Kevin Rue-Albrecht
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/iSEEu |
| git_branch: master |
| git_last_commit: 965aca8 |
| git_last_commit_date: 2022-01-21 08:46:17 -0400 (Fri, 21 Jan 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:50 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the iSEEu package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iSEEu.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 961/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| iSEEu 1.7.1 (landing page) Kevin Rue-Albrecht
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: iSEEu |
| Version: 1.7.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iSEEu.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings iSEEu_1.7.1.tar.gz |
| StartedAt: 2022-03-17 19:23:44 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:28:49 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 305.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: iSEEu.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iSEEu.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings iSEEu_1.7.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/iSEEu.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iSEEu/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iSEEu' version '1.7.1'
* 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 'iSEEu' 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 ... 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 files in 'vignettes' ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: '.setOrganism' is deprecated.
Warning: '.setIdentifierType' is deprecated.
Warning: 'GeneSetTable' is deprecated.
Warning: 'setPValuePattern' is deprecated.
Warning: 'setPValuePattern' is deprecated.
Warning: '.setIdentifierType' is deprecated.
Warning: '.getIdentifierType' is deprecated.
Warning: '.setOrganism' is deprecated.
Warning: '.getOrganism' is deprecated.
Warning: '.getGeneSetCommands' is deprecated.
Warning: '.getOrganism' is deprecated.
Warning: '.getOrganism' is deprecated.
Warning: '.getGeneSetCommands' is deprecated.
Warning: '.getIdentifierType' is deprecated.
Warning: '.getOrganism' is deprecated.
Warning: '.getOrganism' is deprecated.
Warning: '.setGeneSetCommands' is deprecated.
Warning: '.getGeneSetCommands' is deprecated.
Warning: '.getGeneSetCommands' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AggregatedDotPlot 12.09 1.83 15.22
modeReducedDim 9.62 0.56 11.14
DynamicMarkerTable-class 6.73 0.72 8.37
FeatureSetTable-class 6.08 0.75 8.35
DynamicReducedDimensionPlot-class 5.75 0.76 7.51
ReducedDimensionHexPlot-class 5.60 0.64 7.17
GeneSetTable-class 5.40 0.69 7.67
modeGating 4.24 0.56 5.78
registerFeatureSetCollections 4.30 0.35 6.35
* 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
See
'D:/biocbuild/bbs-3.15-bioc/meat/iSEEu.Rcheck/00check.log'
for details.
iSEEu.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL iSEEu
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'iSEEu' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'iSEEu'
finding HTML links ... done
AggregatedDotPlot html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-iSEEu/00new/iSEEu/help/.refineParameters+2CAggregatedDotPlot-method.html
finding level-2 HTML links ... done
DynamicMarkerTable-class html
DynamicReducedDimensionPlot-class html
FeatureSetTable-class html
GeneSetTable-class html
LogFCLogFCPlot-class html
MAPlot-class html
MarkdownBoard-class html
ReducedDimensionHexPlot-class html
VolcanoPlot-class html
createGeneSetCommands html
defunct html
global-FeatureSetCommands html
global-TableExtraFields html
globals-PValuePattern html
iSEEu-pkg html
modeEmpty html
modeGating html
modeReducedDim html
registerDEFields html
registerFeatureSetCollections html
utils-geneset 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
* DONE (iSEEu)
Making 'packages.html' ... done
iSEEu.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(iSEEu)
Loading required package: iSEE
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, 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 objects are masked from 'package:base':
I, expand.grid, unname
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")'.
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: SingleCellExperiment
>
> test_check("iSEEu")
snapshotDate(): 2022-03-16
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
Loading required package: scuttle
Loading required package: ggplot2
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 307 ]
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 307 ]
>
> proc.time()
user system elapsed
57.04 6.76 68.68
iSEEu.Rcheck/iSEEu-Ex.timings
| name | user | system | elapsed | |
| AggregatedDotPlot | 12.09 | 1.83 | 15.22 | |
| DynamicMarkerTable-class | 6.73 | 0.72 | 8.37 | |
| DynamicReducedDimensionPlot-class | 5.75 | 0.76 | 7.51 | |
| FeatureSetTable-class | 6.08 | 0.75 | 8.35 | |
| GeneSetTable-class | 5.40 | 0.69 | 7.67 | |
| LogFCLogFCPlot-class | 0.04 | 0.00 | 0.03 | |
| MAPlot-class | 0.01 | 0.00 | 0.02 | |
| MarkdownBoard-class | 0 | 0 | 0 | |
| ReducedDimensionHexPlot-class | 5.60 | 0.64 | 7.17 | |
| VolcanoPlot-class | 0.01 | 0.00 | 0.01 | |
| createGeneSetCommands | 0 | 0 | 0 | |
| global-FeatureSetCommands | 0 | 0 | 0 | |
| global-TableExtraFields | 0 | 0 | 0 | |
| globals-PValuePattern | 0 | 0 | 0 | |
| modeEmpty | 0.42 | 0.05 | 0.49 | |
| modeGating | 4.24 | 0.56 | 5.78 | |
| modeReducedDim | 9.62 | 0.56 | 11.14 | |
| registerDEFields | 0.03 | 0.00 | 0.03 | |
| registerFeatureSetCollections | 4.30 | 0.35 | 6.35 | |
| utils-geneset | 0 | 0 | 0 | |