Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
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" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 398/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CNVPanelizer 1.38.0 (landing page) Thomas Wolf
| 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 | |||||||||
To the developers/maintainers of the CNVPanelizer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNVPanelizer.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: CNVPanelizer |
Version: 1.38.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNVPanelizer.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CNVPanelizer_1.38.0.tar.gz |
StartedAt: 2024-12-20 00:12:31 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 00:16:09 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 217.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CNVPanelizer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNVPanelizer.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CNVPanelizer_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/CNVPanelizer.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'CNVPanelizer/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CNVPanelizer' version '1.38.0' * 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 'CNVPanelizer' 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 Namespace in Imports field not imported from: 'S4Vectors' All declared Imports should be used. Unexported object imported by a ':::' call: 'utils:::format.object_size' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE countBamInGRanges: no visible global function definition for 'strand<-' Undefined global functions or variables: strand<- * 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 data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed PlotBootstrapDistributions 5.1 0.1 5.2 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'runTests.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 'F:/biocbuild/bbs-3.20-bioc/meat/CNVPanelizer.Rcheck/00check.log' for details.
CNVPanelizer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL CNVPanelizer ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'CNVPanelizer' ... ** using staged installation ** R ** data ** 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 (CNVPanelizer)
CNVPanelizer.Rcheck/tests/runTests.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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. > BiocGenerics:::testPackage("CNVPanelizer") Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Calculating Background for s1 Calculating Background for s2 Calculating Background for s3 Calculating Background for s4 Saving plot to 'F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp2HLRTG/s1_plot.pdf' Saving plot to 'F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp2HLRTG/s2_plot.pdf' Saving plot to 'F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp2HLRTG/s3_plot.pdf' Saving plot to 'F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp2HLRTG/s4_plot.pdf' Saving plot to 'F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp2HLRTG/sample1.pdf' Saving plot to 'F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp2HLRTG/sample2.pdf' Saving plot to 'F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp2HLRTG/sample3.pdf' Saving plot to 'F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp2HLRTG/sample4.pdf' Calculating Background for c:/somefile1.bam Saving file to 'F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp2HLRTG/samples.xlsx' [1] "GENE 1: 0.166666666666667" [1] "GENE 2: 0.356348322549899" RUNIT TEST PROTOCOL -- Fri Dec 20 00:15:58 2024 *********************************************** Number of test functions: 9 Number of errors: 0 Number of failures: 0 1 Test Suite : CNVPanelizer RUnit Tests - 9 test functions, 0 errors, 0 failures Number of test functions: 9 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 43.26 1.51 45.64
CNVPanelizer.Rcheck/CNVPanelizer-Ex.timings
name | user | system | elapsed | |
Background | 0.23 | 0.05 | 0.28 | |
BedToGenomicRanges | 0 | 0 | 0 | |
BootList | 0.12 | 0.02 | 0.14 | |
CNVPanelizerFromReadCounts | 0 | 0 | 0 | |
CNVPanelizerFromReadCountsHelper | 0.02 | 0.00 | 0.01 | |
CollectColumnFromAllReportTables | 0 | 0 | 0 | |
CombinedNormalizedCounts | 0.05 | 0.01 | 0.07 | |
IndexMultipleBams | 0 | 0 | 0 | |
NormalizedCounts | 0.01 | 0.00 | 0.01 | |
PlotBootstrapDistributions | 5.1 | 0.1 | 5.2 | |
ReadCountsFromBam | 0 | 0 | 0 | |
ReadXLSXToList | 0 | 0 | 0 | |
ReportTables | 0.47 | 0.04 | 0.52 | |
RunCNVPanelizerShiny | 0 | 0 | 0 | |
SelectReferenceSetByInterquartileRange | 0 | 0 | 0 | |
SelectReferenceSetByKmeans | 0 | 0 | 0 | |
SelectReferenceSetByPercentil | 0 | 0 | 0 | |
SelectReferenceSetFromReadCounts | 0 | 0 | 0 | |
StatusHeatmap | 0 | 0 | 0 | |
WriteListToXLSX | 0 | 0 | 0 | |