Kevin Rue-Albrecht
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/iSEEu |
| git_branch: RELEASE_3_13 |
| git_last_commit: 51da58e |
| git_last_commit_date: 2021-05-19 12:51:28 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:09 -0400 (Fri, 15 Oct 2021).
|
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 946/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| iSEEu 1.4.0 (landing page) Kevin Rue-Albrecht
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: iSEEu |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iSEEu.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings iSEEu_1.4.0.tar.gz |
| StartedAt: 2021-10-15 00:54:21 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 01:07:22 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 781.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: iSEEu.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iSEEu.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings iSEEu_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/iSEEu.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.4.0'
* 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
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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 22.42 2.81 26.83
modeReducedDim 19.11 0.76 20.66
FeatureSetTable-class 17.03 0.61 18.99
GeneSetTable-class 15.86 0.62 18.01
DynamicMarkerTable-class 14.75 1.46 17.11
DynamicReducedDimensionPlot-class 13.81 0.53 15.28
registerFeatureSetCollections 13.75 0.42 15.55
ReducedDimensionHexPlot-class 13.52 0.53 14.92
modeGating 11.66 0.47 13.09
** running examples for arch 'x64' ... 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 23.34 1.73 26.43
modeReducedDim 19.01 0.51 20.24
GeneSetTable-class 17.50 0.69 19.36
FeatureSetTable-class 17.53 0.59 19.50
registerFeatureSetCollections 14.23 0.63 16.22
DynamicReducedDimensionPlot-class 13.80 0.54 15.27
DynamicMarkerTable-class 13.64 0.62 15.20
ReducedDimensionHexPlot-class 12.60 0.48 13.94
modeGating 11.78 0.47 13.22
* 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: 2 WARNINGs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/iSEEu.Rcheck/00check.log'
for details.
iSEEu.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/iSEEu_1.4.0.tar.gz && rm -rf iSEEu.buildbin-libdir && mkdir iSEEu.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iSEEu.buildbin-libdir iSEEu_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL iSEEu_1.4.0.zip && rm iSEEu_1.4.0.tar.gz iSEEu_1.4.0.zip
###
##############################################################################
##############################################################################
% 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 617k 100 617k 0 0 1465k 0 --:--:-- --:--:-- --:--:-- 1469k
install for i386
* 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: C:/Users/biocbuild/bbs-3.13-bioc/meat/iSEEu.buildbin-libdir/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
install for x64
* installing *source* package 'iSEEu' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iSEEu' as iSEEu_1.4.0.zip
* DONE (iSEEu)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'iSEEu' successfully unpacked and MD5 sums checked
|
iSEEu.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(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
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.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(): 2021-05-18
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 ]
>
> proc.time()
user system elapsed
78.98 8.01 93.82
|
iSEEu.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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
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.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(): 2021-05-18
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 ]
>
> proc.time()
user system elapsed
74.43 5.39 84.87
|
|
iSEEu.Rcheck/examples_i386/iSEEu-Ex.timings
|
iSEEu.Rcheck/examples_x64/iSEEu-Ex.timings
|