Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1446/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
omicsViewer 1.11.0 (landing page) Chen Meng
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the omicsViewer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/omicsViewer.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: omicsViewer |
Version: 1.11.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:omicsViewer.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings omicsViewer_1.11.0.tar.gz |
StartedAt: 2024-12-24 00:32:17 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 00:37:22 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 304.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: omicsViewer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:omicsViewer.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings omicsViewer_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/omicsViewer.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 ‘omicsViewer/DESCRIPTION’ ... OK * this is package ‘omicsViewer’ version ‘1.11.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 33 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘omicsViewer’ 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test_auxi_sparse_converter.R’ Running ‘test_db_vs_esv.R’ Running ‘test_dose_response.R’ Running ‘test_motif.R’ Running ‘test_ora.R’ Running ‘test_shinyAuxi.R’ Running ‘test_stats.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: OK
omicsViewer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL omicsViewer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘omicsViewer’ ... ** 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 (omicsViewer)
omicsViewer.Rcheck/tests/test_auxi_sparse_converter.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(omicsViewer) > library(Matrix) > library(unittest, quietly = TRUE) > > # source("R/auxi_sparse_converter.R") > > m <- matrix(0, 10, 5, dimnames = list(paste0("R", 1:10), paste0("C", 1:5))) > for (i in 2:ncol(m)) { + m[i*2, i] <- 1 + } > > csc <- as(m, "dgCMatrix") > ok(ut_cmp_equal(colSums(csc), colSums(m)), "as sparse") ok - as sparse > > scc <- omicsViewer:::csc2list(csc) > csc2 <- omicsViewer:::list2csc(scc, dimnames = list(rownames(m))) > ok(ut_cmp_equal(colSums(csc2), colSums(m)[-1], check.attributes = FALSE), + "only rownames, missing 0 column") ok - only rownames, missing 0 column > > csc3 <- omicsViewer:::list2csc(scc, dimnames = list(rownames(m), colnames(m))) > ok(ut_cmp_equal(colSums(csc3), colSums(m), check.attributes = FALSE), + "both rownames and columns given") ok - both rownames and columns given > ok(ut_cmp_equal(as(csc3, "matrix"), m, check.attributes = FALSE), + "regular matrix") ok - regular matrix > > scc2 <- scc > scc2$weight <- NULL > csc4 <- omicsViewer:::list2csc(scc2, dimnames = list(rownames(m), colnames(m))) > ok(ut_cmp_equal(colSums(csc4), colSums(m), check.attributes = FALSE), + "as binary matrix") ok - as binary matrix > > > # ================= conversion of hclust object ================= > m <- matrix(rnorm(50), 25, dimnames = list(paste0("g", 1:25), c('c1', 'c2'))) > hc <- hclust(dist(m)) > plot(hc) > te <- omicsViewer:::hclust2str(hc) > hc2 <- omicsViewer:::str2hclust(te) > plot(hc2) > hc_elements <- names(hc) > ok(ut_cmp_equal(all(names(hc2) %in% hc_elements), TRUE), "Element name test") ok - Element name test > j <- sapply(setdiff(hc_elements, "call"), function(x) + all.equal(hc[[x]], hc2[[x]], tol = 5e-5, check.attributes = FALSE)) > ok(ut_cmp_equal(all(j), TRUE), "HCL element conversion test.") ok - HCL element conversion test. > > > # ===================== select highlight block =================== > cl <- list(x = -5:5, y = c(5:0, 1:5)) > line_rect <- omicsViewer:::line_rect > r <- line_rect(coord = cl, l = list(x = 2.5, y = 2.5, corner = "topright")) > ok( + ut_cmp_equal( + r$rect[[1]][c("x0", "y0")], c(2.5, 2.5), check.attributes = FALSE + ), "line_rect - topright" + ) ok - line_rect - topright > > r <- line_rect(coord = cl, l = list(x = 2.5, y = 2.5, corner = "volcano")) > ok( + ut_cmp_identical(length(r$rect), as.integer(2)), + "line_rect - volcano n block" + ) ok - line_rect - volcano n block > ok( + ut_cmp_equal( + r$rect[[1]][c("x1", "y0")], c(-2.5, 2.5), check.attributes = FALSE + ), "line_rect - volcano block 1" + ) ok - line_rect - volcano block 1 > ok( + ut_cmp_equal( + r$rect[[2]][c("x0", "y0")], c(2.5, 2.5), check.attributes = FALSE + ), "line_rect - volcano block 2" + ) ok - line_rect - volcano block 2 > > ok( + ut_cmp_identical( + line_rect(coord = cl, l = list(y = 2.5, corner = "volcano")), NULL + ), "line_rect - NULL 1" + ) ok - line_rect - NULL 1 > > ok( + ut_cmp_identical( + line_rect(coord = cl, l = list(x = 2.5, corner = "volcano")), NULL + ), "line_rect - NULL 2" + ) ok - line_rect - NULL 2 > > ok( + ut_cmp_identical( + line_rect(coord = cl, l = list(x = 2.5, y = 2.5, corner = "None")), NULL + ), "line_rect - NULL 3" + ) ok - line_rect - NULL 3 > > > proc.time() user system elapsed 7.674 0.496 8.163 1..14 # Looks like you passed all 14 tests.
