| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-10-19 13:21:23 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 510/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| derfinder 1.30.0 (landing page) Leonardo Collado-Torres
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: derfinder |
| Version: 1.30.0 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:derfinder.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings derfinder_1.30.0.tar.gz |
| StartedAt: 2022-10-18 23:36:36 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 23:45:29 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 533.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: derfinder.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:derfinder.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings derfinder_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/derfinder.Rcheck' * using R version 4.2.1 (2022-06-23 ucrt) * using platform: x86_64-w64-mingw32 (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 '1.30.0' * 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 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 * 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 'F:/biocbuild/bbs-3.15-bioc/meat/derfinder.Rcheck/00check.log' for details.
derfinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL derfinder ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.15-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 version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 115 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
181.53 5.60 194.82
derfinder.Rcheck/derfinder-Ex.timings
| name | user | system | elapsed | |
| analyzeChr | 1.36 | 0.11 | 1.47 | |
| annotateRegions | 0.30 | 0.07 | 0.36 | |
| calculatePvalues | 1.03 | 0.04 | 1.07 | |
| calculateStats | 0.69 | 0.02 | 0.71 | |
| coerceGR | 0.07 | 0.00 | 0.08 | |
| collapseFullCoverage | 0 | 0 | 0 | |
| coverageToExon | 4.85 | 0.04 | 4.89 | |
| createBw | 0.15 | 0.00 | 0.16 | |
| createBwSample | 0.07 | 0.00 | 0.06 | |
| define_cluster | 0 | 0 | 0 | |
| derfinder-deprecated | 0 | 0 | 0 | |
| extendedMapSeqlevels | 0.11 | 0.02 | 0.13 | |
| filterData | 0.17 | 0.01 | 0.18 | |
| findRegions | 0.61 | 0.03 | 0.64 | |
| fullCoverage | 0.26 | 0.00 | 0.28 | |
| getRegionCoverage | 0.39 | 0.05 | 0.83 | |
| getTotalMapped | 0.00 | 0.00 | 0.02 | |
| loadCoverage | 0.13 | 0.03 | 0.15 | |
| makeGenomicState | 3.75 | 0.09 | 3.93 | |
| makeModels | 0.01 | 0.00 | 0.01 | |
| mergeResults | 0.41 | 0.07 | 0.55 | |
| preprocessCoverage | 0.48 | 0.01 | 0.50 | |
| railMatrix | 0 | 0 | 0 | |
| rawFiles | 0 | 0 | 0 | |
| regionMatrix | 0.95 | 0.13 | 1.08 | |
| sampleDepth | 0.02 | 0.00 | 0.02 | |