Alejandro Reyes
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/SummarizedBenchmark |
| Branch: RELEASE_3_9 |
| Last Commit: 1d60e4d |
| Last Changed Date: 2019-09-18 09:42:01 -0400 (Wed, 18 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:40:49 -0400 (Wed, 16 Oct 2019).
| Package 1607/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SummarizedBenchmark 2.2.3 Alejandro Reyes
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SummarizedBenchmark |
| Version: 2.2.3 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SummarizedBenchmark.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SummarizedBenchmark_2.2.3.tar.gz |
| StartedAt: 2019-10-16 07:25:45 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:31:06 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 320.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SummarizedBenchmark.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SummarizedBenchmark.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SummarizedBenchmark_2.2.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SummarizedBenchmark.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 'SummarizedBenchmark/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SummarizedBenchmark' version '2.2.3'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'tidyr', 'SummarizedExperiment', 'S4Vectors', 'BiocGenerics',
'UpSetR', 'rlang', 'stringr', 'BiocParallel', 'ggplot2', 'mclust',
'dplyr', 'digest', 'sessioninfo', 'crayon', 'tibble'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'SummarizedBenchmark' can be installed ... OK
* checking installed package size ... NOTE
installed size is 11.5Mb
sub-directories of 1Mb or more:
data 10.6Mb
* 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
Package in Depends field not imported from: 'BiocGenerics'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'BiocGenerics:::replaceSlots'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.combineSummarizedBenchmarks: no visible binding for global variable
'colid'
.combineSummarizedBenchmarks: no visible global function definition for
'metadata'
.combineSummarizedBenchmarks: no visible binding for global variable
'label'
.compare.meta: no visible binding for global variable 'label'
.compare.meta : : no visible binding for global variable
'label'
.compare.meta : : no visible binding for global variable '.'
.compare.meta: no visible binding for global variable 'value'
.compare.meta: no visible binding for global variable 'comparison'
.list2mat: no visible binding for global variable '.method'
.list2mat: no visible binding for global variable '.val'
.list2mat: no visible binding for global variable '.id'
.printUpdateBench: no visible binding for global variable 'f'
.printUpdateBench: no visible binding for global variable 'meta'
.printUpdateBench: no visible binding for global variable 'params'
.printUpdateBench: no visible binding for global variable 'post'
.printUpdateBench: no visible binding for global variable 'rerun'
.printUpdateBench: no visible binding for global variable 'overlap'
.printUpdateBench: no visible binding for global variable '.'
.show.BDData: no visible global function definition for 'head'
.show.BDMethodList: no visible global function definition for 'head'
.show.BenchDesign: no visible global function definition for 'head'
.tidyForComparison: no visible binding for global variable 'slot'
BDData: no visible global function definition for '.valueClassTest'
BDMethod: no visible global function definition for '.valueClassTest'
BDMethodList: no visible global function definition for
'.valueClassTest'
BenchDesign: no visible global function definition for
'.valueClassTest'
plotROC: no visible binding for global variable 'FDR'
plotROC: no visible binding for global variable 'TPR'
plotROC: no visible binding for global variable 'method'
sb.correlation: no visible global function definition for 'cor'
sb.sdad: no visible global function definition for 'sd'
tidyUpMetrics: no visible binding for global variable 'key'
tidyUpMetrics: no visible binding for global variable 'value'
updateBench: no visible global function definition for 'metadata'
updateBench: no visible binding for global variable 'overlap'
updateBench: no visible binding for global variable 'f'
updateBench: no visible binding for global variable 'meta'
updateBench: no visible binding for global variable 'params'
updateBench: no visible binding for global variable 'post'
show,BDData: no visible global function definition for 'head'
show,BDMethodList: no visible global function definition for 'head'
show,BenchDesign: no visible global function definition for 'head'
Undefined global functions or variables:
. .id .method .val .valueClassTest FDR TPR colid comparison cor f
head key label meta metadata method overlap params post rerun sd slot
value
Consider adding
importFrom("methods", ".valueClassTest", "slot")
importFrom("stats", "cor", "sd")
importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/SummarizedBenchmark.Rcheck/00check.log'
for details.
