Peter M. Haverty
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/genoset |
| Branch: RELEASE_3_10 |
| Last Commit: 8bd8fd5 |
| Last Changed Date: 2019-10-29 13:08:20 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:06:20 -0400 (Wed, 15 Apr 2020).
| Package 689/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| genoset 1.42.0 Peter M. Haverty
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: genoset |
| Version: 1.42.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:genoset.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings genoset_1.42.0.tar.gz |
| StartedAt: 2020-04-15 00:59:20 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:02:29 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 189.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genoset.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:genoset.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings genoset_1.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/genoset.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genoset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoset’ version ‘1.42.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/genoset.Rcheck/00check.log’
for details.
genoset.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL genoset ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘genoset’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bounds.c -o bounds.o gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rangeSummaries.c -o rangeSummaries.o gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o genoset.so bounds.o init.o rangeSummaries.o utils.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-genoset/00new/genoset/libs ** 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=<environment: 0x55bfc98e1688>, where2=<environment: namespace:genoset>] From .checkSubclasses(): subclass "UnstitchedGPos" of class "GenomicRanges" is not local and is not updated for new inheritance information currently; [where=<environment: 0x55bfc98e1688>, where2=<environment: namespace:genoset>] From .checkSubclasses(): subclass "StitchedGPos" of class "GenomicRanges" is not local and is not updated for new inheritance information currently; [where=<environment: 0x55bfc98e1688>, where2=<environment: namespace:genoset>] From .checkSubclasses(): subclass "UnstitchedGPos" of class "GenomicRanges" is not local and is not updated for new inheritance information currently; [where=<environment: 0x55bfc98e1688>, where2=<environment: namespace:genoset>] From .checkSubclasses(): subclass "StitchedGPos" of class "GenomicRanges" is not local and is not updated for new inheritance information currently; [where=<environment: 0x55bfc98e1688>, where2=<environment: namespace:genoset>] ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (genoset)
genoset.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
> 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
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
15.076 0.396 15.538
genoset.Rcheck/genoset-Ex.timings
| name | user | system | elapsed | |
| GenoSet-class | 0.104 | 0.000 | 0.102 | |
| RleDataFrame-class | 0.760 | 0.004 | 0.766 | |
| RleDataFrame-views | 0.048 | 0.000 | 0.049 | |
| baf2mbaf | 0.088 | 0.000 | 0.085 | |
| boundingIndices | 0.000 | 0.000 | 0.001 | |
| calcGC | 0 | 0 | 0 | |
| calcGC2 | 0 | 0 | 0 | |
| chr-methods | 0.020 | 0.008 | 0.027 | |
| chrIndices-methods | 0.020 | 0.000 | 0.021 | |
| chrInfo-methods | 0.056 | 0.000 | 0.058 | |
| chrNames-methods | 0.036 | 0.004 | 0.039 | |
| chrOrder | 0.000 | 0.000 | 0.001 | |
| gcCorrect | 0.004 | 0.000 | 0.005 | |
| genoPlot-methods | 0.128 | 0.004 | 0.135 | |
| genoPos-methods | 0.028 | 0.000 | 0.029 | |
| genome | 0.012 | 0.000 | 0.014 | |
| genomeAxis | 0.032 | 0.012 | 0.045 | |
| genoset-methods | 0.040 | 0.004 | 0.044 | |
| genoset-subset | 0.216 | 0.016 | 0.233 | |
| isGenomeOrder | 0.020 | 0.000 | 0.018 | |
| modeCenter | 0.000 | 0.004 | 0.005 | |
| pos-methods | 0.020 | 0.000 | 0.019 | |
| rangeSampleMeans | 0.036 | 0.004 | 0.039 | |
| readGenoSet | 0 | 0 | 0 | |
| runCBS | 1.456 | 0.012 | 1.469 | |
| segPairTable-methods | 0.016 | 0.000 | 0.017 | |
| segTable-methods | 1.268 | 0.000 | 1.269 | |
| segs2Rle | 0.956 | 0.000 | 0.959 | |
| segs2RleDataFrame | 0.952 | 0.000 | 0.951 | |
| toGenomeOrder | 0.044 | 0.000 | 0.043 | |