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CHECK report for genoset on tokay2

This page was generated on 2019-10-16 12:25:00 -0400 (Wed, 16 Oct 2019).

Package 663/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoset 1.40.0
Peter M. Haverty
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/genoset
Branch: RELEASE_3_9
Last Commit: 102035f
Last Changed Date: 2019-05-02 11:53:24 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: genoset
Version: 1.40.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genoset.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings genoset_1.40.0.tar.gz
StartedAt: 2019-10-16 03:59:33 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:04:17 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 284.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: genoset.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genoset.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings genoset_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/genoset.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 'genoset/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genoset' version '1.40.0'
* package encoding: UTF-8
* 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 'genoset' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .Call("RleViews_viewMaxs", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewMeans", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewMins", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewSums", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewWhichMaxs", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewWhichMins", ..., PACKAGE = "IRanges")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* 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 ... WARNING
Undocumented code objects:
  'lengths'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... 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 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/genoset.Rcheck/00check.log'
for details.



Installation output

genoset.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/genoset_1.40.0.tar.gz && rm -rf genoset.buildbin-libdir && mkdir genoset.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genoset.buildbin-libdir genoset_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL genoset_1.40.0.zip && rm genoset_1.40.0.tar.gz genoset_1.40.0.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  108k  100  108k    0     0  1985k      0 --:--:-- --:--:-- --:--:-- 2209k

install for i386

* installing *source* package 'genoset' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c bounds.c -o bounds.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c rangeSummaries.c -o rangeSummaries.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o genoset.dll tmp.def bounds.o init.o rangeSummaries.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/genoset.buildbin-libdir/00LOCK-genoset/00new/genoset/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
From .checkSubclasses(): subclass "GenomicPos" of class "GenomicRanges" is not local and is not updated for new inheritance information currently; 
[where=, where2=]
** help
*** installing help indices
  converting help for package 'genoset'
    finding HTML links ... done
    GenoSet-class                           html  
    finding level-2 HTML links ... done

    RleDataFrame-class                      html  
    RleDataFrame-views                      html  
    baf2mbaf                                html  
    boundingIndices                         html  
    boundingIndicesByChr                    html  
    bounds2Rle                              html  
    calcGC                                  html  
    calcGC2                                 html  
    chr-methods                             html  
    chrIndices-methods                      html  
    chrInfo-methods                         html  
    chrNames-methods                        html  
    chrOrder                                html  
    chrPartitioning                         html  
    cn2lr-methods                           html  
    do_rledf_range_summary                  html  
    do_rledf_views                          html  
    fixSegNAs                               html  
    gcCorrect                               html  
    genoPlot-methods                        html  
    genoPos-methods                         html  
    genome                                  html  
    genomeAxis                              html  
    genomicranges-methods                   html  
    genoset-dataset                         html  
    genoset-methods                         html  
    genoset-package                         html  
    genoset-subset                          html  
    isGenomeOrder                           html  
    lr2cn                                   html  
    modeCenter                              html  
    numCallable                             html  
    pos-methods                             html  
    rangeSampleMeans                        html  
    rangeSegMeanLength-methods              html  
    rbindDataframe                          html  
    readGenoSet                             html  
    runCBS                                  html  
    segPairTable-methods                    html  
    segTable-methods                        html  
    segs2Granges                            html  
    segs2Rle                                html  
    segs2RleDataFrame                       html  
    toGenomeOrder                           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 'genoset' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c bounds.c -o bounds.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rangeSummaries.c -o rangeSummaries.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o genoset.dll tmp.def bounds.o init.o rangeSummaries.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/genoset.buildbin-libdir/genoset/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genoset' as genoset_1.40.0.zip
* DONE (genoset)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'genoset' successfully unpacked and MD5 sums checked

Tests output

genoset.Rcheck/tests_i386/testthat.Rout


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.

> library(testthat)
> library(genoset)
Loading required package: BiocGenerics
Loading required package: parallel

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

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

> 
> test_check("genoset")
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
== testthat results  ===========================================================
[ OK: 162 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  13.29    0.70   13.96 

genoset.Rcheck/tests_x64/testthat.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-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.

> library(testthat)
> library(genoset)
Loading required package: BiocGenerics
Loading required package: parallel

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

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

> 
> test_check("genoset")
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
== testthat results  ===========================================================
[ OK: 162 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  11.48    0.35   11.81 

Example timings

genoset.Rcheck/examples_i386/genoset-Ex.timings

nameusersystemelapsed
GenoSet-class0.390.083.12
RleDataFrame-class0.470.000.47
RleDataFrame-views0.070.000.06
baf2mbaf0.090.000.09
boundingIndices000
calcGC000
calcGC2000
chr-methods0.030.000.03
chrIndices-methods0.020.010.03
chrInfo-methods0.060.000.07
chrNames-methods0.030.000.03
chrOrder000
gcCorrect000
genoPlot-methods0.110.020.12
genoPos-methods0.030.000.03
genome0.020.010.04
genomeAxis0.070.000.06
genoset-methods0.060.020.08
genoset-subset0.250.030.28
isGenomeOrder0.010.000.02
modeCenter0.000.020.01
pos-methods0.030.000.04
rangeSampleMeans0.050.000.04
readGenoSet000
runCBS2.330.012.35
segPairTable-methods0.020.000.01
segTable-methods2.280.002.28
segs2Rle1.870.021.89
segs2RleDataFrame2.110.002.11
toGenomeOrder0.060.000.06

genoset.Rcheck/examples_x64/genoset-Ex.timings

nameusersystemelapsed
GenoSet-class0.160.000.15
RleDataFrame-class0.250.000.25
RleDataFrame-views0.050.000.04
baf2mbaf0.030.010.05
boundingIndices000
calcGC000
calcGC20.000.020.02
chr-methods0.000.010.01
chrIndices-methods0.010.000.02
chrInfo-methods0.040.000.03
chrNames-methods0.010.000.02
chrOrder0.020.000.01
gcCorrect000
genoPlot-methods0.060.020.08
genoPos-methods0.020.020.03
genome0.000.010.02
genomeAxis0.030.000.03
genoset-methods0.030.020.04
genoset-subset0.150.000.16
isGenomeOrder0.020.000.01
modeCenter000
pos-methods0.010.000.02
rangeSampleMeans0.030.010.04
readGenoSet000
runCBS2.190.002.19
segPairTable-methods000
segTable-methods1.580.001.58
segs2Rle1.560.001.56
segs2RleDataFrame1.520.001.52
toGenomeOrder0.040.000.04