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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:25:00 -0400 (Wed, 16 Oct 2019).
| Package 663/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| genoset 1.40.0 Peter M. Haverty
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| 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 |
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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
###
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* 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.
genoset.Rcheck/00install.out
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###
### 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
###
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% 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
|
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
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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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