Mike Morgan
| Snapshot Date: 2022-04-05 01:55:07 -0400 (Tue, 05 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/miloR |
| git_branch: RELEASE_3_14 |
| git_last_commit: e95c921 |
| git_last_commit_date: 2021-12-17 09:16:47 -0400 (Fri, 17 Dec 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-06 12:06:52 -0400 (Wed, 06 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4322 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4076 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4135 |
| 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 miloR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/miloR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1150/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miloR 1.2.0 (landing page) Mike Morgan
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: miloR |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:miloR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings miloR_1.2.0.tar.gz |
| StartedAt: 2022-04-05 23:20:22 -0400 (Tue, 05 Apr 2022) |
| EndedAt: 2022-04-05 23:37:42 -0400 (Tue, 05 Apr 2022) |
| EllapsedTime: 1040.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: miloR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:miloR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings miloR_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/miloR.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'miloR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'miloR' version '1.2.0'
* 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 'miloR' 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 ... NOTE
Unexported object imported by a ':::' call: 'S4Vectors:::disableValidity'
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
plotDAbeeswarm: no visible binding for global variable 'SpatialFDR'
plotDAbeeswarm: no visible binding for global variable 'is_signif'
plotDAbeeswarm: no visible binding for global variable 'logFC'
plotDAbeeswarm: no visible binding for global variable 'Nhood'
plotDAbeeswarm: no visible binding for global variable 'logFC_color'
plotNhoodExpressionDA: no visible binding for global variable 'Nhood'
plotNhoodExpressionDA: no visible binding for global variable 'logFC'
plotNhoodExpressionDA: no visible binding for global variable
'SpatialFDR'
plotNhoodExpressionDA: no visible binding for global variable
'logFC_rank'
plotNhoodExpressionDA: no visible binding for global variable '.'
plotNhoodExpressionDA: no visible binding for global variable
'is_signif'
plotNhoodExpressionDA: no visible binding for global variable 'feature'
plotNhoodExpressionDA: no visible binding for global variable
'avg_expr'
plotNhoodExpressionDA: no visible binding for global variable 'label'
plotNhoodExpressionGroups: no visible binding for global variable
'Nhood'
plotNhoodExpressionGroups: no visible binding for global variable
'NhoodGroup'
plotNhoodExpressionGroups: no visible binding for global variable
'logFC'
plotNhoodExpressionGroups: no visible binding for global variable
'feature'
plotNhoodExpressionGroups: no visible binding for global variable
'logFC_rank'
plotNhoodExpressionGroups: no visible binding for global variable
'avg_expr'
plotNhoodExpressionGroups: no visible binding for global variable '.'
plotNhoodExpressionGroups: no visible binding for global variable
'label'
plotNhoodGraph: no visible binding for global variable 'weight'
plotNhoodGraph: no visible binding for global variable 'size'
plotNhoodGraphDA: no visible binding for global variable 'layout'
plotNhoodGroups: no visible binding for global variable 'layout'
plotNhoodMA: no visible binding for global variable 'logCPM'
plotNhoodMA: no visible binding for global variable 'logFC'
plotNhoodMA: no visible binding for global variable 'Sig'
plotNhoodSizeHist: no visible binding for global variable 'nh_size'
Undefined global functions or variables:
. Nhood NhoodGroup Sig SpatialFDR avg_expr feature is_signif label
layout logCPM logFC logFC_color logFC_rank nh_size size weight
Consider adding
importFrom("graphics", "layout")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: findNhoodGroupMarkers.Rd:79-81: Dropping empty section \examples
* 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
findNhoodMarkers 7.52 0.03 7.65
testNhoods 5.28 0.03 5.32
testDiffExp 5.18 0.11 5.28
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findNhoodMarkers 5.71 0.03 5.73
testNhoods 5.09 0.03 5.13
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/miloR.Rcheck/00check.log'
for details.
