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This page was generated on 2021-09-20 15:05:09 -0400 (Mon, 20 Sep 2021).

CHECK results for CNVPanelizer on tokay2

To the developers/maintainers of the CNVPanelizer package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNVPanelizer.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 352/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVPanelizer 1.24.0  (landing page)
Thomas Wolf
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/CNVPanelizer
git_branch: RELEASE_3_13
git_last_commit: b0dc959
git_last_commit_date: 2021-05-19 12:14:20 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CNVPanelizer
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVPanelizer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CNVPanelizer_1.24.0.tar.gz
StartedAt: 2021-09-19 20:40:51 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 20:45:34 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 283.1 seconds
RetCode: 0
Status:   OK  
CheckDir: CNVPanelizer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVPanelizer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CNVPanelizer_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CNVPanelizer.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNVPanelizer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNVPanelizer' 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 'CNVPanelizer' 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
* 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 ... NOTE
Namespace in Imports field not imported from: 'S4Vectors'
  All declared Imports should be used.
Unexported object imported by a ':::' call: 'utils:::format.object_size'
  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 ...
** 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-3.13-bioc/meat/CNVPanelizer.Rcheck/00check.log'
for details.



Installation output

CNVPanelizer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CNVPanelizer_1.24.0.tar.gz && rm -rf CNVPanelizer.buildbin-libdir && mkdir CNVPanelizer.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNVPanelizer.buildbin-libdir CNVPanelizer_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CNVPanelizer_1.24.0.zip && rm CNVPanelizer_1.24.0.tar.gz CNVPanelizer_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 87124  100 87124    0     0   172k      0 --:--:-- --:--:-- --:--:--  172k
100 87124  100 87124    0     0   172k      0 --:--:-- --:--:-- --:--:--  172k

install for i386

* installing *source* package 'CNVPanelizer' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CNVPanelizer'
    finding HTML links ... done
    Background                              html  
    BedToGenomicRanges                      html  
    BootList                                html  
    CNVPanelizer-package                    html  
    CNVPanelizerFromReadCounts              html  
    CNVPanelizerFromReadCountsHelper        html  
    CollectColumnFromAllReportTables        html  
    CombinedNormalizedCounts                html  
    IndexMultipleBams                       html  
    NormalizedCounts                        html  
    PlotBootstrapDistributions              html  
    ReadCountsFromBam                       html  
    ReadXLSXToList                          html  
    ReportTables                            html  
    RunCNVPanelizerShiny                    html  
    SelectReferenceSetByInterquartileRange
                                            html  
    SelectReferenceSetByKmeans              html  
    SelectReferenceSetByPercentil           html  
    SelectReferenceSetFromReadCounts        html  
    StatusHeatmap                           html  
    WriteListToXLSX                         html  
    referenceReadCounts                     html  
    sampleReadCounts                        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 'CNVPanelizer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNVPanelizer' as CNVPanelizer_1.24.0.zip
* DONE (CNVPanelizer)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CNVPanelizer' successfully unpacked and MD5 sums checked

Tests output

CNVPanelizer.Rcheck/tests_i386/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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("CNVPanelizer")

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


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows

Calculating Background for s1
Calculating Background for s2
Calculating Background for s3
Calculating Background for s4
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpKsRxtF/s1_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpKsRxtF/s2_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpKsRxtF/s3_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpKsRxtF/s4_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpKsRxtF/sample1.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpKsRxtF/sample2.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpKsRxtF/sample3.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpKsRxtF/sample4.pdf'
Calculating Background for c:/somefile1.bam
Saving file to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpKsRxtF/samples.xlsx'
[1] "GENE 1:  0.166666666666667"
[1] "GENE 2:  0.356348322549899"


RUNIT TEST PROTOCOL -- Sun Sep 19 20:44:42 2021 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CNVPanelizer RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  35.43    1.01   36.73 

CNVPanelizer.Rcheck/tests_x64/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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("CNVPanelizer")

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


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows

Calculating Background for s1
Calculating Background for s2
Calculating Background for s3
Calculating Background for s4
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpUPDZcD/s1_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpUPDZcD/s2_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpUPDZcD/s3_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpUPDZcD/s4_plot.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpUPDZcD/sample1.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpUPDZcD/sample2.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpUPDZcD/sample3.pdf'
Saving plot to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpUPDZcD/sample4.pdf'
Calculating Background for c:/somefile1.bam
Saving file to 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpUPDZcD/samples.xlsx'
[1] "GENE 1:  0.166666666666667"
[1] "GENE 2:  0.356348322549899"


RUNIT TEST PROTOCOL -- Sun Sep 19 20:45:26 2021 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CNVPanelizer RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  42.46    0.48   42.96 

Example timings

CNVPanelizer.Rcheck/examples_i386/CNVPanelizer-Ex.timings

nameusersystemelapsed
Background0.220.000.22
BedToGenomicRanges000
BootList0.090.020.11
CNVPanelizerFromReadCounts000
CNVPanelizerFromReadCountsHelper000
CollectColumnFromAllReportTables000
CombinedNormalizedCounts0.050.000.04
IndexMultipleBams000
NormalizedCounts0.020.000.02
PlotBootstrapDistributions3.350.093.45
ReadCountsFromBam000
ReadXLSXToList000
ReportTables0.320.000.31
RunCNVPanelizerShiny000
SelectReferenceSetByInterquartileRange000
SelectReferenceSetByKmeans000
SelectReferenceSetByPercentil000
SelectReferenceSetFromReadCounts000
StatusHeatmap000
WriteListToXLSX000

CNVPanelizer.Rcheck/examples_x64/CNVPanelizer-Ex.timings

nameusersystemelapsed
Background0.180.060.24
BedToGenomicRanges000
BootList0.090.000.10
CNVPanelizerFromReadCounts000
CNVPanelizerFromReadCountsHelper000
CollectColumnFromAllReportTables000
CombinedNormalizedCounts0.030.000.03
IndexMultipleBams000
NormalizedCounts000
PlotBootstrapDistributions3.740.043.78
ReadCountsFromBam000
ReadXLSXToList000
ReportTables0.390.020.40
RunCNVPanelizerShiny000
SelectReferenceSetByInterquartileRange000
SelectReferenceSetByKmeans000
SelectReferenceSetByPercentil000
SelectReferenceSetFromReadCounts000
StatusHeatmap000
WriteListToXLSX000