Peter M. Haverty
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/genoset |
| Branch: RELEASE_3_6 |
| Last Commit: cd3de97 |
| Last Changed Date: 2017-10-30 12:39:33 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:20:48 -0400 (Thu, 12 Apr 2018).
| Package 571/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| genoset 1.34.0 Peter M. Haverty
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: genoset |
| Version: 1.34.0 |
| Command: rm -rf genoset.buildbin-libdir genoset.Rcheck && mkdir genoset.buildbin-libdir genoset.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genoset.buildbin-libdir genoset_1.34.0.tar.gz >genoset.Rcheck\00install.out 2>&1 && cp genoset.Rcheck\00install.out genoset-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=genoset.buildbin-libdir --install="check:genoset-install.out" --force-multiarch --no-vignettes --timings genoset_1.34.0.tar.gz |
| StartedAt: 2018-04-12 00:19:30 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:24:18 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 288.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genoset.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf genoset.buildbin-libdir genoset.Rcheck && mkdir genoset.buildbin-libdir genoset.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genoset.buildbin-libdir genoset_1.34.0.tar.gz >genoset.Rcheck\00install.out 2>&1 && cp genoset.Rcheck\00install.out genoset-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=genoset.buildbin-libdir --install="check:genoset-install.out" --force-multiarch --no-vignettes --timings genoset_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/genoset.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 'genoset/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genoset' version '1.34.0'
* 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 '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 ... NOTE
Unexported object imported by a ':::' call: 'BiocGenerics:::testPackage'
See the note in ?`:::` about the use of this operator.
* 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 S4 methods:
generic '[' and siglist 'GenoSet,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/genoset.buildbin-libdir/genoset/libs/i386/genoset.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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 'prove.R'
Comparing 'prove.Rout' to 'prove.Rout.save' ...15c15
< IQR, mad, sd, var, xtabs
---
> IQR, mad, xtabs
20,32c20,24
< 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
---
> as.data.frame, as.vector, cbind, colnames, 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, rep.int, rownames, sapply, setdiff, sort, table,
> tapply, union, unique, unlist, unsplit
41,57c33,37
< Attaching package: 'matrixStats'
<
< The following objects are masked from 'package:Biobase':
<
< anyMissing, rowMedians
<
<
< Attaching package: 'DelayedArray'
<
< The following objects are masked from 'package:matrixStats':
<
< colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
<
< The following object is masked from 'package:base':
<
< apply
<
---
> *** Genoset API Changes ***
> The genoset class is transitioning to extending
> RangedSummarizedExperiment rather than eSet. For this release,
> please use the RSE API as the eSet API has been deprecated
> (e.g. colnames instead of sampleNames). ***
59a40
> Using mclapply for segmentation ...
61a43
> Using mclapply for segmentation ...
63a46
> Using mclapply for segmentation ...
65a49
> Using mclapply for segmentation ...
67a52
> Using mclapply for segmentation ...
72c57
< RUNIT TEST PROTOCOL -- Thu Apr 12 00:23:46 2018
---
> RUNIT TEST PROTOCOL -- Sat Sep 12 10:57:59 2015
74c59
< Number of test functions: 32
---
> Number of test functions: 36
80,81c65,66
< genoset RUnit Tests - 32 test functions, 0 errors, 0 failures
< Number of test functions: 32
---
> genoset RUnit Tests - 36 test functions, 0 errors, 0 failures
> Number of test functions: 36
83a69
> There were 19 warnings (use warnings() to see them)
Warning message:
running command '"diff" -bw "C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\Rtmp6jXkg5\Rdiffa19dc471522f4" "C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\Rtmp6jXkg5\Rdiffb19dc513a5275"' had status 1
OK
** running tests for arch 'x64' ...
Running 'prove.R'
Comparing 'prove.Rout' to 'prove.Rout.save' ...15c15
< IQR, mad, sd, var, xtabs
---
> IQR, mad, xtabs
20,32c20,24
< 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
---
> as.data.frame, as.vector, cbind, colnames, 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, rep.int, rownames, sapply, setdiff, sort, table,
> tapply, union, unique, unlist, unsplit
41,57c33,37
< Attaching package: 'matrixStats'
<
< The following objects are masked from 'package:Biobase':
<
< anyMissing, rowMedians
<
<
< Attaching package: 'DelayedArray'
<
< The following objects are masked from 'package:matrixStats':
<
< colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
<
< The following object is masked from 'package:base':
<
< apply
<
---
> *** Genoset API Changes ***
> The genoset class is transitioning to extending
> RangedSummarizedExperiment rather than eSet. For this release,
> please use the RSE API as the eSet API has been deprecated
> (e.g. colnames instead of sampleNames). ***
59a40
> Using mclapply for segmentation ...
61a43
> Using mclapply for segmentation ...
