797 | 0.072 | 1.870 | |
annotateRegions | 0.427 | 0.024 | 0.451 | |
calculatePvalues | 1.593 | 0.028 | 1.620 | |
calculateStats | 1.943 | 0.076 | 2.019 | |
coerceGR | 0.105 | 0.000 | 0.107 | |
collapseFullCoverage | 0.008 | 0.000 | 0.008 | |
coverageToExon | 6.109 | 0.432 | 6.541 | |
createBw | 0.245 | 0.000 | 0.245 | |
createBwSample | 0.088 | 0.000 | 0.088 | |
define_cluster | 0.008 | 0.000 | 0.008 | |
derfinder-deprecated | 0.000 | 0.002 | 0.003 | |
extendedMapSeqlevels | 0.094 | 0.005 | 0.099 | |
filterData | 0.170 | 0.004 | 0.175 | |
findRegions | 0.962 | 0.028 | 0.990 | |
fullCoverage | 0.362 | 0.008 | 0.372 | |
getRegionCoverage | 0.395 | 0.008 | 1.231 | |
getTotalMapped | 0.011 | 0.000 | 0.013 | |
loadCoverage | 0.221 | 0.004 | 0.224 | |
makeGenomicState | 5.340 | 0.032 | 5.374 | |
makeModels | 0.022 | 0.000 | 0.022 | |
mergeResults | 0.518 | 0.008 | 0.528 | |
preprocessCoverage | 0.723 | 0.012 | 0.735 | |
railMatrix | 11.999 | 0.303 | 12.365 | |
rawFiles | 0.002 | 0.000 | 0.002 | |
regionMatrix | 1.252 | 0.012 | 1.263 | |
sampleDepth | 0.019 | 0.000 | 0.019 | |