Helena L. Crowell
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/CATALYST |
| Branch: RELEASE_3_11 |
| Last Commit: 3846718 |
| Last Changed Date: 2020-07-02 09:14:54 -0400 (Thu, 02 Jul 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:12 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE CATALYST PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 234/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CATALYST 1.12.2 Helena L. Crowell
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: CATALYST |
| Version: 1.12.2 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CATALYST.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CATALYST_1.12.2.tar.gz |
| StartedAt: 2020-10-17 02:16:52 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:42:57 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 1565.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CATALYST.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CATALYST.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CATALYST_1.12.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CATALYST.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CATALYST/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CATALYST' version '1.12.2'
* 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 whether package 'CATALYST' 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* 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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotPbExprs 18.94 0.04 18.99
plotDR 18.07 0.06 21.92
plotDiffHeatmap 14.71 0.02 15.07
plotExprHeatmap 13.55 0.05 13.76
plotMultiHeatmap 12.62 0.06 12.67
plotClusterExprs 10.70 0.04 11.40
plotFreqHeatmap 10.63 0.00 10.63
sce2fcs 9.76 0.19 9.95
mergeClusters 9.76 0.05 9.82
plotCodes 8.91 0.08 10.35
pbMDS 8.47 0.05 8.51
plotAbundances 7.95 0.00 7.96
SCE-accessors 6.97 0.32 7.61
extractClusters 6.86 0.02 6.88
runDR 6.83 0.00 6.83
plotExprs 6.61 0.11 6.75
plotYields 5.99 0.03 6.01
plotMahal 5.78 0.06 5.84
cluster 5.75 0.00 5.75
clrDR 5.52 0.20 5.72
filterSCE 5.53 0.06 5.59
plotScatter 5.14 0.10 5.23
plotSpillmat 5.07 0.08 5.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotDR 21.21 0.04 21.25
plotMultiHeatmap 15.11 0.06 15.17
plotClusterExprs 12.94 0.11 13.06
plotPbExprs 12.78 0.01 12.82
plotDiffHeatmap 12.45 0.08 12.54
plotExprHeatmap 11.50 0.02 11.51
plotCodes 10.78 0.04 10.83
sce2fcs 10.34 0.12 10.47
plotAbundances 10.12 0.05 10.19
pbMDS 9.67 0.03 9.77
SCE-accessors 9.27 0.23 9.50
mergeClusters 8.40 0.00 8.40
plotMahal 8.28 0.04 8.32
clrDR 7.97 0.05 9.22
filterSCE 7.95 0.06 8.01
adaptSpillmat 7.70 0.09 9.26
plotFreqHeatmap 7.58 0.04 7.62
runDR 6.68 0.00 6.67
cluster 6.62 0.01 7.48
extractClusters 6.49 0.02 6.50
plotExprs 6.27 0.11 6.38
estCutoffs 6.06 0.04 6.11
compCytof 6.02 0.05 7.89
applyCutoffs 5.25 0.10 5.83
plotYields 5.24 0.03 5.26
* 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: OK
CATALYST.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CATALYST_1.12.2.tar.gz && rm -rf CATALYST.buildbin-libdir && mkdir CATALYST.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CATALYST.buildbin-libdir CATALYST_1.12.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CATALYST_1.12.2.zip && rm CATALYST_1.12.2.tar.gz CATALYST_1.12.2.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 3591k 100 3591k 0 0 38.0M 0 --:--:-- --:--:-- --:--:-- 41.2M
install for i386
* installing *source* package 'CATALYST' ...
** 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 'CATALYST'
finding HTML links ... done
SCE-accessors html
finding level-2 HTML links ... done
adaptSpillmat html
applyCutoffs html
assignPrelim html
clrDR html
cluster html
compCytof html
computeSpillmat html
data html
estCutoffs html
extractClusters html
filterSCE html
guessPanel html
mergeClusters html
normCytof html
pbMDS html
plotAbundances html
plotClusterExprs html
plotClusterHeatmap html
plotCodes html
plotCounts html
plotDR html
plotDiffHeatmap html
plotEvents html
plotExprHeatmap html
plotExprs html
plotFreqHeatmap html
plotMahal html
plotMultiHeatmap html
plotNRS html
plotPbExprs html
plotScatter html
plotSpillmat html
plotYields html
prepData html
runDR html
sce2fcs 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 'CATALYST' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CATALYST' as CATALYST_1.12.2.zip
* DONE (CATALYST)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CATALYST' successfully unpacked and MD5 sums checked
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CATALYST.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(CATALYST)
Loading required package: SingleCellExperiment
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: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
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("CATALYST")
== testthat results ===========================================================
[ OK: 732 | SKIPPED: 0 | WARNINGS: 37 | FAILED: 0 ]
>
> proc.time()
user system elapsed
178.48 3.56 184.18
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CATALYST.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(CATALYST)
Loading required package: SingleCellExperiment
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: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
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("CATALYST")
== testthat results ===========================================================
[ OK: 732 | SKIPPED: 0 | WARNINGS: 37 | FAILED: 0 ]
>
> proc.time()
user system elapsed
185.04 1.68 186.73
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CATALYST.Rcheck/examples_i386/CATALYST-Ex.timings
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CATALYST.Rcheck/examples_x64/CATALYST-Ex.timings
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