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CHECK report for focalCall on tokay1

This page was generated on 2021-05-06 12:31:21 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the focalCall package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 644/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
focalCall 1.24.0  (landing page)
Oscar Krijgsman
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/focalCall
Branch: RELEASE_3_12
Last Commit: 7d9c40f
Last Changed Date: 2020-10-27 10:59:54 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: focalCall
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:focalCall.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings focalCall_1.24.0.tar.gz
StartedAt: 2021-05-06 02:54:27 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:55:48 -0400 (Thu, 06 May 2021)
EllapsedTime: 81.4 seconds
RetCode: 1
Status:   ERROR   
CheckDir: focalCall.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:focalCall.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings focalCall_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/focalCall.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.24.0'
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'focalCall' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/focalCall.Rcheck/00install.out' for details.
* 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 '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 '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 '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 png points
  segmented write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "axis", "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' ... ERROR
Running examples in 'focalCall-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: singleSample
> ### Title: Detection focal aberrations with 1 sample only
> ### Aliases: singleSample
> 
> ### ** Examples
> 
> 
> # generate object of cghCall class object and input files
> data(BierkensCNA)
> 
> # Extract focal aberrations and distinguish somatic from germ-line copy number aberrations (CNA) in a single sample
> singleSample(CGHset[,1], CNVset, focalSize=3)
Array resolution too low for calling aberrations smaller than 3MB. 
Counted number of segments for tumor sample 
Generated matrix with detected aberrations <3MB. 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'plot.cghCall' for signature '"cghCall"'
Calls: singleSample -> plot -> plot.cghCall -> <Anonymous>
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'focalCall-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: singleSample
> ### Title: Detection focal aberrations with 1 sample only
> ### Aliases: singleSample
> 
> ### ** Examples
> 
> 
> # generate object of cghCall class object and input files
> data(BierkensCNA)
> 
> # Extract focal aberrations and distinguish somatic from germ-line copy number aberrations (CNA) in a single sample
> singleSample(CGHset[,1], CNVset, focalSize=3)
Array resolution too low for calling aberrations smaller than 3MB. 
Counted number of segments for tumor sample 
Generated matrix with detected aberrations <3MB. 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'plot.cghCall' for signature '"cghCall"'
Calls: singleSample -> plot -> plot.cghCall -> <Anonymous>
Execution halted
* 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 ERRORs, 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/focalCall.Rcheck/00check.log'
for details.

Installation output

focalCall.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/focalCall_1.24.0.tar.gz && rm -rf focalCall.buildbin-libdir && mkdir focalCall.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=focalCall.buildbin-libdir focalCall_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL focalCall_1.24.0.zip && rm focalCall_1.24.0.tar.gz focalCall_1.24.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  376k  100  376k    0     0  16.6M      0 --:--:-- --:--:-- --:--:-- 17.4M

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
Warning: Package 'focalCall' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'focalCall' is deprecated and will be removed from Bioconductor
  version 3.13
** 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
Warning: Package 'focalCall' is deprecated and will be removed from Bioconductor
  version 3.13
* MD5 sums
packaged installation of 'focalCall' as focalCall_1.24.0.zip
* DONE (focalCall)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'focalCall' successfully unpacked and MD5 sums checked

Tests output

focalCall.Rcheck/tests_i386/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.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 -- Thu May 06 02:55:39 2021 
*********************************************** 
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 
Warning message:
Package 'focalCall' is deprecated and will be removed from Bioconductor
  version 3.13 
> 
> proc.time()
   user  system elapsed 
   1.17    0.14    1.29

focalCall.Rcheck/tests_x64/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.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 -- Thu May 06 02:55:41 2021 
*********************************************** 
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 
Warning message:
Package 'focalCall' is deprecated and will be removed from Bioconductor
  version 3.13 
> 
> proc.time()
   user  system elapsed 
   1.17    0.07    1.25

Example timings

focalCall.Rcheck/examples_i386/focalCall-Ex.timings

nameusersystemelapsed
BierkensCNA0.430.010.46
FreqPlot0.440.000.44
FreqPlotfocal1.600.051.64
focalCall4.150.024.17
igvFiles2.990.063.05

focalCall.Rcheck/examples_x64/focalCall-Ex.timings

nameusersystemelapsed
BierkensCNA0.280.050.32
FreqPlot0.410.030.44
FreqPlotfocal1.180.031.22
focalCall3.890.063.95
igvFiles2.610.032.64