Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 2013/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
smoppix 1.1.4 (landing page) Stijn Hawinkel
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | TIMEOUT | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
To the developers/maintainers of the smoppix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/smoppix.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: smoppix |
Version: 1.1.4 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:smoppix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings smoppix_1.1.4.tar.gz |
StartedAt: 2025-08-08 21:41:45 -0400 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 21:44:12 -0400 (Fri, 08 Aug 2025) |
EllapsedTime: 147.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: smoppix.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:smoppix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings smoppix_1.1.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/smoppix.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘smoppix/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘smoppix’ version ‘1.1.4’ * 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 ‘smoppix’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... NOTE plotCells: no visible binding for global variable ‘gene’ plotCells: no visible binding for global variable ‘cell’ plotWf: no visible binding for global variable ‘minP’ plotWf: no visible binding for global variable ‘maxP’ plotWf: no visible binding for global variable ‘Weight’ Undefined global functions or variables: Weight cell gene maxP minP * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotTopResults 4.265 1.623 3.669 estPis 4.324 1.157 1.355 fitLMMs 3.245 1.929 2.478 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: <character> <character> <list> <numeric> 1 section1 lowres #### 0.0510334 2 section2 lowres #### 0.0510334 [ FAIL 1 | WARN 2 | SKIP 0 | PASS 187 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-weightFun.R:16:5'): Adding the weight function works ───────── predNew > evalWeightFunction(objBG$Wfs[["nn"]], newdata = data.frame(NP = 2)) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 1 | WARN 2 | SKIP 0 | PASS 187 ] Error: Test failures Execution halted * 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: 1 ERROR, 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/smoppix.Rcheck/00check.log’ for details.
smoppix.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL smoppix ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘smoppix’ ... ** this is package ‘smoppix’ version ‘1.1.4’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c crossdistFast.cpp -o crossdistFast.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c findRanksDist.cpp -o findRanksDist.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o smoppix.so RcppExports.o crossdistFast.o findRanksDist.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-smoppix/00new/smoppix/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help Loading required namespace: smoppix *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (smoppix)
smoppix.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-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(smoppix) > library(spatstat.random) Loading required package: spatstat.data Loading required package: spatstat.univar spatstat.univar 3.1-4 Loading required package: spatstat.geom spatstat.geom 3.5-0 spatstat.random 3.4-1 > library(BiocParallel) > n <- 4000 # number of molecules > ng <- 8 # number of genes > nfov <- 3 # Number of fields of view > conditions <- 3 > # sample xy-coordinates in [0, 1] > x <- runif(n) > y <- runif(n) > # assign each molecule to some gene-cell pair > gs <- paste0("gene", seq(ng)) > gene <- sample(gs, n, TRUE) > fov <- as.character(sample(nfov, n, TRUE)) > condition <- as.character(sample(conditions, n, TRUE)) > f = paste(fov, condition, sep = "_") > age = unsplit(lapply(split(integer(n), f = f), function(x) {rep(runif(1, 18, 98))}), f = f) > # construct data.frame of molecule coordinates > df <- data.frame(gene, x, y, fov, condition = condition, age = age) > # A list of point patterns > listPPP <- tapply(seq(nrow(df)), df$fov, function(i) { + ppp(x = df$x[i], y = df$y[i], marks = df[i, c("gene", "condition", "fov", "age"), drop = FALSE]) + }, simplify = FALSE) > # Regions of interest (roi): Diamond in the center plus four triangles > w1 <- owin(poly = list(x = c(0, 0.5, 1, 0.5), y = c(0.5, 0, 0.5, 1))) > w2 <- owin(poly = list(x = c(0, 0, 0.5), y = c(0.5, 0, 0))) > w3 <- owin(poly = list(x = c(0, 0, 0.5), y = c(1, 0.5, 1))) > w4 <- owin(poly = list(x = c(1, 1, 0.5), y = c(0.5, 1, 1))) > w5 <- owin(poly = list(x = c(1, 1, 0.5), y = c(0, 0.5, 0))) > wWrong <- owin(poly = list(x = c(0, 1, 1, 0), y = c(0.75, 0.5, 0.75, 1))) > hypFrame <- buildHyperFrame(df, coordVars = c("x", "y"), imageVars = c( + "condition", "fov", "age" + ), imageIdentifier = c("fov", "condition")) Found 9 unique images > nDesignFactors <- length(unique(hypFrame$image)) > wList <- lapply(seq_len(nDesignFactors), function(x) { + Li <- list(w1 = w1, w2 = w2, w3 = w3, w4 = w4, w5 = w5) + names(Li) <- paste0(names(Li), "_", x) + Li + }) > wList2 <- lapply(seq_len(nDesignFactors), function(x) { + list(w1 = w1, w2 = w2, w3 = w3, w4 = w4, w5 = w5, wWrong = wWrong) + }) > unCells <- unlist(lapply(wList, names)) > cellTypesDf <- data.frame(cell = unCells, cellType = sample(paste0("CellType_", LETTERS[seq_len(5)]), + length(unCells), + replace = TRUE + )) > names(wList) <- names(wList2) <- rownames(hypFrame) > hypFrame2 <- addCell(hypFrame, wList, cellTypes = cellTypesDf, verbose = FALSE) > # The nuclei > n1 <- owin(poly = list(x = c(0.2, .4, 0.8, .4), y = c(.4, .2, .4, .8))) > n2 <- owin(poly = list(x = c(0.1, 0.1, .4), y = c(.4, .1, .1))) > n3 <- owin(poly = list(x = c(0.1, 0.1, .4), y = c(1, .75, 1))) > n4 <- owin(poly = list(x = c(1, 1, .6), y = c(.7, .9, .9))) > n5 <- owin(poly = list(x = c(.95, .95, .7), y = c(.1, .4, .1))) > nLarge <- owin(poly = list(x = c(1.1, 1.1, .7), y = c(.1, .4, .1))) > nList <- lapply(seq_len(nDesignFactors), function(x) { + Li <- list("w1" = n1, "w2" = n2, "w3" = n3, "w4" = n4, "w5" = n5) + names(Li) <- paste0(names(Li), "_", x) + Li + }) > nList2 <- lapply(seq_len(nDesignFactors), function(x) { + Li <- list("w1" = n1, "w2" = n2, "w3" = n3, "w4" = n4, "w5" = nLarge) + names(Li) <- paste0(names(Li), "_", x) + Li + }) > names(nList) <- names(nList2) <- rownames(hypFrame) # Matching names is necessary > hypFrame2 <- addNuclei(hypFrame2, nList, verbose = FALSE) > # Register the parallel backend > nCores <- 2 > if(.Platform$OS.type == "unix"){ + #On unix-based systems, use MulticoreParam + register(MulticoreParam(nCores)) + } else { + #On windows, use makeCluster + library(doParallel) + Clus = makeCluster(nCores) + registerDoParallel(Clus) + register(DoparParam(), default = TRUE) + } > #register(SerialParam()) # Switch on when mapping test coverage > pis <- c("nn", "nnPair", "edge", "centroid", "nnCell", "nnPairCell") > piEstsBG <- estPis(hypFrame2, pis = pis, null = "background", verbose = FALSE) > piEstsCSR <- estPis(hypFrame2, pis = pis, null = "CSR", verbose = FALSE) > piEstsBG2 <- estPis(hypFrame2[, c("ppp", "image", "tabObs")], + pis = "nn", null = "background", + verbose = FALSE + ) > # Add weight functions > objBG <- addWeightFunction(piEstsBG, designVars = "condition") > objCSR <- addWeightFunction(piEstsCSR, designVars = "condition") > # Fit Yang models too > data(Yang) > hypYang <- buildHyperFrame(Yang[Yang$section %in% paste0("section", seq_len(3)),], + coordVars = c("x", "y"), imageVars = c("day", "root", "section" + )) #Subset for speed Found 18 unique images > yangPims <- estPis(hypYang, features = getFeatures(hypYang)[12:21], + pis = c("nn", "nnPair"), verbose = FALSE, nPointsAll = 2e3) > yangPims <- addWeightFunction(yangPims, lowestLevelVar = "section") > data(Eng) > hypEng <- buildHyperFrame(Eng, coordVars = c("x", "y"), imageVars = c("fov", "experiment")) Found 17 unique images There were 13 warnings (use warnings() to see them) > hypEng <- addCell(hypEng, EngRois, verbose = FALSE) > test_check("smoppix") rd10xV> dir <- system.file( rd10xV+ file.path("extdata", "10xVisium"), rd10xV+ package = "SpatialExperiment") rd10xV> sample_ids <- c("section1", "section2") rd10xV> samples <- file.path(dir, sample_ids, "outs") rd10xV> list.files(samples[1]) [1] "raw_feature_bc_matrix" "spatial" rd10xV> list.files(file.path(samples[1], "spatial")) [1] "scalefactors_json.json" "tissue_lowres_image.png" [3] "tissue_positions_list.csv" rd10xV> file.path(samples[1], "raw_feature_bc_matrix") [1] "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/SpatialExperiment/extdata/10xVisium/section1/outs/raw_feature_bc_matrix" rd10xV> (spe <- read10xVisium(samples, sample_ids, rd10xV+ type = "sparse", data = "raw", rd10xV+ images = "lowres", load = FALSE)) class: SpatialExperiment dim: 50 99 metadata(0): assays(1): counts rownames(50): ENSMUSG00000051951 ENSMUSG00000089699 ... ENSMUSG00000005886 ENSMUSG00000101476 rowData names(1): symbol colnames(99): AAACAACGAATAGTTC-1 AAACAAGTATCTCCCA-1 ... AAAGTCGACCCTCAGT-1 AAAGTGCCATCAATTA-1 colData names(4): in_tissue array_row array_col sample_id reducedDimNames(0): mainExpName: NULL altExpNames(0): spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres imgData names(4): sample_id image_id data scaleFactor rd10xV> # base directory 'outs/' from Space Ranger can also be omitted rd10xV> samples2 <- file.path(dir, sample_ids) rd10xV> (spe2 <- read10xVisium(samples2, sample_ids, rd10xV+ type = "sparse", data = "raw", rd10xV+ images = "lowres", load = FALSE)) class: SpatialExperiment dim: 50 99 metadata(0): assays(1): counts rownames(50): ENSMUSG00000051951 ENSMUSG00000089699 ... ENSMUSG00000005886 ENSMUSG00000101476 rowData names(1): symbol colnames(99): AAACAACGAATAGTTC-1 AAACAAGTATCTCCCA-1 ... AAAGTCGACCCTCAGT-1 AAAGTGCCATCAATTA-1 colData names(4): in_tissue array_row array_col sample_id reducedDimNames(0): mainExpName: NULL altExpNames(0): spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres imgData names(4): sample_id image_id data scaleFactor rd10xV> # tabulate number of spots mapped to tissue rd10xV> cd <- colData(spe) rd10xV> table( rd10xV+ in_tissue = cd$in_tissue, rd10xV+ sample_id = cd$sample_id) sample_id in_tissue section1 section2 FALSE 28 27 TRUE 22 22 rd10xV> # view available images rd10xV> imgData(spe) DataFrame with 2 rows and 4 columns sample_id image_id data scaleFactor <character> <character> <list> <numeric> 1 section1 lowres #### 0.0510334 2 section2 lowres #### 0.0510334 [ FAIL 1 | WARN 2 | SKIP 0 | PASS 187 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-weightFun.R:16:5'): Adding the weight function works ───────── predNew > evalWeightFunction(objBG$Wfs[["nn"]], newdata = data.frame(NP = 2)) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 1 | WARN 2 | SKIP 0 | PASS 187 ] Error: Test failures Execution halted
smoppix.Rcheck/smoppix-Ex.timings
name | user | system | elapsed | |
addCell | 1.322 | 0.128 | 1.352 | |
addNuclei | 0.136 | 0.213 | 0.208 | |
buildDataFrame | 1.171 | 0.585 | 1.295 | |
buildHyperFrame | 0.610 | 0.039 | 0.650 | |
estGradients | 1.058 | 0.633 | 4.698 | |
estPis | 4.324 | 1.157 | 1.355 | |
evalWeightFunction | 1.848 | 1.813 | 2.249 | |
findOverlap | 0.040 | 0.071 | 0.104 | |
fitLMMs | 3.245 | 1.929 | 2.478 | |
getFeatures | 0.589 | 0.063 | 0.655 | |
getGp | 0.000 | 0.001 | 0.000 | |
makePairs | 0.001 | 0.000 | 0.000 | |
plotCells | 0.133 | 0.169 | 0.208 | |
plotExplore | 1.928 | 0.140 | 2.086 | |
plotTopResults | 4.265 | 1.623 | 3.669 | |
plotWf | 1.120 | 0.586 | 1.256 | |
sund | 0 | 0 | 0 | |
writeToXlsx | 3.057 | 1.820 | 2.584 | |