| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:13 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2039/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SummarizedBenchmark 2.18.0 (landing page) Patrick Kimes
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK |  | |||||||
|
To the developers/maintainers of the SummarizedBenchmark package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SummarizedBenchmark |
| Version: 2.18.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SummarizedBenchmark.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SummarizedBenchmark_2.18.0.tar.gz |
| StartedAt: 2023-10-19 05:24:09 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 05:31:15 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 425.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SummarizedBenchmark.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SummarizedBenchmark.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SummarizedBenchmark_2.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SummarizedBenchmark.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SummarizedBenchmark/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SummarizedBenchmark’ version ‘2.18.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SummarizedBenchmark’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.3Mb
sub-directories of 1Mb or more:
data 6.4Mb
* 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:::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: no visible binding for global variable ‘value’
.compare.meta: no visible binding for global variable ‘comparison’
.list2mat: no visible binding for global variable ‘.id’
.list2mat: no visible binding for global variable ‘.val’
.list2mat: no visible binding for global variable ‘.method’
.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’
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 LazyData ... WARNING
LazyData DB of 6.4 MB without LazyDataCompression set
See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
buildBench 2.589 0.206 5.493
* 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, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SummarizedBenchmark.Rcheck/00check.log’
for details.
SummarizedBenchmark.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SummarizedBenchmark ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * 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 *** 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 * DONE (SummarizedBenchmark)
SummarizedBenchmark.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, aperm, 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.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:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
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: BiocParallel
Loading required package: ggplot2
Loading required package: mclust
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: dplyr
Attaching package: 'dplyr'
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:matrixStats':
count
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")
Attaching package: 'iCOBRA'
The following objects are masked from 'package:GenomicRanges':
score, score<-
The following objects are masked from 'package:BiocGenerics':
score, score<-
Option rerun is set to `FALSE`:
Rerunning performance metrics only for the following methods: BH2
Found already estimated performance metrics, replacing these
Found already estimated performance metrics, replacing these
Found already estimated performance metrics, replacing these
Found already estimated performance metrics, replacing these
[ FAIL 0 | WARN 108 | SKIP 0 | PASS 224 ]
[ FAIL 0 | WARN 108 | SKIP 0 | PASS 224 ]
>
> proc.time()
user system elapsed
35.293 2.744 71.732
SummarizedBenchmark.Rcheck/SummarizedBenchmark-Ex.timings
| name | user | system | elapsed | |
| BDData-setter | 0.033 | 0.002 | 0.063 | |
| BDData | 0.011 | 0.001 | 0.022 | |
| BDMethod-setter | 0.045 | 0.002 | 0.082 | |
| BDMethod | 0.009 | 0.001 | 0.022 | |
| BDMethodList-setter | 0.014 | 0.001 | 0.028 | |
| BDMethodList | 0.025 | 0.002 | 0.050 | |
| BenchDesign | 0.020 | 0.002 | 0.042 | |
| SummarizedBenchmark-class | 0.867 | 0.071 | 1.679 | |
| SummarizedBenchmark | 0.226 | 0.006 | 0.420 | |
| addMethod | 0.035 | 0.003 | 0.068 | |
| addPerformanceMetric | 0.057 | 0.005 | 0.114 | |
| allSB | 0.001 | 0.002 | 0.003 | |
| assayNames-setter | 0.069 | 0.004 | 0.127 | |
| availableMetrics | 0.002 | 0.001 | 0.006 | |
| buildBench | 2.589 | 0.206 | 5.493 | |
| compareBDData | 0.004 | 0.001 | 0.010 | |
| compareBDMethod | 0.207 | 0.015 | 0.404 | |
| compareBenchDesigns | 0.357 | 0.034 | 0.689 | |
| dropMethod | 0.043 | 0.005 | 0.085 | |
| estimateMetrics | 0.660 | 0.042 | 1.254 | |
| expandMethod | 0.049 | 0.002 | 0.085 | |
| modifyMethod | 0.045 | 0.001 | 0.077 | |
| performanceMetrics-setter | 0.059 | 0.004 | 0.110 | |
| performanceMetrics | 0.056 | 0.003 | 0.104 | |
| plotMethodsOverlap | 0.002 | 0.002 | 0.008 | |
| plotROC | 0.001 | 0.003 | 0.007 | |
| printMethod | 0.030 | 0.002 | 0.056 | |
| sb | 0.001 | 0.002 | 0.007 | |
| tdat | 0.002 | 0.002 | 0.007 | |
| tidyUpMetrics | 0.229 | 0.006 | 0.406 | |
| updateBench | 1.219 | 0.042 | 2.261 | |