| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-06 12:10 -0500 (Thu, 06 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4769 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4504 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4527 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4480 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4416 |
| 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 550/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| derfinder 1.40.0 (landing page) Leonardo Collado-Torres
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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. |
| Package: derfinder |
| Version: 1.40.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:derfinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings derfinder_1.40.0.tar.gz |
| StartedAt: 2025-03-04 17:28:00 -0500 (Tue, 04 Mar 2025) |
| EndedAt: 2025-03-04 17:39:13 -0500 (Tue, 04 Mar 2025) |
| EllapsedTime: 673.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: derfinder.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:derfinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings derfinder_1.40.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/derfinder.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘derfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘derfinder’ version ‘1.40.0’
* 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 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 10.038 0.657 10.782
coverageToExon 6.125 0.260 6.390
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/derfinder.Rcheck/00check.log’
for details.
derfinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL derfinder ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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
300.433 7.793 309.586
derfinder.Rcheck/derfinder-Ex.timings
| name | user | system | elapsed | |
| analyzeChr | 1.151 | 0.076 | 1.230 | |
| annotateRegions | 0.378 | 0.031 | 0.426 | |
| calculatePvalues | 0.846 | 0.026 | 0.872 | |
| calculateStats | 0.443 | 0.024 | 0.466 | |
| coerceGR | 0.099 | 0.006 | 0.104 | |
| collapseFullCoverage | 0.005 | 0.002 | 0.007 | |
| coverageToExon | 6.125 | 0.260 | 6.390 | |
| createBw | 0.191 | 0.004 | 0.197 | |
| createBwSample | 0.067 | 0.002 | 0.069 | |
| define_cluster | 0.007 | 0.001 | 0.007 | |
| derfinder-deprecated | 0.003 | 0.001 | 0.003 | |
| extendedMapSeqlevels | 0.068 | 0.012 | 0.081 | |
| filterData | 0.177 | 0.008 | 0.187 | |
| findRegions | 0.518 | 0.018 | 0.536 | |
| fullCoverage | 0.280 | 0.025 | 0.305 | |
| getRegionCoverage | 0.384 | 0.043 | 1.134 | |
| getTotalMapped | 0.011 | 0.002 | 0.013 | |
| loadCoverage | 0.181 | 0.017 | 0.199 | |
| makeGenomicState | 3.798 | 0.049 | 3.852 | |
| makeModels | 0.014 | 0.002 | 0.015 | |
| mergeResults | 0.354 | 0.020 | 0.374 | |
| preprocessCoverage | 0.315 | 0.003 | 0.318 | |
| railMatrix | 10.038 | 0.657 | 10.782 | |
| rawFiles | 0.003 | 0.002 | 0.005 | |
| regionMatrix | 1.025 | 0.067 | 1.110 | |
| sampleDepth | 0.011 | 0.001 | 0.013 | |