Leonardo Collado-Torres
| Snapshot Date: 2025-10-22 13:45 -0400 (Wed, 22 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/derfinder |
| git_branch: devel |
| git_last_commit: 6a63646 |
| git_last_commit_date: 2025-07-25 18:41:35 -0400 (Fri, 25 Jul 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-23 12:07 -0400 (Thu, 23 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4894 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4684 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4629 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 567/2355 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| derfinder 1.43.1 (landing page) Leonardo Collado-Torres
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: derfinder |
| Version: 1.43.1 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:derfinder.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings derfinder_1.43.1.tar.gz |
| StartedAt: 2025-10-21 07:24:31 -0000 (Tue, 21 Oct 2025) |
| EndedAt: 2025-10-21 07:36:37 -0000 (Tue, 21 Oct 2025) |
| EllapsedTime: 725.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: derfinder.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:derfinder.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings derfinder_1.43.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/derfinder.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘derfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘derfinder’ version ‘1.43.1’
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'analyzeChr.Rd':
‘[TxDb.Hsapiens.UCSC.hg19.knownGene:package]{TxDb.Hsapiens.UCSC.hg19.knownGene}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 10.113 0.175 10.387
makeGenomicState 5.380 0.027 5.429
coverageToExon 4.976 0.088 5.078
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/derfinder.Rcheck/00check.log’
for details.
derfinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL derfinder ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘derfinder’ ... ** this is package ‘derfinder’ version ‘1.43.1’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 9 | SKIP 0 | PASS 137 ]
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 137 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
316.405 3.308 320.625
derfinder.Rcheck/derfinder-Ex.timings
| name | user | system | elapsed | |
| analyzeChr | 1.583 | 0.119 | 1.708 | |
| annotateRegions | 0.446 | 0.004 | 0.452 | |
| calculatePvalues | 1.267 | 0.036 | 1.307 | |
| calculateStats | 0.641 | 0.036 | 0.679 | |
| coerceGR | 0.108 | 0.000 | 0.109 | |
| collapseFullCoverage | 0.003 | 0.004 | 0.008 | |
| coverageToExon | 4.976 | 0.088 | 5.078 | |
| createBw | 0.239 | 0.008 | 0.247 | |
| createBwSample | 0.09 | 0.00 | 0.09 | |
| define_cluster | 0.008 | 0.000 | 0.008 | |
| derfinder-deprecated | 0.002 | 0.000 | 0.003 | |
| extendedMapSeqlevels | 0.089 | 0.008 | 0.097 | |
| filterData | 0.193 | 0.008 | 0.201 | |
| findRegions | 0.724 | 0.000 | 0.726 | |
| fullCoverage | 0.330 | 0.008 | 0.342 | |
| getRegionCoverage | 0.413 | 0.004 | 0.419 | |
| getTotalMapped | 0.010 | 0.000 | 0.012 | |
| loadCoverage | 0.202 | 0.004 | 0.206 | |
| makeGenomicState | 5.380 | 0.027 | 5.429 | |
| makeModels | 0.020 | 0.000 | 0.021 | |
| mergeResults | 0.485 | 0.008 | 0.497 | |
| preprocessCoverage | 0.503 | 0.000 | 0.505 | |
| railMatrix | 10.113 | 0.175 | 10.387 | |
| rawFiles | 0.003 | 0.000 | 0.003 | |
| regionMatrix | 1.275 | 0.016 | 1.296 | |
| sampleDepth | 0.021 | 0.000 | 0.021 | |