Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:55:54 -0400 (Wed, 16 Oct 2019).
Package 310/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
CNVPanelizer 1.16.0 Thomas Wolf
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: CNVPanelizer |
Version: 1.16.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNVPanelizer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNVPanelizer_1.16.0.tar.gz |
StartedAt: 2019-10-16 01:37:21 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 01:42:43 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 322.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CNVPanelizer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNVPanelizer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNVPanelizer_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CNVPanelizer.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CNVPanelizer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CNVPanelizer’ version ‘1.16.0’ * 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 for sufficient/correct file permissions ... 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 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 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 ... 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 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 or elapsed time > 5s user system elapsed PlotBootstrapDistributions 6.202 0.357 6.566 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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 ‘/Users/biocbuild/bbs-3.9-bioc/meat/CNVPanelizer.Rcheck/00check.log’ for details.
CNVPanelizer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CNVPanelizer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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. > BiocGenerics:::testPackage("CNVPanelizer") Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Calculating Background for s1 Calculating Background for s2 Calculating Background for s3 Calculating Background for s4 Saving plot to '/tmp/RtmpFZ3PfE/s1_plot.pdf' Saving plot to '/tmp/RtmpFZ3PfE/s2_plot.pdf' Saving plot to '/tmp/RtmpFZ3PfE/s3_plot.pdf' Saving plot to '/tmp/RtmpFZ3PfE/s4_plot.pdf' Saving plot to '/tmp/RtmpFZ3PfE/sample1.pdf' Saving plot to '/tmp/RtmpFZ3PfE/sample2.pdf' Saving plot to '/tmp/RtmpFZ3PfE/sample3.pdf' Saving plot to '/tmp/RtmpFZ3PfE/sample4.pdf' Calculating Background for c:/somefile1.bam Saving file to '/tmp/RtmpFZ3PfE/samples.xlsx' Note: zip::zip() is deprecated, please use zip::zipr() instead [1] "GENE 1: 0.166666666666667" [1] "GENE 2: 0.356348322549899" RUNIT TEST PROTOCOL -- Wed Oct 16 01:42:36 2019 *********************************************** 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 69.773 2.435 72.260
CNVPanelizer.Rcheck/CNVPanelizer-Ex.timings
name | user | system | elapsed | |
Background | 0.532 | 0.091 | 0.625 | |
BedToGenomicRanges | 0.000 | 0.000 | 0.001 | |
BootList | 0.155 | 0.015 | 0.170 | |
CNVPanelizerFromReadCounts | 0.000 | 0.000 | 0.001 | |
CNVPanelizerFromReadCountsHelper | 0.001 | 0.001 | 0.001 | |
CollectColumnFromAllReportTables | 0 | 0 | 0 | |
CombinedNormalizedCounts | 0.046 | 0.012 | 0.058 | |
IndexMultipleBams | 0.000 | 0.000 | 0.001 | |
NormalizedCounts | 0.003 | 0.003 | 0.006 | |
PlotBootstrapDistributions | 6.202 | 0.357 | 6.566 | |
ReadCountsFromBam | 0.000 | 0.001 | 0.001 | |
ReadXLSXToList | 0.000 | 0.000 | 0.001 | |
ReportTables | 0.761 | 0.017 | 0.777 | |
RunCNVPanelizerShiny | 0.001 | 0.000 | 0.001 | |
SelectReferenceSetByInterquartileRange | 0.000 | 0.000 | 0.001 | |
SelectReferenceSetByKmeans | 0.000 | 0.000 | 0.001 | |
SelectReferenceSetByPercentil | 0 | 0 | 0 | |
SelectReferenceSetFromReadCounts | 0.001 | 0.001 | 0.001 | |
StatusHeatmap | 0 | 0 | 0 | |
WriteListToXLSX | 0.000 | 0.000 | 0.001 | |