omicsViewer.Rcheck/tests/test_db_vs_esv.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(unittest, quietly = TRUE) > library(RSQLite) > library(omicsViewer) > > > f <- system.file(package = 'omicsViewer', 'extdata/demo.RDS') > obj <- readRDS(f) > dd <- tools::R_user_dir("omicsViewer", which="cache") > dir.create(dd) Warning message: In dir.create(dd) : '/home/biocbuild/.cache/R/omicsViewer' already exists > db <- tempfile(tmpdir = dd, fileext = ".db") > savedPath <- saveOmicsViewerDb(obj, db) > ok(ut_cmp_identical(is.character(savedPath), TRUE), "save sqlite database") ok - save sqlite database > > esv1 <- readESVObj(f) > ok(ut_cmp_identical(inherits(esv1, "ExpressionSet"), TRUE), "read expressionset") ok - read expressionset > > esv2 <- readESVObj(db) > ok(ut_cmp_identical(inherits(esv2, "SQLiteConnection"), TRUE), "connect to database") ok - connect to database > > getExprs <- omicsViewer:::getExprs > expr1 <- getExprs(esv1) > expr2 <- getExprs(esv2) > ok(ut_cmp_identical(expr1, expr2), "db vs esv - expression") ok - db vs esv - expression > > getExprsImpute <- omicsViewer:::getExprsImpute > expr1 <- getExprsImpute(esv1) > expr2 <- getExprsImpute(esv2) > ok(ut_cmp_identical(expr1, expr2), "db vs esv - expression imputed") ok - db vs esv - expression imputed > > > getPData <- omicsViewer:::getPData > getFData <- omicsViewer:::getFData > getAx <- omicsViewer:::getAx > getDend <- omicsViewer:::getDend > > pd1 <- getPData(esv1) > pd2 <- getPData(esv2) > ok(ut_cmp_identical(colnames(pd1), colnames(pd2)), "db vs esv - phenotype 1") ok - db vs esv - phenotype 1 > ok(ut_cmp_identical(rownames(pd1), rownames(pd2)), "db vs esv - phenotype 2") ok - db vs esv - phenotype 2 > > fd1 <- getFData(esv1) > fd2 <- getFData(esv2) > ok(ut_cmp_identical(rownames(fd1), rownames(fd2)), "db vs esv - feature data") ok - db vs esv - feature data > > for (i in c("sx", "sy", "fx", "fy")) { + ax1 <- getAx(esv1, i) + ax2 <- getAx(esv2, i) + ok(ut_cmp_identical(ax1, ax2), sprintf("db vs esv - get axis - %s", i)) + } ok - db vs esv - get axis - sx ok - db vs esv - get axis - sy ok - db vs esv - get axis - fx ok - db vs esv - get axis - fy > > dd2 <- getDend(esv2) > ok(ut_cmp_identical(dd2, NULL), "db get dend") ok - db get dend > > > proc.time() user system elapsed 10.291 0.635 10.915 1..13 # Looks like you passed all 13 tests.
