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CHECK report for panelcn.mops on malbec2

This page was generated on 2019-10-16 12:12:06 -0400 (Wed, 16 Oct 2019).

Package 1164/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
panelcn.mops 1.6.1
Gundula Povysil
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/panelcn.mops
Branch: RELEASE_3_9
Last Commit: b3dcdbe
Last Changed Date: 2019-10-13 19:35:37 -0400 (Sun, 13 Oct 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: panelcn.mops
Version: 1.6.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:panelcn.mops.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings panelcn.mops_1.6.1.tar.gz
StartedAt: 2019-10-16 03:45:11 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:47:38 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 146.7 seconds
RetCode: 0
Status:  OK 
CheckDir: panelcn.mops.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:panelcn.mops.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings panelcn.mops_1.6.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/panelcn.mops.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.1’
* 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 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-3.9-bioc/meat/panelcn.mops.Rcheck/00check.log’
for details.



Installation output

panelcn.mops.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL panelcn.mops
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

Tests output

panelcn.mops.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-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("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 Oct 16 03:47:33 2019 
*********************************************** 
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 
  6.448   0.208   6.719 

Example timings

panelcn.mops.Rcheck/panelcn.mops-Ex.timings

nameusersystemelapsed
control0.0730.0040.077
countBamListInGRanges0.0200.0000.216
countWindows0.0210.0080.030
createResultTable0.1650.0000.165
getWindows0.0080.0040.012
panelcn.mops0.7110.0120.742
plotBoxplot0.0540.0000.055
read.width0.0020.0000.001
resultlist0.0300.0040.034
runPanelcnMops0.7850.0000.788
splitROIs0.1660.0040.170
test0.0130.0000.013