Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-02-22 12:48:05 -0500 (Thu, 22 Feb 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4657 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4397 |
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 533/2244 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
deltaCaptureC 1.17.0 (landing page) Michael Shapiro
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the deltaCaptureC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/deltaCaptureC.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: deltaCaptureC |
Version: 1.17.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:deltaCaptureC.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings deltaCaptureC_1.17.0.tar.gz |
StartedAt: 2024-02-21 22:12:46 -0500 (Wed, 21 Feb 2024) |
EndedAt: 2024-02-21 22:18:45 -0500 (Wed, 21 Feb 2024) |
EllapsedTime: 358.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: deltaCaptureC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:deltaCaptureC.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings deltaCaptureC_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/deltaCaptureC.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘deltaCaptureC/DESCRIPTION’ ... OK * this is package ‘deltaCaptureC’ version ‘1.17.0’ * 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 ‘deltaCaptureC’ 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘tictoc’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE getDeltaSE: warning in SummarizedExperiment(assay = list(delta = delta), colData = colData): partial argument match of 'assay' to 'assays' plotSignificantRegions: no visible binding for global variable ‘ctr’ plotSignificantRegions: no visible binding for global variable ‘delta’ plotSignificantRegions: no visible binding for global variable ‘significance’ Undefined global functions or variables: ctr delta significance * 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 binSummarizedExperiment 75.598 0.515 76.117 getOverlapWeights 12.173 0.039 12.214 * 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-3.19-bioc/meat/deltaCaptureC.Rcheck/00check.log’ for details.
deltaCaptureC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL deltaCaptureC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘deltaCaptureC’ ... ** 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 (deltaCaptureC)
deltaCaptureC.Rcheck/deltaCaptureC-Ex.timings
name | user | system | elapsed | |
binSummarizedExperiment | 75.598 | 0.515 | 76.117 | |
downshiftDFtoMatrix | 0.002 | 0.000 | 0.002 | |
generatePermutation | 0.017 | 0.000 | 0.016 | |
getDeltaSE | 0.258 | 0.000 | 0.259 | |
getLopsidedness | 0.064 | 0.000 | 0.064 | |
getMeanNormalizedCountsSE | 0.142 | 0.000 | 0.141 | |
getNormalizedCountsSE | 0.12 | 0.00 | 0.12 | |
getOverlapWeights | 12.173 | 0.039 | 12.214 | |
getPValueCutoff | 0.001 | 0.000 | 0.001 | |
getRunTotals | 0.091 | 0.004 | 0.096 | |
getSizeFactorsDF | 0.002 | 0.000 | 0.002 | |
getSizeFactorsSE | 0.015 | 0.000 | 0.014 | |
plotSignificantRegions | 0.059 | 0.000 | 0.058 | |
rebinToMultiple | 0.471 | 0.000 | 0.471 | |