SummarizedBenchmark.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/SummarizedBenchmark_2.2.3.tar.gz && rm -rf SummarizedBenchmark.buildbin-libdir && mkdir SummarizedBenchmark.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SummarizedBenchmark.buildbin-libdir SummarizedBenchmark_2.2.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SummarizedBenchmark_2.2.3.zip && rm SummarizedBenchmark_2.2.3.tar.gz SummarizedBenchmark_2.2.3.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 4404k 100 4404k 0 0 41.3M 0 --:--:-- --:--:-- --:--:-- 44.8M
install for i386
* installing *source* package 'SummarizedBenchmark' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SummarizedBenchmark'
finding HTML links ... done
BDData-class html
BDData html
BDMethod-class html
BDMethod html
BDMethodList-accessors html
BDMethodList-class html
BDMethodList html
BenchDesign-accessors html
BenchDesign-class html
BenchDesign html
SummarizedBenchmark-accessors html
SummarizedBenchmark-class html
finding level-2 HTML links ... done
SummarizedBenchmark html
addMethod html
addPerformanceMetric html
allSB html
availableMetrics html
buildBench html
compareBDData html
compareBDMethod html
compareBenchDesigns html
dropMethod html
estimateMetrics html
expandMethod html
hashBDData html
modifyMethod html
modmethod html
performanceMetrics html
plotMethodsOverlap html
plotROC html
printMethod html
sb html
tdat html
tidyBDMethod html
tidyUpMetrics html
updateBench 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 'SummarizedBenchmark' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SummarizedBenchmark' as SummarizedBenchmark_2.2.3.zip
* DONE (SummarizedBenchmark)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SummarizedBenchmark' successfully unpacked and MD5 sums checked
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SummarizedBenchmark.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("SummarizedBenchmark")
Loading required package: tidyr
Attaching package: 'tidyr'
The following object is masked from 'package:testthat':
matches
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:tidyr':
expand
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: 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
Loading required package: UpSetR
Loading required package: rlang
Attaching package: 'rlang'
The following object is masked from 'package:Biobase':
exprs
The following objects are masked from 'package:testthat':
is_false, is_null, is_true
Loading required package: stringr
Loading required package: ggplot2
Loading required package: mclust
Package 'mclust' version 5.4.5
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:matrixStats':
count
The following object is masked from 'package:Biobase':
combine
The following objects are masked from 'package:GenomicRanges':
intersect, setdiff, union
The following object is masked from 'package:GenomeInfoDb':
intersect
The following objects are masked from 'package:IRanges':
collapse, desc, intersect, setdiff, slice, union
The following objects are masked from 'package:S4Vectors':
first, intersect, rename, setdiff, setequal, union
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: digest
Loading required package: sessioninfo
Loading required package: crayon
Attaching package: 'crayon'
The following object is masked from 'package:ggplot2':
%+%
The following object is masked from 'package:rlang':
chr
Loading required package: tibble
>
> test_check("SummarizedBenchmark")
Option rerun is set to `FALSE`:
Rerunning performance metrics only for the following methods: BH2
== testthat results ===========================================================
[ OK: 224 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
>
> proc.time()
user system elapsed
25.92 3.32 29.98
|
SummarizedBenchmark.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("SummarizedBenchmark")
Loading required package: tidyr
Attaching package: 'tidyr'
The following object is masked from 'package:testthat':
matches
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:tidyr':
expand
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: 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
Loading required package: UpSetR
Loading required package: rlang
Attaching package: 'rlang'
The following object is masked from 'package:Biobase':
exprs
The following objects are masked from 'package:testthat':
is_false, is_null, is_true
Loading required package: stringr
Loading required package: ggplot2
Loading required package: mclust
Package 'mclust' version 5.4.5
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:matrixStats':
count
The following object is masked from 'package:Biobase':
combine
The following objects are masked from 'package:GenomicRanges':
intersect, setdiff, union
The following object is masked from 'package:GenomeInfoDb':
intersect
The following objects are masked from 'package:IRanges':
collapse, desc, intersect, setdiff, slice, union
The following objects are masked from 'package:S4Vectors':
first, intersect, rename, setdiff, setequal, union
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: digest
Loading required package: sessioninfo
Loading required package: crayon
Attaching package: 'crayon'
The following object is masked from 'package:ggplot2':
%+%
The following object is masked from 'package:rlang':
chr
Loading required package: tibble
>
> test_check("SummarizedBenchmark")
Option rerun is set to `FALSE`:
Rerunning performance metrics only for the following methods: BH2
== testthat results ===========================================================
[ OK: 224 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
>
> proc.time()
user system elapsed
30.31 3.37 36.89
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SummarizedBenchmark.Rcheck/examples_i386/SummarizedBenchmark-Ex.timings
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SummarizedBenchmark.Rcheck/examples_x64/SummarizedBenchmark-Ex.timings
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