Package: focalCall

Version: 1.18.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:focalCall.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings focalCall_1.18.0.tar.gz

StartedAt: 2019-10-16 03:47:21 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:49:07 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 105.3 seconds

RetCode: 0

Status:  OK

CheckDir: focalCall.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:focalCall.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings focalCall_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/focalCall.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'focalCall/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'focalCall' version '1.18.0'
* 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 'focalCall' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.match_CNV2CGH: no visible global function definition for 'bpstart'
.match_CNV2CGH: no visible global function definition for 'chromosomes'
.match_CNV2CGH: no visible global function definition for 'bpend'
FreqPlot: no visible global function definition for 'chromosomes'
FreqPlot: no visible global function definition for 'plot'
FreqPlot: no visible global function definition for 'points'
FreqPlot: no visible global function definition for 'abline'
FreqPlot: no visible global function definition for 'axis'
FreqPlotfocal: no visible global function definition for 'chromosomes'
FreqPlotfocal: no visible global function definition for
  'assayDataElement'
FreqPlotfocal: no visible global function definition for 'fData'
FreqPlotfocal: no visible global function definition for 'plot'
FreqPlotfocal: no visible global function definition for 'points'
FreqPlotfocal: no visible global function definition for 'abline'
FreqPlotfocal: no visible global function definition for 'axis'
focalCall: no visible global function definition for 'calls'
focalCall: no visible global function definition for 'featureNames'
focalCall: no visible global function definition for 'segmented'
focalCall: no visible global function definition for 'chromosomes'
focalCall: no visible global function definition for 'bpstart'
focalCall: no visible global function definition for
  'assayDataElement<-'
focalCall: no visible global function definition for 'assayDataElement'
focalCall: no visible global function definition for 'bpend'
focalCall: no visible global function definition for 'fData'
focalCall: no visible global function definition for 'fData<-'
focalCall: no visible global function definition for 'write.table'
igvFiles: no visible global function definition for 'calls'
igvFiles: no visible global function definition for 'chromosomes'
igvFiles: no visible global function definition for 'bpstart'
igvFiles: no visible global function definition for 'bpend'
igvFiles: no visible global function definition for 'featureNames'
igvFiles: no visible global function definition for 'segmented'
igvFiles: no visible global function definition for 'write.table'
igvFiles: no visible global function definition for 'assayDataElement'
singleSample: no visible global function definition for 'calls'
singleSample: no visible global function definition for 'featureNames'
singleSample: no visible global function definition for 'fData'
singleSample: no visible global function definition for 'fData<-'
singleSample: no visible global function definition for
  'assayDataElement<-'
singleSample: no visible global function definition for 'segmented'
singleSample: no visible global function definition for 'chromosomes'
singleSample: no visible global function definition for 'bpend'
singleSample: no visible global function definition for 'bpstart'
singleSample: no visible global function definition for
  'assayDataElement'
singleSample: no visible global function definition for 'median'
singleSample: no visible global function definition for 'png'
singleSample: no visible global function definition for 'plot'
singleSample: no visible global function definition for 'dev.off'
singleSample: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline assayDataElement assayDataElement<- axis bpend bpstart calls
  chromosomes dev.off fData fData<- featureNames median plot png points
  segmented write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 ...
** 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/focalCall.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/focalCall_1.18.0.tar.gz && rm -rf focalCall.buildbin-libdir && mkdir focalCall.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=focalCall.buildbin-libdir focalCall_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL focalCall_1.18.0.zip && rm focalCall_1.18.0.tar.gz focalCall_1.18.0.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  374k  100  374k    0     0  4898k      0 --:--:-- --:--:-- --:--:-- 5429k

install for i386

* installing *source* package 'focalCall' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'focalCall'
    finding HTML links ... done
    BierkensCNA                             html  
    FreqPlot                                html  
    FreqPlotfocal                           html  
    focalCall                               html  
    igvFiles                                html  
    singleSample                            html  
** 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

install for x64

* installing *source* package 'focalCall' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'focalCall' as focalCall_1.18.0.zip
* DONE (focalCall)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'focalCall' successfully unpacked and MD5 sums checked

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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("focalCall")

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA


Attaching package: 'snow'

The following objects are masked from 'package:BiocGenerics':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, parApply, parCapply,
    parLapply, parRapply, parSapply

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
    parCapply, parLapply, parRapply, parSapply, splitIndices,
    stopCluster


Attaching package: 'CGHcall'

The following object is masked from 'package:BiocGenerics':

    normalize



RUNIT TEST PROTOCOL -- Wed Oct 16 03:48:56 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
focalCall RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.21    0.15    1.37 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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("focalCall")

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA


Attaching package: 'snow'

The following objects are masked from 'package:BiocGenerics':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, parApply, parCapply,
    parLapply, parRapply, parSapply

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
    parCapply, parLapply, parRapply, parSapply, splitIndices,
    stopCluster


Attaching package: 'CGHcall'

The following object is masked from 'package:BiocGenerics':

    normalize



RUNIT TEST PROTOCOL -- Wed Oct 16 03:48:57 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
focalCall RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.21    0.07    1.28