Thomas Wolf
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/CNVPanelizer |
| Branch: master |
| Last Commit: 75c8f1a |
| Last Changed Date: 2019-10-29 13:39:34 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:42:43 -0500 (Thu, 16 Jan 2020).
| Package 326/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CNVPanelizer 1.19.0 Thomas Wolf
| malbec2 | Linux (Ubuntu 18.04.3 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: 1.19.0 |
| 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_1.19.0.tar.gz |
| StartedAt: 2020-01-16 03:04:35 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 03:10:24 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 349.5 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CNVPanelizer.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.19.0’
* 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 (user + system) or elapsed time > 5s
user system elapsed
PlotBootstrapDistributions 6.184 0.342 6.532
* 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-3.11-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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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/RtmpmEvSWp/s1_plot.pdf'
Saving plot to '/tmp/RtmpmEvSWp/s2_plot.pdf'
Saving plot to '/tmp/RtmpmEvSWp/s3_plot.pdf'
Saving plot to '/tmp/RtmpmEvSWp/s4_plot.pdf'
Saving plot to '/tmp/RtmpmEvSWp/sample1.pdf'
Saving plot to '/tmp/RtmpmEvSWp/sample2.pdf'
Saving plot to '/tmp/RtmpmEvSWp/sample3.pdf'
Saving plot to '/tmp/RtmpmEvSWp/sample4.pdf'
Calculating Background for c:/somefile1.bam
Saving file to '/tmp/RtmpmEvSWp/samples.xlsx'
[1] "GENE 1: 0.166666666666667"
[1] "GENE 2: 0.356348322549899"
RUNIT TEST PROTOCOL -- Thu Jan 16 03:10:16 2020
***********************************************
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
71.827 2.411 74.588
CNVPanelizer.Rcheck/CNVPanelizer-Ex.timings
| name | user | system | elapsed | |
| Background | 0.462 | 0.034 | 0.847 | |
| BedToGenomicRanges | 0 | 0 | 0 | |
| BootList | 0.176 | 0.015 | 0.190 | |
| CNVPanelizerFromReadCounts | 0.000 | 0.001 | 0.001 | |
| CNVPanelizerFromReadCountsHelper | 0.000 | 0.001 | 0.001 | |
| CollectColumnFromAllReportTables | 0 | 0 | 0 | |
| CombinedNormalizedCounts | 0.046 | 0.008 | 0.054 | |
| IndexMultipleBams | 0.001 | 0.000 | 0.001 | |
| NormalizedCounts | 0.005 | 0.003 | 0.008 | |
| PlotBootstrapDistributions | 6.184 | 0.342 | 6.532 | |
| ReadCountsFromBam | 0.000 | 0.000 | 0.001 | |
| ReadXLSXToList | 0.000 | 0.001 | 0.000 | |
| ReportTables | 0.711 | 0.027 | 0.738 | |
| RunCNVPanelizerShiny | 0.000 | 0.000 | 0.001 | |
| SelectReferenceSetByInterquartileRange | 0.000 | 0.001 | 0.000 | |
| SelectReferenceSetByKmeans | 0 | 0 | 0 | |
| SelectReferenceSetByPercentil | 0.000 | 0.001 | 0.001 | |
| SelectReferenceSetFromReadCounts | 0.001 | 0.000 | 0.000 | |
| StatusHeatmap | 0.001 | 0.001 | 0.000 | |
| WriteListToXLSX | 0 | 0 | 0 | |