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CHECK report for panelcn.mops on tokay1

This page was generated on 2018-04-12 13:30:31 -0400 (Thu, 12 Apr 2018).

Package 994/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
panelcn.mops 1.0.0
Gundula Povysil
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/panelcn.mops
Branch: RELEASE_3_6
Last Commit: 465858b
Last Changed Date: 2017-10-30 12:41:53 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: panelcn.mops
Version: 1.0.0
Command: rm -rf panelcn.mops.buildbin-libdir panelcn.mops.Rcheck && mkdir panelcn.mops.buildbin-libdir panelcn.mops.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=panelcn.mops.buildbin-libdir panelcn.mops_1.0.0.tar.gz >panelcn.mops.Rcheck\00install.out 2>&1 && cp panelcn.mops.Rcheck\00install.out panelcn.mops-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=panelcn.mops.buildbin-libdir --install="check:panelcn.mops-install.out" --force-multiarch --no-vignettes --timings panelcn.mops_1.0.0.tar.gz
StartedAt: 2018-04-12 01:59:20 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:02:21 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 181.3 seconds
RetCode: 0
Status:  OK  
CheckDir: panelcn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf panelcn.mops.buildbin-libdir panelcn.mops.Rcheck && mkdir panelcn.mops.buildbin-libdir panelcn.mops.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=panelcn.mops.buildbin-libdir panelcn.mops_1.0.0.tar.gz >panelcn.mops.Rcheck\00install.out 2>&1 && cp panelcn.mops.Rcheck\00install.out panelcn.mops-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=panelcn.mops.buildbin-libdir --install="check:panelcn.mops-install.out" --force-multiarch --no-vignettes --timings panelcn.mops_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/panelcn.mops.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'panelcn.mops/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'panelcn.mops' version '1.0.0'
* 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 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/panelcn.mops.Rcheck/00check.log'
for details.



Installation output

panelcn.mops.Rcheck/00install.out


install for i386

* installing *source* package 'panelcn.mops' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'panelcn.mops'
    finding HTML links ... done
    control                                 html  
    countBamListInGRanges                   html  
    countWindows                            html  
    createResultTable                       html  
    getWindows                              html  
    panelcn.mops                            html  
    plotBoxplot                             html  
    read.width                              html  
    resultlist                              html  
    runPanelcnMops                          html  
    splitROIs                               html  
    test                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'panelcn.mops' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'panelcn.mops' as panelcn.mops_1.0.0.zip
* DONE (panelcn.mops)
In R CMD INSTALL
In R CMD INSTALL

Tests output

panelcn.mops.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, cbind, colMeans, colSums, colnames, 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


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

"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 -- Thu Apr 12 02:02:07 2018 
*********************************************** 
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 
   5.85    0.20    6.04 

panelcn.mops.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, cbind, colMeans, colSums, colnames, 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


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

"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 -- Thu Apr 12 02:02:14 2018 
*********************************************** 
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 
   6.50    0.10    6.59 

Example timings

panelcn.mops.Rcheck/examples_i386/panelcn.mops-Ex.timings

nameusersystemelapsed
control0.290.000.30
countBamListInGRanges0.030.000.03
countWindows0.030.000.04
createResultTable0.440.040.46
getWindows0.060.000.07
panelcn.mops2.000.002.54
plotBoxplot0.050.000.05
read.width000
resultlist0.080.000.08
runPanelcnMops0.980.000.98
splitROIs0.200.010.22
test0.020.000.02

panelcn.mops.Rcheck/examples_x64/panelcn.mops-Ex.timings

nameusersystemelapsed
control0.450.000.46
countBamListInGRanges0.010.000.01
countWindows000
createResultTable0.190.000.19
getWindows0.010.000.02
panelcn.mops1.410.011.56
plotBoxplot0.050.000.05
read.width000
resultlist0.110.000.11
runPanelcnMops1.090.001.09
splitROIs0.170.000.17
test000