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 13:09:31 -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: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings genoset_1.34.0.tar.gz |
| StartedAt: 2018-04-11 23:51:29 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:54:15 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 165.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genoset.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings genoset_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/genoset.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.34.0’
* 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 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 ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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). ***
77c57
< RUNIT TEST PROTOCOL -- Wed Apr 11 23:54:12 2018
---
> RUNIT TEST PROTOCOL -- Sat Sep 12 10:57:59 2015
79c59
< Number of test functions: 32
---
> Number of test functions: 36
85,86c65,66
< 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
88a69
> There were 19 warnings (use warnings() to see them)
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-3.6-bioc/meat/genoset.Rcheck/00check.log’
for details.
genoset.Rcheck/00install.out
* installing *source* package ‘genoset’ ... ** libs gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bounds.c -o bounds.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rangeSummaries.c -o rangeSummaries.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o genoset.so bounds.o init.o rangeSummaries.o utils.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.6-bioc/meat/genoset.Rcheck/genoset/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (genoset)
genoset.Rcheck/tests/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-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.
> 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()
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 -- Wed Apr 11 23:54:12 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
22.608 0.396 20.053
genoset.Rcheck/tests/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/genoset-Ex.timings
| name | user | system | elapsed | |
| GenoSet-class | 0.236 | 0.024 | 0.259 | |
| RleDataFrame-class | 0.784 | 0.012 | 0.798 | |
| RleDataFrame-views | 0.044 | 0.000 | 0.044 | |
| baf2mbaf | 0.028 | 0.000 | 0.028 | |
| boundingIndices | 0.004 | 0.000 | 0.001 | |
| calcGC | 0.000 | 0.000 | 0.001 | |
| calcGC2 | 0.000 | 0.000 | 0.001 | |
| chr-methods | 0.016 | 0.000 | 0.018 | |
| chrIndices-methods | 0.016 | 0.000 | 0.015 | |
| chrInfo-methods | 0.036 | 0.004 | 0.041 | |
| chrNames-methods | 0.036 | 0.000 | 0.038 | |
| chrOrder | 0.000 | 0.000 | 0.001 | |
| gcCorrect | 0.004 | 0.000 | 0.004 | |
| genoPlot-methods | 0.060 | 0.000 | 0.057 | |
| genoPos-methods | 0.02 | 0.00 | 0.02 | |
| genome | 0.068 | 0.000 | 0.068 | |
| genomeAxis | 0.032 | 0.000 | 0.030 | |
| genoset-methods | 0.084 | 0.000 | 0.087 | |
| genoset-subset | 0.240 | 0.004 | 0.246 | |
| isGenomeOrder | 0.020 | 0.000 | 0.016 | |
| modeCenter | 0.008 | 0.004 | 0.015 | |
| pos-methods | 0.008 | 0.004 | 0.015 | |
| rangeSampleMeans | 0.024 | 0.000 | 0.025 | |
| readGenoSet | 0.000 | 0.000 | 0.001 | |
| runCBS | 1.660 | 0.004 | 1.666 | |
| segPairTable-methods | 0.004 | 0.004 | 0.009 | |
| segTable-methods | 0.904 | 0.000 | 0.905 | |
| segs2Rle | 1.040 | 0.008 | 1.050 | |
| segs2RleDataFrame | 0.956 | 0.000 | 0.960 | |
| toGenomeOrder | 0.052 | 0.004 | 0.055 | |