Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 2021/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
standR 1.9.0 (landing page) Ning Liu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the standR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/standR.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: standR |
Version: 1.9.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:standR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings standR_1.9.0.tar.gz |
StartedAt: 2024-06-10 10:47:40 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 10:58:26 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 645.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: standR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:standR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings standR_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/standR.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘standR/DESCRIPTION’ ... OK * this is package ‘standR’ version ‘1.9.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘standR’ 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 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed prepareSpatialDecon 18.032 2.531 27.040 findBestK 12.465 0.356 14.093 readGeoMx 10.086 1.095 10.178 plotClusterEvalStats 5.276 0.058 5.785 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
standR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL standR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘standR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘drawPCA’ with signature ‘"DGEList"’: no definition for class “DGEList” in method for ‘drawPCA’ with signature ‘"SpatialExperiment"’: no definition for class “SpatialExperiment” in method for ‘plotDR’ with signature ‘"SpatialExperiment","ANY"’: no definition for class “SpatialExperiment” in method for ‘plotMDS’ with signature ‘"DGEList","ANY","ANY","ANY"’: no definition for class “DGEList” in method for ‘plotMDS’ with signature ‘"SpatialExperiment"’: no definition for class “SpatialExperiment” in method for ‘plotRLExpr’ with signature ‘"DGEList","ANY"’: no definition for class “DGEList” ** help *** installing help indices *** copying figures ** 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 (standR)
standR.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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(standR) > > test_check("standR") Loading required package: SpatialExperiment 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 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, 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 New names: * `cv` -> `cv...1` * `cv` -> `cv...2` * `cv` -> `cv...3` * `cv` -> `cv...4` * `cv` -> `cv...5` * `cv` -> `cv...6` * `cv` -> `cv...7` New names: * `cv` -> `cv...1` * `cv` -> `cv...2` * `cv` -> `cv...3` * `cv` -> `cv...4` * `cv` -> `cv...5` * `cv` -> `cv...6` * `cv` -> `cv...7` Rows: 18504 Columns: 232 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (1): TargetName dbl (231): disease3_scan | 001 | PanCK, disease3_scan | 001 | neg, disease3_... i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 231 Columns: 25 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (8): SlideName, ScanName, SegmentLabel, SegmentDisplayName, Sample_ID, ... dbl (17): ROILabel, AOISurfaceArea, AOINucleiCount, ROICoordinateX, ROICoord... i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 18504 Columns: 232 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (1): TargetName dbl (231): disease3_scan | 001 | PanCK, disease3_scan | 001 | neg, disease3_... i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 18504 Columns: 232 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (1): TargetName dbl (231): disease3_scan | 001 | PanCK, disease3_scan | 001 | neg, disease3_... i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 231 Columns: 25 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (8): SlideName, ScanName, SegmentLabel, SegmentDisplayName, Sample_ID, ... dbl (17): ROILabel, AOISurfaceArea, AOINucleiCount, ROICoordinateX, ROICoord... i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Loading required namespace: scater Loading required package: scuttle Loading required package: ggplot2 Attaching package: 'scater' The following object is masked from 'package:standR': plotMDS Loading required package: AnnotationHub Loading required package: BiocFileCache Loading required package: dbplyr Attaching package: 'AnnotationHub' The following object is masked from 'package:Biobase': cache see ?standR and browseVignettes('standR') for documentation loading from cache see ?standR and browseVignettes('standR') for documentation loading from cache Rows: 18504 Columns: 232 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (1): TargetName dbl (231): disease3_scan | 001 | PanCK, disease3_scan | 001 | neg, disease3_... i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 231 Columns: 25 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (8): SlideName, ScanName, SegmentLabel, SegmentDisplayName, Sample_ID, ... dbl (17): ROILabel, AOISurfaceArea, AOINucleiCount, ROICoordinateX, ROICoord... i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 104 ] > > proc.time() user system elapsed 125.053 7.935 146.082
standR.Rcheck/standR-Ex.timings
name | user | system | elapsed | |
addPerROIQC | 2.865 | 0.111 | 3.298 | |
computeClusterEvalStats | 3.969 | 0.150 | 4.358 | |
dkd_spe_subset | 0.081 | 0.006 | 0.091 | |
drawPCA | 0.773 | 0.091 | 0.910 | |
findBestK | 12.465 | 0.356 | 14.093 | |
findNCGs | 2.095 | 0.139 | 2.432 | |
geomxBatchCorrection | 3.403 | 0.155 | 4.018 | |
geomxNorm | 2.531 | 0.124 | 2.988 | |
plotClusterEvalStats | 5.276 | 0.058 | 5.785 | |
plotDR | 1.106 | 0.037 | 1.305 | |
plotGeneQC | 2.923 | 0.027 | 3.241 | |
plotMDS | 1.341 | 0.064 | 1.486 | |
plotPCAbiplot | 0.826 | 0.010 | 0.885 | |
plotPairPCA | 2.166 | 0.029 | 2.353 | |
plotRLExpr | 3.812 | 0.027 | 4.174 | |
plotROIQC | 2.306 | 0.049 | 2.547 | |
plotSampleInfo | 1.888 | 0.018 | 2.117 | |
plotScreePCA | 0.569 | 0.007 | 0.622 | |
prepareSpatialDecon | 18.032 | 2.531 | 27.040 | |
readGeoMx | 10.086 | 1.095 | 10.178 | |
readGeoMxFromDGE | 0.629 | 0.007 | 0.692 | |
spe2dge | 1.249 | 0.050 | 1.398 | |