omicsViewer.Rcheck/tests/test_dose_response.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(unittest) > library(drc) Loading required package: MASS 'drc' has been loaded. Please cite R and 'drc' if used for a publication, for references type 'citation()' and 'citation('drc')'. Attaching package: 'drc' The following objects are masked from 'package:stats': gaussian, getInitial > > ds <- c(0.1, 0.2, 0.4, 0.8, 1.6, 3.2, 6.4, 12.8, 25.6, 51.2, 102.4) > > > testPar <- function( pars, cid = "(Intercept)", b, c, d, e, f, tol = 0.1 ) { + r <- TRUE + nr <- nrow(pars) + id <- paste("ResponseCurve", cid, sep = "|") + + iae <- function(x, y, tolerance) isTRUE(all.equal(x, y, tolerance = tolerance)) + if (!missing(b)) { + rb <- iae(pars[, sprintf("%s|b_hill.slope", id)], rep(b, nr), tolerance = tol) + r <- r && rb + } + + if (!missing(c)) { + rc <- iae(pars[, sprintf("%s|c_min.response", id)], rep(c, nr), tolerance = tol) + r <- r && rc + } + + if (!missing(d)) { + rd <- iae(pars[, sprintf("%s|d_max.response", id)], rep(d, nr), tolerance = tol) + r <- r && rd + } + + if (!missing(e)) { + re <- iae(pars[, sprintf("%s|e_inflection", id)], rep(e, nr), tolerance = tol) + r <- r && re + } + + if (!missing(f)) { + rf <- iae(pars[, sprintf("%s|f_asym.factor", id)], rep(f, nr), tolerance = tol) + r <- r && rf + } + + ok(r) + } > > d_log <- -(10:-1) > dd <- 2^d_log > > for (eb in c(1, -1)) { + ec <- 0 + ed <- 1 + ee <- 0.005 + ef <- 1 + + m1 <- sapply(1:20, function(n) { + y_sim <- omicsViewer:::.modelFormula(dd, b = eb, c = ec, d = ed, e = ee, f = ef) + y_sim + rnorm(length(y_sim), sd = 0.0001) + }) + m1 <- t(m1) + + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL.5()") + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, c = ec, d = ed, e = ee, f = ef) + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL2.5()") + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, c = ec, d = ed, e = ee, f = ef) + + # + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL.4()") + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, c = ec, d = ed, e = ee) + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL2.4()") + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, c = ec, d = ed, e = ee) + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL.3()") + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, d = ed, e = ee) + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL2.3()") + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, d = ed, e = ee) + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL.3u()") + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, c = ec, e = ee) + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL2.3u()") + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, c = ec, e = ee) + + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL.2()") + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, e = ee) + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL2.2()") + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, e = ee) + } ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r > > d_log <- rep(-(10:-1), 2) > dd <- 2^d_log > > for (eb in c(1, -1)) { + ec <- 0 + ed <- 1 + ee <- 0.005 + ef <- 1 + + m1 <- sapply(1:5, function(n) { + y_sim <- omicsViewer:::.modelFormula(dd, b = eb, c = ec, d = ed, e = ee, f = ef) + y_sim + rnorm(length(y_sim), sd = 0.0001) + }) + m1 <- t(m1) + curve <- rep(c("a", "b"), each = 12) + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL.5()", curveid = curve) + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, c = ec, d = ed, e = ee, f = ef, cid = "a") + testPar(pp, b = eb, c = ec, d = ed, e = ee, f = ef, cid = "b") + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL2.5()", curveid = curve) + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, c = ec, d = ed, e = ee, f = ef, cid = "a") + testPar(pp, b = eb, c = ec, d = ed, e = ee, f = ef, cid = "b") + # + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL.4()", curveid = curve) + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, c = ec, d = ed, e = ee, cid = "a") + testPar(pp, b = eb, c = ec, d = ed, e = ee, cid = "b") + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL2.4()", curveid = curve) + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, c = ec, d = ed, e = ee, cid = "a") + testPar(pp, b = eb, c = ec, d = ed, e = ee, cid = "b") + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL.3()", curveid = curve) + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, d = ed, e = ee, cid = "a") + testPar(pp, b = eb, d = ed, e = ee, cid = "b") + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL2.3()", curveid = curve) + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, d = ed, e = ee, cid = "a") + testPar(pp, b = eb, d = ed, e = ee, cid = "b") + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL.3u()", curveid = curve) + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, c = ec, e = ee, cid = "a") + testPar(pp, b = eb, c = ec, e = ee, cid = "b") + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL2.3u()", curveid = curve) + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, c = ec, e = ee, cid = "a") + testPar(pp, b = eb, c = ec, e = ee, cid = "b") + + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL.2()", curveid = curve) + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, e = ee, cid = "a") + testPar(pp, b = eb, e = ee, cid = "b") + + mod <- omicsViewer:::drmMat(m1, fitvar = dd, fitvar.name = "Dose", fct.name = "LL2.2()", curveid = curve) + pp <- omicsViewer:::extractParamDCList(mod) + testPar(pp, b = eb, e = ee, cid = "a") + testPar(pp, b = eb, e = ee, cid = "b") + } ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r ok - r > > > proc.time() user system elapsed 32.606 0.825 33.422 1..60 # Looks like you passed all 60 tests.
