Gundula Povysil
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/panelcn.mops |
| Branch: RELEASE_3_10 |
| Last Commit: 3f3f728 |
| Last Changed Date: 2019-10-29 13:10:45 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:46:04 -0400 (Wed, 15 Apr 2020).
| Package 1214/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| panelcn.mops 1.8.0 Gundula Povysil
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: panelcn.mops |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:panelcn.mops.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings panelcn.mops_1.8.0.tar.gz |
| StartedAt: 2020-04-15 04:25:33 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:28:21 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 168.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: panelcn.mops.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:panelcn.mops.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings panelcn.mops_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/panelcn.mops.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘panelcn.mops/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘panelcn.mops’ version ‘1.8.0’ * 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 ‘panelcn.mops’ 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: ‘cn.mops:::.cn.mopsC’ 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 * 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-3.10-bioc/meat/panelcn.mops.Rcheck/00check.log’ for details.
panelcn.mops.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL panelcn.mops ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘panelcn.mops’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (panelcn.mops)
panelcn.mops.Rcheck/tests/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
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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
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> BiocGenerics:::testPackage("panelcn.mops")
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
Attaching package: 'cn.mops'
The following object is masked from 'package:S4Vectors':
params
Calculating results for sample(s) SAMPLE1.bam
SAMPLE1.bam
Building table...
SAMPLE1.bam
Finished
naming without chr prefix chosen, but BED contains chr -> removing chr
Analyzing sample(s) SAMPLE1.bam
new sampleThresh 235.95
Cannot use exon PMS2.E2.chr7.6045492.6045693
Cannot use exon CHEK2.E15.chr22.29083854.29084005
Cannot use exon CHEK2.E14.chr22.29085092.29085234
Cannot use exon CHEK2.E13.chr22.29089989.29090136
Analyzing sample SAMPLE1.bam
"corrThresh" is set to 0.99
"maxControls" is set to 25
1
0.997060493255309
0.996941831461954
0.996599322273787
0.995380799421952
0.930827189241917
Low correlation.
Selected 5 out of 5 controls:
SAMPLE4.bam
SAMPLE3.bam
SAMPLE6.bam
SAMPLE2.bam
SAMPLE5.bam
Normalizing...
Removed bad control sample(s) SAMPLE5.bam
Normalizing again...
Remaining samples: SAMPLE1.bam
Remaining samples: SAMPLE4.bam
Remaining samples: SAMPLE3.bam
Remaining samples: SAMPLE6.bam
Remaining samples: SAMPLE2.bam
Low quality exon(s):
7_6012999_6013204
7_6017188_6017419
7_6018196_6018358
17_29422297_29422418
Computing results...
Creating CNVDetectionResult
Finished genepanelcn.mops
RUNIT TEST PROTOCOL -- Wed Apr 15 04:28:15 2020
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
panelcn.mops RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
6.038 0.346 6.495
panelcn.mops.Rcheck/panelcn.mops-Ex.timings
| name | user | system | elapsed | |
| control | 0.150 | 0.008 | 0.281 | |
| countBamListInGRanges | 0.026 | 0.001 | 0.048 | |
| countWindows | 0.050 | 0.015 | 0.113 | |
| createResultTable | 0.266 | 0.022 | 0.508 | |
| getWindows | 0.013 | 0.001 | 0.030 | |
| panelcn.mops | 1.032 | 0.011 | 1.442 | |
| plotBoxplot | 0.159 | 0.003 | 0.164 | |
| read.width | 0.002 | 0.001 | 0.003 | |
| resultlist | 0.054 | 0.003 | 0.057 | |
| runPanelcnMops | 0.924 | 0.005 | 0.935 | |
| splitROIs | 0.161 | 0.006 | 0.167 | |
| test | 0.021 | 0.002 | 0.023 | |