miloR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/miloR_1.2.0.tar.gz && rm -rf miloR.buildbin-libdir && mkdir miloR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=miloR.buildbin-libdir miloR_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL miloR_1.2.0.zip && rm miloR_1.2.0.tar.gz miloR_1.2.0.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
27 5825k 27 1592k 0 0 1945k 0 0:00:02 --:--:-- 0:00:02 1944k
82 5825k 82 4780k 0 0 2633k 0 0:00:02 0:00:01 0:00:01 2633k
100 5825k 100 5825k 0 0 2784k 0 0:00:02 0:00:02 --:--:-- 2786k
install for i386
* installing *source* package 'miloR' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'graph' in package 'miloR'
** help
*** installing help indices
converting help for package 'miloR'
finding HTML links ... done
Milo html
finding level-2 HTML links ... done
annotateNhoods html
buildFromAdjacency html
buildGraph html
buildNhoodGraph html
calcNhoodDistance html
calcNhoodExpression html
countCells html
findNhoodGroupMarkers html
findNhoodMarkers html
graphSpatialFDR html
groupNhoods html
makeNhoods html
matrixORMatrix-class html
methods html
miloR-package html
plotDAbeeswarm html
plotNhoodExpressionDA html
plotNhoodGraph html
plotNhoodGraphDA html
plotNhoodMA html
plotNhoodSizeHist html
sim_discrete html
sim_trajectory html
testDiffExp html
testNhoods 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 'miloR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'miloR' as miloR_1.2.0.zip
* DONE (miloR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'miloR' successfully unpacked and MD5 sums checked
|
miloR.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(miloR)
Loading required package: edgeR
Loading required package: limma
> require(mvtnorm)
Loading required package: mvtnorm
> require(scran)
Loading required package: scran
Loading required package: SingleCellExperiment
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 object is masked from 'package:limma':
plotMA
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
Attaching package: 'SingleCellExperiment'
The following object is masked from 'package:edgeR':
cpm
Loading required package: scuttle
> require(scater)
Loading required package: scater
Loading required package: ggplot2
Attaching package: 'scater'
The following object is masked from 'package:limma':
plotMDS
> require(MASS)
Loading required package: MASS
>
> test_check("miloR")
A patchwork composed of 2 patches
- Autotagging is turned off
- Guides are collected
Layout:
2 patch areas, spanning 2 columns and 1 rows
t l b r
1: 1 1 1 1
2: 1 2 1 2
A patchwork composed of 2 patches
- Autotagging is turned off
- Guides are collected
Layout:
2 patch areas, spanning 2 columns and 1 rows
t l b r
1: 1 1 1 1
2: 1 2 1 2
Coefficients not estimable: ConditionA
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 167 ]
>
> proc.time()
user system elapsed
361.34 6.78 368.42
|
miloR.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(miloR)
Loading required package: edgeR
Loading required package: limma
> require(mvtnorm)
Loading required package: mvtnorm
> require(scran)
Loading required package: scran
Loading required package: SingleCellExperiment
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 object is masked from 'package:limma':
plotMA
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
Attaching package: 'SingleCellExperiment'
The following object is masked from 'package:edgeR':
cpm
Loading required package: scuttle
> require(scater)
Loading required package: scater
Loading required package: ggplot2
Attaching package: 'scater'
The following object is masked from 'package:limma':
plotMDS
> require(MASS)
Loading required package: MASS
>
> test_check("miloR")
A patchwork composed of 2 patches
- Autotagging is turned off
- Guides are collected
Layout:
2 patch areas, spanning 2 columns and 1 rows
t l b r
1: 1 1 1 1
2: 1 2 1 2
A patchwork composed of 2 patches
- Autotagging is turned off
- Guides are collected
Layout:
2 patch areas, spanning 2 columns and 1 rows
t l b r
1: 1 1 1 1
2: 1 2 1 2
Coefficients not estimable: ConditionA
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 167 ]
>
> proc.time()
user system elapsed
352.68 4.92 357.62
|
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miloR.Rcheck/examples_i386/miloR-Ex.timings
|
miloR.Rcheck/examples_x64/miloR-Ex.timings
|