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 08:55:01 -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: /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_1.12.0.tar.gz |
| StartedAt: 2018-10-16 20:35:58 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:39:48 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 229.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CNVPanelizer.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/CNVPanelizer.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.12.0’
* 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 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 5.135 0.194 5.367
* 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-3.7-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/3.5/Resources/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-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, 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/RtmpWQjHn3/s1_plot.pdf'
Saving plot to '/tmp/RtmpWQjHn3/s2_plot.pdf'
Saving plot to '/tmp/RtmpWQjHn3/s3_plot.pdf'
Saving plot to '/tmp/RtmpWQjHn3/s4_plot.pdf'
Saving plot to '/tmp/RtmpWQjHn3/sample1.pdf'
Saving plot to '/tmp/RtmpWQjHn3/sample2.pdf'
Saving plot to '/tmp/RtmpWQjHn3/sample3.pdf'
Saving plot to '/tmp/RtmpWQjHn3/sample4.pdf'
Calculating Background for c:/somefile1.bam
Saving file to '/tmp/RtmpWQjHn3/samples.xlsx'
[1] "GENE 1: 0.125"
[1] "GENE 2: 0.330289129537908"
RUNIT TEST PROTOCOL -- Tue Oct 16 20:39:42 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
54.788 0.957 56.181
CNVPanelizer.Rcheck/CNVPanelizer-Ex.timings
| name | user | system | elapsed | |
| Background | 0.412 | 0.028 | 0.444 | |
| BedToGenomicRanges | 0.001 | 0.000 | 0.001 | |
| BootList | 0.136 | 0.006 | 0.143 | |
| CNVPanelizerFromReadCounts | 0.002 | 0.000 | 0.002 | |
| CNVPanelizerFromReadCountsHelper | 0.001 | 0.000 | 0.002 | |
| CollectColumnFromAllReportTables | 0.002 | 0.000 | 0.002 | |
| CombinedNormalizedCounts | 0.038 | 0.008 | 0.045 | |
| IndexMultipleBams | 0.002 | 0.000 | 0.002 | |
| NormalizedCounts | 0.004 | 0.002 | 0.005 | |
| PlotBootstrapDistributions | 5.135 | 0.194 | 5.367 | |
| ReadCountsFromBam | 0.002 | 0.000 | 0.001 | |
| ReadXLSXToList | 0.002 | 0.000 | 0.002 | |
| ReportTables | 0.644 | 0.008 | 0.660 | |
| RunCNVPanelizerShiny | 0.001 | 0.000 | 0.002 | |
| SelectReferenceSetByInterquartileRange | 0.002 | 0.000 | 0.002 | |
| SelectReferenceSetByKmeans | 0.001 | 0.000 | 0.001 | |
| SelectReferenceSetByPercentil | 0.001 | 0.000 | 0.002 | |
| SelectReferenceSetFromReadCounts | 0.001 | 0.000 | 0.002 | |
| StatusHeatmap | 0.001 | 0.000 | 0.001 | |
| WriteListToXLSX | 0.001 | 0.000 | 0.001 | |