Nils Eling
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/cytomapper |
| git_branch: RELEASE_3_13 |
| git_last_commit: edd9a70 |
| git_last_commit_date: 2021-05-21 05:14:02 -0400 (Fri, 21 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:02 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the cytomapper package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cytomapper.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 434/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cytomapper 1.4.1 (landing page) Nils Eling
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: cytomapper |
| Version: 1.4.1 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cytomapper.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings cytomapper_1.4.1.tar.gz |
| StartedAt: 2021-10-14 21:50:51 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 22:29:17 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 2306.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cytomapper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cytomapper.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings cytomapper_1.4.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/cytomapper.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 'cytomapper/DESCRIPTION' ... OK
* this is package 'cytomapper' version '1.4.1'
* 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 'cytomapper' 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
plotting-param 6.85 0.03 6.88
plotCells 5.03 0.35 5.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotting-param 6.78 0.03 6.81
plotCells 5.96 0.11 6.08
measureObjects 5.49 0.05 5.53
* 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
cytomapper.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/cytomapper_1.4.1.tar.gz && rm -rf cytomapper.buildbin-libdir && mkdir cytomapper.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cytomapper.buildbin-libdir cytomapper_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL cytomapper_1.4.1.zip && rm cytomapper_1.4.1.tar.gz cytomapper_1.4.1.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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
10 17.8M 10 1911k 0 0 1804k 0 0:00:10 0:00:01 0:00:09 1805k
27 17.8M 27 5026k 0 0 2444k 0 0:00:07 0:00:02 0:00:05 2445k
48 17.8M 48 8884k 0 0 2895k 0 0:00:06 0:00:03 0:00:03 2894k
72 17.8M 72 13.0M 0 0 3281k 0 0:00:05 0:00:04 0:00:01 3281k
100 17.8M 100 17.8M 0 0 3688k 0 0:00:04 0:00:04 --:--:-- 3733k
install for i386
* installing *source* package 'cytomapper' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cytomapper'
finding HTML links ... done
CytoImageList-manipulation html
finding level-2 HTML links ... done
CytoImageList-naming html
CytoImageList-subsetting html
CytoImageList html
cytomapperShiny html
loadImages html
measureObjects html
pancreasImages html
pancreasMasks html
pancreasSCE html
plotCells html
plotPixels html
plotting-param 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 'cytomapper' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cytomapper' as cytomapper_1.4.1.zip
* DONE (cytomapper)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'cytomapper' successfully unpacked and MD5 sums checked
|
cytomapper.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(cytomapper)
Loading required package: EBImage
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
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 objects are masked from 'package:EBImage':
resize, tile
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
The following object is masked from 'package:EBImage':
channel
Attaching package: 'cytomapper'
The following objects are masked from 'package:Biobase':
channelNames, channelNames<-
>
> test_check("cytomapper")
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
== Skipped tests ===============================================================
* On CRAN (5)
* empty test (5)
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 2914 ]
>
> proc.time()
user system elapsed
643.87 26.89 926.79
|
cytomapper.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(cytomapper)
Loading required package: EBImage
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
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 objects are masked from 'package:EBImage':
resize, tile
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
The following object is masked from 'package:EBImage':
channel
Attaching package: 'cytomapper'
The following objects are masked from 'package:Biobase':
channelNames, channelNames<-
>
> test_check("cytomapper")
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
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be deactivated with `verify_fa = FALSE`
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be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
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be deactivated with `verify_fa = FALSE`
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* if providing a custom `html_dependency` these `name` checks can
be deactivated with `verify_fa = FALSE`
== Skipped tests ===============================================================
* On CRAN (5)
* empty test (5)
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 2914 ]
>
> proc.time()
user system elapsed
671.73 21.43 938.35
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cytomapper.Rcheck/examples_i386/cytomapper-Ex.timings
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cytomapper.Rcheck/examples_x64/cytomapper-Ex.timings
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