Thomas Wolf
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/CNVPanelizer |
| Branch: RELEASE_3_7 |
| Last Commit: e941efc |
| Last Changed Date: 2018-04-30 10:35:37 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:27:46 -0400 (Wed, 17 Oct 2018).
| Package 279/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CNVPanelizer 1.12.0 Thomas Wolf
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: CNVPanelizer |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CNVPanelizer.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CNVPanelizer_1.12.0.tar.gz |
| StartedAt: 2018-10-15 23:22:52 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 23:25:22 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 150.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CNVPanelizer.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CNVPanelizer.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CNVPanelizer_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/CNVPanelizer.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-pc-linux-gnu (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 ‘1.12.0’ * 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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 ‘/home/biocbuild/bbs-3.7-bioc/meat/CNVPanelizer.Rcheck/00check.log’ for details.
CNVPanelizer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL CNVPanelizer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘CNVPanelizer’ ... ** 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 * DONE (CNVPanelizer)
CNVPanelizer.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, 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/RtmpxC5osY/s1_plot.pdf'
Saving plot to '/tmp/RtmpxC5osY/s2_plot.pdf'
Saving plot to '/tmp/RtmpxC5osY/s3_plot.pdf'
Saving plot to '/tmp/RtmpxC5osY/s4_plot.pdf'
Saving plot to '/tmp/RtmpxC5osY/sample1.pdf'
Saving plot to '/tmp/RtmpxC5osY/sample2.pdf'
Saving plot to '/tmp/RtmpxC5osY/sample3.pdf'
Saving plot to '/tmp/RtmpxC5osY/sample4.pdf'
Calculating Background for c:/somefile1.bam
Saving file to '/tmp/RtmpxC5osY/samples.xlsx'
[1] "GENE 1: 0.125"
[1] "GENE 2: 0.330289129537908"
RUNIT TEST PROTOCOL -- Mon Oct 15 23:25:20 2018
***********************************************
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
36.324 0.248 36.659
CNVPanelizer.Rcheck/CNVPanelizer-Ex.timings
| name | user | system | elapsed | |
| Background | 0.228 | 0.016 | 0.243 | |
| BedToGenomicRanges | 0 | 0 | 0 | |
| BootList | 0.072 | 0.000 | 0.075 | |
| CNVPanelizerFromReadCounts | 0 | 0 | 0 | |
| CNVPanelizerFromReadCountsHelper | 0 | 0 | 0 | |
| CollectColumnFromAllReportTables | 0 | 0 | 0 | |
| CombinedNormalizedCounts | 0.016 | 0.000 | 0.016 | |
| IndexMultipleBams | 0.000 | 0.000 | 0.001 | |
| NormalizedCounts | 0.004 | 0.000 | 0.002 | |
| PlotBootstrapDistributions | 3.176 | 0.048 | 3.226 | |
| ReadCountsFromBam | 0.004 | 0.000 | 0.001 | |
| ReadXLSXToList | 0 | 0 | 0 | |
| ReportTables | 0.348 | 0.000 | 0.346 | |
| RunCNVPanelizerShiny | 0.000 | 0.000 | 0.001 | |
| SelectReferenceSetByInterquartileRange | 0 | 0 | 0 | |
| SelectReferenceSetByKmeans | 0 | 0 | 0 | |
| SelectReferenceSetByPercentil | 0.000 | 0.000 | 0.001 | |
| SelectReferenceSetFromReadCounts | 0.000 | 0.000 | 0.001 | |
| StatusHeatmap | 0 | 0 | 0 | |
| WriteListToXLSX | 0 | 0 | 0 | |