63a46
> Using mclapply for segmentation ...
65a49
> Using mclapply for segmentation ...
67a52
> Using mclapply for segmentation ...
72c57
< RUNIT TEST PROTOCOL -- Thu Apr 12 00:24:12 2018
---
> RUNIT TEST PROTOCOL -- Sat Sep 12 10:57:59 2015
74c59
< Number of test functions: 32
---
> Number of test functions: 36
80,81c65,66
< genoset RUnit Tests - 32 test functions, 0 errors, 0 failures
< Number of test functions: 32
---
> genoset RUnit Tests - 36 test functions, 0 errors, 0 failures
> Number of test functions: 36
83a69
> There were 19 warnings (use warnings() to see them)
Warning message:
running command '"diff" -bw "C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\RtmpK8nKED\Rdiffa11c07bbb4746" "C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\RtmpK8nKED\Rdiffb11c079371872"' had status 1
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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/genoset.Rcheck/00check.log'
for details.
genoset.Rcheck/00install.out
install for i386
* installing *source* package 'genoset' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o genoset.dll tmp.def bounds.o init.o rangeSummaries.o utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/genoset.buildbin-libdir/genoset/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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
In R CMD INSTALL
install for x64
* installing *source* package 'genoset' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o genoset.dll tmp.def bounds.o init.o rangeSummaries.o utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/genoset.buildbin-libdir/genoset/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genoset' as genoset_1.34.0.zip
* DONE (genoset)
In R CMD INSTALL
In R CMD INSTALL
|
genoset.Rcheck/tests_i386/prove.Rout.save
R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (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.
> require("genoset") || stop("unable to load genoset package")
Loading required package: 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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, 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, rep.int, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
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: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
*** Genoset API Changes ***
The genoset class is transitioning to extending
RangedSummarizedExperiment rather than eSet. For this release,
please use the RSE API as the eSet API has been deprecated
(e.g. colnames instead of sampleNames). ***
[1] TRUE
> genoset:::.test()
Using mclapply for segmentation ...
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Using mclapply for segmentation ...
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Using mclapply for segmentation ...
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Using mclapply for segmentation ...
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Using mclapply for segmentation ...
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
RUNIT TEST PROTOCOL -- Sat Sep 12 10:57:59 2015
***********************************************
Number of test functions: 36
Number of errors: 0
Number of failures: 0
1 Test Suite :
genoset RUnit Tests - 36 test functions, 0 errors, 0 failures
Number of test functions: 36
Number of errors: 0
Number of failures: 0
There were 19 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
20.799 1.830 20.257
|
genoset.Rcheck/tests_x64/prove.Rout.save
R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (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.
> require("genoset") || stop("unable to load genoset package")
Loading required package: 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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, 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, rep.int, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
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: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
*** Genoset API Changes ***
The genoset class is transitioning to extending
RangedSummarizedExperiment rather than eSet. For this release,
please use the RSE API as the eSet API has been deprecated
(e.g. colnames instead of sampleNames). ***
[1] TRUE
> genoset:::.test()
Using mclapply for segmentation ...
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Using mclapply for segmentation ...
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Using mclapply for segmentation ...
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Using mclapply for segmentation ...
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Using mclapply for segmentation ...
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
RUNIT TEST PROTOCOL -- Sat Sep 12 10:57:59 2015
***********************************************
Number of test functions: 36
Number of errors: 0
Number of failures: 0
1 Test Suite :
genoset RUnit Tests - 36 test functions, 0 errors, 0 failures
Number of test functions: 36
Number of errors: 0
Number of failures: 0
There were 19 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
20.799 1.830 20.257
|
|
genoset.Rcheck/tests_i386/prove.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.
> require("genoset") || stop("unable to load genoset package")
Loading required package: 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, 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
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
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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
[1] TRUE
> genoset:::.test()
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
RUNIT TEST PROTOCOL -- Thu Apr 12 00:23:46 2018
***********************************************
Number of test functions: 32
Number of errors: 0
Number of failures: 0
1 Test Suite :
genoset RUnit Tests - 32 test functions, 0 errors, 0 failures
Number of test functions: 32
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
25.29 0.34 25.75
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genoset.Rcheck/tests_x64/prove.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.
> require("genoset") || stop("unable to load genoset package")
Loading required package: 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, 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
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
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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
[1] TRUE
> genoset:::.test()
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
RUNIT TEST PROTOCOL -- Thu Apr 12 00:24:12 2018
***********************************************
Number of test functions: 32
Number of errors: 0
Number of failures: 0
1 Test Suite :
genoset RUnit Tests - 32 test functions, 0 errors, 0 failures
Number of test functions: 32
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
23.51 0.23 23.75
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genoset.Rcheck/examples_i386/genoset-Ex.timings
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genoset.Rcheck/examples_x64/genoset-Ex.timings
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