Back to Build/check report for BioC 3.21 experimental data |
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This page was generated on 2024-12-10 15:01 -0500 (Tue, 10 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4749 |
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 |
Package 201/430 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
imcdatasets 1.15.0 (landing page) Nicolas Damond
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||
To the developers/maintainers of the imcdatasets package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: imcdatasets |
Version: 1.15.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:imcdatasets.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings imcdatasets_1.15.0.tar.gz |
StartedAt: 2024-12-10 12:45:54 -0500 (Tue, 10 Dec 2024) |
EndedAt: 2024-12-10 13:04:59 -0500 (Tue, 10 Dec 2024) |
EllapsedTime: 1145.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: imcdatasets.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:imcdatasets.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings imcdatasets_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/imcdatasets.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘imcdatasets/DESCRIPTION’ ... OK * this is package ‘imcdatasets’ version ‘1.15.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘imcdatasets’ 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 code 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 loading without being on the library search path ... 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: Damond_2019_Pancreas.Rd: HDF5Array-class, CytoImageList-class, SingleCellExperiment-class, SpatialExperiment-class HochSchulz_2022_Melanoma.Rd: HDF5Array-class, CytoImageList-class, SingleCellExperiment-class, SpatialExperiment-class IMMUcan_2022_CancerExample.Rd: HDF5Array-class, CytoImageList-class, SingleCellExperiment-class, SpatialExperiment-class JacksonFischer_2020_BreastCancer.Rd: HDF5Array-class, CytoImageList-class, SingleCellExperiment-class, SpatialExperiment-class Zanotelli_2020_Spheroids.Rd: HDF5Array-class, CytoImageList-class, SingleCellExperiment-class, SpatialExperiment-class listDatasets.Rd: DataFrame-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Zanotelli_2020_Spheroids 41.523 2.227 44.417 HochSchulz_2022_Melanoma 28.606 2.489 31.780 Damond_2019_Pancreas 24.247 1.502 26.448 JacksonFischer_2020_BreastCancer 23.404 1.995 26.070 IMMUcan_2022_CancerExample 5.547 0.385 6.572 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-data-experiment/meat/imcdatasets.Rcheck/00check.log’ for details.
imcdatasets.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL imcdatasets ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘imcdatasets’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (imcdatasets)
imcdatasets.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(imcdatasets) 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: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges 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: SpatialExperiment Loading required package: cytomapper Loading required package: EBImage Attaching package: 'EBImage' The following object is masked from 'package:SummarizedExperiment': resize The following object is masked from 'package:Biobase': channel The following objects are masked from 'package:GenomicRanges': resize, tile The following objects are masked from 'package:IRanges': resize, tile Attaching package: 'cytomapper' The following objects are masked from 'package:Biobase': channelNames, channelNames<- > test_check("imcdatasets") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ] > > proc.time() user system elapsed 295.787 51.148 394.389
imcdatasets.Rcheck/imcdatasets-Ex.timings
name | user | system | elapsed | |
Damond_2019_Pancreas | 24.247 | 1.502 | 26.448 | |
HochSchulz_2022_Melanoma | 28.606 | 2.489 | 31.780 | |
IMMUcan_2022_CancerExample | 5.547 | 0.385 | 6.572 | |
JacksonFischer_2020_BreastCancer | 23.404 | 1.995 | 26.070 | |
Zanotelli_2020_Spheroids | 41.523 | 2.227 | 44.417 | |
listDatasets | 0.011 | 0.001 | 0.012 | |