omicsViewer.Rcheck/tests/test_motif.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(unittest) > > seqs <- c("PFERVGTATIDNLPT", "MCWPEYCHCLKPIAS", "HRPQTSVNMQDMDPC", "HRPQTSVNMQDMDPCUU") > aaFreq <- omicsViewer:::aaFreq > fq <- aaFreq(seqs[1:3]) > ok( + ut_cmp_equal(dim(fq), c(20, 15)), + "aaFreq - dimension check" + ) ok - aaFreq - dimension check > ok( + ut_cmp_equal(colSums(fq), rep(1, 15)), + "aaFreq - colSum check" + ) ok - aaFreq - colSum check > ok( + ut_cmp_error(aaFreq(seqs), "Different length in x!"), + "aaFreq - length check" + ) ok - aaFreq - length check > > > seqs <- c("PFERVGTATIDNLPT", "MCWPEYCHCLKPIAS", "HRPQTSVNMQDMDPC", "HRPQTSVNMQDMDPC", "HRPQTSVNMQDMDPC") > motifRF <- omicsViewer:::motifRF > sq <- motifRF(fg.seqs = seqs[3:5], bg.seqs = seqs, fg.pfm = NULL, bg.pfm=NULL) > ok( + ut_cmp_equal(dim(sq), c(20, 15)), + "motifRF - dim check" + ) ok - motifRF - dim check > ok( + ut_cmp_equal(unique(c(sq)), c(0, 1)), + "motifRF - value check" + ) ok - motifRF - value check > ok( + ut_cmp_equal(c(table(sq)), c(285, 15), check.attributes = FALSE), + "motifRF - value count check" + ) ok - motifRF - value count check > > proc.time() user system elapsed 7.562 0.503 8.055 1..6 # Looks like you passed all 6 tests.
omicsViewer.Rcheck/tests/test_ora.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(omicsViewer) > library(unittest, quietly = TRUE) > library(Matrix) > library(fastmatch) > > # =========================== conversion ======================== > gs <- cbind( + s1 = c(1, 1, 1, 1, 0, 0, 0, 0), + s2 = c(0, 0, 0, 0, 1, 1, 1, 1), + s3 = c(0, 0, 1, 1, 1, 1, 0, 0)) > stats <- 1:8 > rownames(gs) <- names(stats) <- paste0("g", 1:8) > gss <- as(gs, "dgCMatrix") > ok(ut_cmp_equal(omicsViewer:::csc2list(gs), omicsViewer:::csc2list(gss)), + "convert matrix to data.frame for fgsea") ok - convert matrix to data.frame for fgsea > df <- omicsViewer:::csc2list(gs) > ok( + ut_cmp_equal( + gss, omicsViewer:::list2csc(df, dimnames = dimnames(gs)), check.attributes = FALSE + ), "convert data.frame to matrix" + ) ok - convert data.frame to matrix > > vectORA <- omicsViewer:::vectORA > r1 <- vectORA( gs, i = 1:4, minOverlap = 1, minSize = 1 ) > r2 <- vectORA( gss, i = 1:4, minOverlap = 1, minSize = 1 ) > vectORATall <- omicsViewer:::vectORATall > r3 <- vectORATall( df, i=rownames(gs)[1:4], background=8 ) > > ok( + ut_cmp_equal(r1$pathway, c("s1", "s3"), check.attributes = FALSE), + "vectORA 1" + ) ok - vectORA 1 > ok(ut_cmp_equal(r1, r2, check.attributes = FALSE), "vectORA 2") ok - vectORA 2 > ok(ut_cmp_equal(r1, r3), "vectORATall") ok - vectORATall > > > > res <- omicsViewer:::fgsea1( + gs = gss, stats = stats, minSize = 1, maxSize = 500, sampleSize = 3) Warning message: In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : All values in the stats vector are greater than zero and scoreType is "std", maybe you should switch to scoreType = "pos". > ut_cmp_identical(res$pathway, colnames(gss)) > ok(ut_cmp_equal(res$pval[1] < 0.2, TRUE), "fgsea significant pathway 1") ok - fgsea significant pathway 1 > ok(ut_cmp_equal(res$pval[2] < 0.2, TRUE), "fgsea significant pathway 2") ok - fgsea significant pathway 2 > ok(ut_cmp_equal(res$pval[3] > 0.6, TRUE), "fgsea insignificant pathway") ok - fgsea insignificant pathway > > totall <- omicsViewer:::totall > tgs <- totall(gs) > ok(ut_cmp_identical(colnames(tgs), c("featureId", "gsId", "weight")), + "totall 1") ok - totall 1 > ok(ut_cmp_equal(nrow(tgs), 12), "totall 2") ok - totall 2 > > > # ====================== trisetters ========================== > > expr <- matrix(1:6, 3, 2) > rownames(expr) <- c("g1", "g2", "g3") > colnames(expr) <- c("s1", "s2") > > m1 <- data.frame( + "F1|pos2|pos3" = 1:3, + "F2|pos2|pos3" = 1:3, + check.names = FALSE + ) > rownames(m1) <- rownames(expr) > > m2 <- data.frame( + "var1|pos2|pos3" = 1:2, + "var2|pos2|pos3" = 1:2, + check.names = FALSE + ) > rownames(m2) <- colnames(expr) > > trisetter <- omicsViewer:::trisetter > > f1 <- rbind(c("F1", "pos2", "pos3"), + c("F2", "pos2", "pos3")) > ok( + ut_cmp_equal( + trisetter(meta = m1, expr=NULL, combine="none"), f1, + check.attributes = FALSE + ), + "trisetter feature meta" + ) ok - trisetter feature meta > > var1 <- rbind(c("var1", "pos2", "pos3"), + c("var2", "pos2", "pos3")) > ok( + ut_cmp_equal( + trisetter(meta = m2, expr=NULL, combine="none"), var1, + check.attributes = FALSE + ), + "trisetter pheno meta" + ) ok - trisetter pheno meta > > cf1 <- rbind(f1, c("Sample", "Auto", "s1"), + c("Sample", "Auto", "s2")) > ok( + ut_cmp_equal( + trisetter(meta = m1, expr=expr, combine="feature"), cf1, + check.attributes = FALSE + ), + "trisetter feature combined with expr" + ) ok - trisetter feature combined with expr > cvar1 <- rbind(var1, + c("Feature", "Auto", "g1"), + c("Feature", "Auto", "g2"), + c("Feature", "Auto", "g3")) > ok( + ut_cmp_equal( + trisetter(meta = m2, expr=expr, combine="pheno"), cvar1, + check.attributes = FALSE + ), + "trisetter pheno combined with expr" + ) ok - trisetter pheno combined with expr > > varSelector <- omicsViewer:::varSelector > l1 <- list(analysis = "Feature", subset= "Auto", variable = "g1") > ok( + ut_cmp_equal( + varSelector(x = l1, expr = expr, meta = m2), + c(1, 4), + check.attributes = FALSE + ), + "select from triselector - feature" + ) ok - select from triselector - feature > > l1 <- list(analysis = "Sample", subset= "Auto", variable = "s1") > ok( + ut_cmp_equal( + varSelector(x = l1, expr = expr, meta = m2), + 1:3, + check.attributes = FALSE), + "select from triselector - sample" + ) ok - select from triselector - sample > text2num <- omicsViewer:::text2num > ok(ut_cmp_equal(text2num("-log10(0.01)"), -log10(0.01)), "text2num - 1") ok - text2num - 1 > ok(ut_cmp_equal(text2num("0.05"), 0.05), "text2num - 2") ok - text2num - 2 > > ###################################### > terms <- data.frame( + id = c("ID1", "ID2", "ID1", "ID2", "ID8", "ID10"), + term = c("T1", "T1", "T2", "T2", "T2", "T2"), + stringsAsFactors = FALSE + ) > features <- list(c("ID1", "ID2"), c("ID13"), c("ID4", "ID8", "ID10")) > gsAnnotIdList(idList = features, gsIdMap = terms, minSize = 1, maxSize = 500) 3 x 2 sparse Matrix of class "dgCMatrix" T1 T2 [1,] 1 1 [2,] . . [3,] . 1 > > terms <- data.frame( + id = c("ID1", "ID2", "ID1", "ID2", "ID8", "ID10", "ID4", "ID4"), + term = c("T1", "T1", "T2", "T2", "T2", "T2", "T1", "T2"), + stringsAsFactors = FALSE + ) > features <- list(F1 = c("ID1", "ID2", "ID4"), F2 = c("ID13"), F3 = c("ID4", "ID8", "ID10")) > > res <- data.frame( + featureId = c(1, 1, 3, 3), + gsId = c("T1", "T2", "T2", "T1"), + weight = rep(1, 4), + stringsAsFactors = FALSE + ) > r1 <- gsAnnotIdList(features, gsIdMap = terms, data.frame = TRUE, minSize = 1) > ok(ut_cmp_equal(r1, res, check.attributes = FALSE), + "gsAnnotIdList data.frame" + ) ok - gsAnnotIdList data.frame > > res <- sparseMatrix(i = c(1, 1, 3, 3), j = c(1, 2, 1, 2), x = 1) > colnames(res) <- c("T1", "T2") > r2 <- gsAnnotIdList(features, gsIdMap = terms, data.frame = FALSE, minSize = 1) > ok(ut_cmp_equal(r2, res), "gsAnnotIdList sparseMatrix") ok - gsAnnotIdList sparseMatrix > > # ============================================== > xq <- rbind(c(4, 2, 4), + c(20, 40, 10), + c(11, 234, 10), + c(200, 1000, 100)) > > vectORA.core <- omicsViewer:::vectORA.core > r1 <- vectORA.core(xq[1, ], xq[2, ], xq[3, ], xq[4, ]) > r2 <- vectORA.core(xq[1, ], xq[2, ], xq[3, ], xq[4, ], unconditional.or = FALSE) > > ok(ut_cmp_equal(r1$p.value, r2$p.value), "vecORA.core 1") ok - vecORA.core 1 > > # fisher's test > pv <- t(apply(xq, 2, function(x1) { + m <- rbind(c(x1[1], x1[2]-x1[1]), + c(x1[3]-x1[1], x1[4] - x1[2] - x1[3] + x1[1])) + v <- fisher.test(m, alternative = "greater") + c(p.value = v$p.value, v$estimate) + })) > > ok(ut_cmp_equal(r1$p.value, pv[, "p.value"]), "vectORA.core - conditional OR") ok - vectORA.core - conditional OR > ok(ut_cmp_equal(r2$OR, pv[, "odds ratio"]), "vectORA - unconditional OR") ok - vectORA - unconditional OR > > > proc.time() user system elapsed 10.511 0.616 11.124 1..23 # Looks like you passed all 23 tests.
