Patrick Kimes
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/SummarizedBenchmark |
| Branch: RELEASE_3_10 |
| Last Commit: 5fc84cb |
| Last Changed Date: 2019-10-29 13:11:00 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:30:04 -0400 (Wed, 15 Apr 2020).
| Package 1684/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SummarizedBenchmark 2.4.0 Patrick Kimes
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SummarizedBenchmark |
| Version: 2.4.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SummarizedBenchmark.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings SummarizedBenchmark_2.4.0.tar.gz |
| StartedAt: 2020-04-15 06:58:17 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 07:03:54 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 337.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SummarizedBenchmark.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SummarizedBenchmark.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings SummarizedBenchmark_2.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/SummarizedBenchmark.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '2.4.0'
* 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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5guFh/R.INSTALL21983cab5379/SummarizedBenchmark/man/addMethod.Rd:47: file link 'quotation' in package 'rlang' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5guFh/R.INSTALL21983cab5379/SummarizedBenchmark/man/addMethod.Rd:17: file link 'quotation' in package 'rlang' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5guFh/R.INSTALL21983cab5379/SummarizedBenchmark/man/addMethod.Rd:76: file link 'quotation' in package 'rlang' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5guFh/R.INSTALL21983cab5379/SummarizedBenchmark/man/modifyMethod.Rd:14: file link 'quotation' in package 'rlang' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/SummarizedBenchmark.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 11.6Mb
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
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 binding for global variable
'label'
.compare.meta: no visible binding for global variable 'label'
.compare.meta : <anonymous>: no visible binding for global variable
'label'
.compare.meta : <anonymous>: 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 'post'
.printUpdateBench: no visible binding for global variable 'rerun'
.printUpdateBench: no visible binding for global variable 'overlap'
.printUpdateBench: no visible binding for global variable '.'
plotROC: no visible binding for global variable 'FDR'
plotROC: no visible binding for global variable 'TPR'
plotROC: no visible binding for global variable 'method'
tidyUpMetrics: no visible binding for global variable 'key'
tidyUpMetrics: no visible binding for global variable 'value'
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 'post'
Undefined global functions or variables:
. .id .method .val FDR TPR colid comparison f key label meta method
overlap post rerun value
* 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: 1 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-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://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/SummarizedBenchmark_2.4.0.tar.gz && rm -rf SummarizedBenchmark.buildbin-libdir && mkdir SummarizedBenchmark.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SummarizedBenchmark.buildbin-libdir SummarizedBenchmark_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL SummarizedBenchmark_2.4.0.zip && rm SummarizedBenchmark_2.4.0.tar.gz SummarizedBenchmark_2.4.0.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 5649k 100 5649k 0 0 18.6M 0 --:--:-- --:--:-- --:--:-- 18.8M
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-setter html
BDData-show html
BDData html
BDMethod-class html
BDMethod-setter html
BDMethod-show html
BDMethod html
BDMethodList-class html
BDMethodList-setter html
BDMethodList-show html
BDMethodList html
BenchDesign-class html
BenchDesign-show html
BenchDesign html
SummarizedBenchmark-class html
finding level-2 HTML links ... done
SummarizedBenchmark html
addMethod html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5guFh/R.INSTALL21983cab5379/SummarizedBenchmark/man/addMethod.Rd:47: file link 'quotation' in package 'rlang' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5guFh/R.INSTALL21983cab5379/SummarizedBenchmark/man/addMethod.Rd:17: file link 'quotation' in package 'rlang' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5guFh/R.INSTALL21983cab5379/SummarizedBenchmark/man/addMethod.Rd:76: file link 'quotation' in package 'rlang' does not exist and so has been treated as a topic
addPerformanceMetric html
allSB html
assayNames-setter html
availableMetrics html
buildBench html
compareBDData html
compareBDMethod html
compareBenchDesigns html
dropMethod html
estimateMetrics html
expandMethod html
groundTruths-setter html
groundTruths html
hashBDData html
mcols-setter html
modifyMethod html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5guFh/R.INSTALL21983cab5379/SummarizedBenchmark/man/modifyMethod.Rd:14: file link 'quotation' in package 'rlang' does not exist and so has been treated as a topic
modmethod html
performanceMetrics-setter html
performanceMetrics html
plotMethodsOverlap html
plotROC html
printMethod html
sb html
tdat html
tidyBDMethod html
tidyUpMetrics html
updateBench html
*** copying figures
** 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_2.4.0.zip
* DONE (SummarizedBenchmark)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'SummarizedBenchmark' successfully unpacked and MD5 sums checked
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SummarizedBenchmark.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 5.4.6
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
35.84 3.93 40.21
|
SummarizedBenchmark.Rcheck/tests_x64/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-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 5.4.6
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
32.92 2.53 36.03
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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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