Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:39 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 |
Package 546/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
derfinder 1.39.0 (landing page) Leonardo Collado-Torres
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the derfinder package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: derfinder |
Version: 1.39.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:derfinder.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings derfinder_1.39.0.tar.gz |
StartedAt: 2024-08-26 22:17:03 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 22:28:09 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 666.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: derfinder.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:derfinder.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings derfinder_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/derfinder.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘derfinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘derfinder’ version ‘1.39.0’ * 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 code 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 loading without being on the library search path ... 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 ... NOTE checkRd: (-1) createBwSample.Rd:59: Lost braces 59 | link{coerceGR} | ^ checkRd: (-1) derfinder-deprecated.Rd:30-31: Lost braces in \itemize; meant \describe ? checkRd: (-1) sampleDepth.Rd:41-47: Lost braces 41 | equal to quantiles of interest. The resulting values are transformed {log2(x | ^ * 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 8.285 0.580 8.886 coverageToExon 4.578 0.484 5.062 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-all.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/derfinder.Rcheck/00check.log’ for details.
derfinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL derfinder ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 3 | SKIP 0 | PASS 137 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 137 ] Warning message: call dbDisconnect() when finished working with a connection > > proc.time() user system elapsed 166.545 5.632 172.491
derfinder.Rcheck/derfinder-Ex.timings
name | user | system | elapsed | |
analyzeChr | 1.028 | 0.064 | 1.091 | |
annotateRegions | 0.306 | 0.044 | 0.350 | |
calculatePvalues | 0.811 | 0.007 | 0.819 | |
calculateStats | 0.404 | 0.016 | 0.420 | |
coerceGR | 0.079 | 0.003 | 0.083 | |
collapseFullCoverage | 0.002 | 0.003 | 0.005 | |
coverageToExon | 4.578 | 0.484 | 5.062 | |
createBw | 0.161 | 0.000 | 0.161 | |
createBwSample | 0.063 | 0.000 | 0.063 | |
define_cluster | 0.005 | 0.000 | 0.005 | |
derfinder-deprecated | 0.002 | 0.000 | 0.002 | |
extendedMapSeqlevels | 0.066 | 0.000 | 0.066 | |
filterData | 0.127 | 0.000 | 0.127 | |
findRegions | 0.481 | 0.008 | 0.489 | |
fullCoverage | 0.257 | 0.005 | 0.261 | |
getRegionCoverage | 0.357 | 0.035 | 0.861 | |
getTotalMapped | 0.009 | 0.000 | 0.009 | |
loadCoverage | 0.206 | 0.020 | 0.226 | |
makeGenomicState | 3.567 | 0.344 | 3.911 | |
makeModels | 0.016 | 0.000 | 0.015 | |
mergeResults | 0.351 | 0.024 | 0.376 | |
preprocessCoverage | 0.320 | 0.028 | 0.348 | |
railMatrix | 8.285 | 0.580 | 8.886 | |
rawFiles | 0.000 | 0.001 | 0.003 | |
regionMatrix | 0.884 | 0.045 | 0.928 | |
sampleDepth | 0.012 | 0.000 | 0.012 | |