omicsViewer.Rcheck/tests/test_shinyAuxi.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(unittest) > library(RColorBrewer) > > nColors <- omicsViewer:::nColors > ok(ut_cmp_equal(nColors(k=0, stop = FALSE), NULL), "nColors - return NULL when not stop") ok - nColors - return NULL when not stop > ok(ut_cmp_error(nColors(k=0, stop = TRUE), "k should be an integer between 1 and 60!"), + "nColors - stop only when stop") ok - nColors - stop only when stop > > null2empty <- omicsViewer:::null2empty > ok(ut_cmp_identical(null2empty(NULL), ""), "null2empty") ok - null2empty > > getSearchCols <- omicsViewer:::getSearchCols > ok(ut_cmp_identical(getSearchCols(NULL), NULL), "getSearchCols - return NULL when NULL given") ok - getSearchCols - return NULL when NULL given > > getOrderCols <- omicsViewer:::getOrderCols > ok(ut_cmp_identical(getOrderCols(NULL), NULL), "getOrderCols - return NULL when NULL given") ok - getOrderCols - return NULL when NULL given > > exprsImpute <- omicsViewer:::getExprsImpute > ok(ut_cmp_identical(exprsImpute("5"), NULL), "exprsImpute - return NULL when error") ok - exprsImpute - return NULL when error > > > value2color <- omicsViewer:::value2color > l <- value2color(1:100, n=10) > ok( + ut_cmp_equal(names(l), c("color", "key")), + "value2color - return color and key" + ) ok - value2color - return color and key > ok( + ut_cmp_equal(length(l$color), 100), + "value2color - return color correct length" + ) ok - value2color - return color correct length > ok( + ut_cmp_equal(c(table(l$color)), rep(10, 10), check.attributes = FALSE), + "value2color - return key correct length" + ) ok - value2color - return key correct length > ok( + ut_cmp_equal(length(unique(l$key)), 10), + "value2color - return color correct unique length" + ) ok - value2color - return color correct unique length > > proc.time() user system elapsed 7.475 0.543 8.008 1..10 # Looks like you passed all 10 tests.
omicsViewer.Rcheck/tests/test_stats.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(unittest) > correlationAnalysis <- omicsViewer:::correlationAnalysis > > ph <- data.frame( + set = 1:15 + ) > expr <- rbind(1:15, matrix(rnorm(150), 10, 15)) > res <- correlationAnalysis(expr, ph, prefix = "test") > ok(ut_cmp_equal( + colnames(res), + c("test|set|R", "test|set|N", "test|set|P", "test|set|logP", "test|set|range")), + "correlationAnalysis - colnames" + ) ok - correlationAnalysis - colnames > ok( + ut_cmp_equal( nrow(res), 11 ), + "correlationAnalysis - row numbers" + ) ok - correlationAnalysis - row numbers > ok( + ut_cmp_equal( res[1, 1], 1 ), + "correlationAnalysis - correlation 1" + ) ok - correlationAnalysis - correlation 1 > > > ph <- data.frame( + var1 = rep(LETTERS[1:2], each = 6), + var2 = rep(c("C", "D", "C", "D"), each = 3), + stringsAsFactors = FALSE, + row.names = paste("S", 1:12, sep = "") + ) > cmp <- rbind( + c("var1", "A", "B"), + c("var2", "C", "D") + ) > expr <- cbind(matrix(rnorm(60), 10), matrix(rnorm(60, mean = 3), 10)) > colnames(expr) <- rownames(ph) > rownames(expr) <- paste("P", 1:10, sep = "") > > multi.t.test <- omicsViewer:::multi.t.test > res <- multi.t.test(x = expr, pheno = ph, compare = cmp) > ok( + ut_cmp_equal(all(res$`ttest|A_vs_B|pvalue` < res$`ttest|C_vs_D|pvalue`), TRUE), + "multi.t.test - significance" + ) ok - multi.t.test - significance > > exprspca <- omicsViewer:::exprspca > pcres <- exprspca(expr, n = 3) > ok(ut_cmp_equal(dim(pcres$samples), c(12, 3)), "exprspca sample") ok - exprspca sample > ok(ut_cmp_equal(dim(pcres$features), c(10, 3)), "exprspca sample") ok - exprspca sample > > exprNA <- expr > exprNA[1, 1:11] <- NA > fillNA <- omicsViewer:::fillNA > res <- fillNA(exprNA) > ok(ut_cmp_equal(length(unique(res[1, 1:11])), 1), "fillNA") ok - fillNA > > proc.time() user system elapsed 7.716 0.480 8.185 1..7 # Looks like you passed all 7 tests.
omicsViewer.Rcheck/omicsViewer-Ex.timings
name | user | system | elapsed | |
app_module | 0.001 | 0.000 | 0.000 | |
app_ui | 0 | 0 | 0 | |
correlationAnalysis | 0.015 | 0.007 | 0.023 | |
draw_roc_pr | 0.103 | 0.014 | 0.118 | |
exprspca | 0.196 | 0.012 | 0.210 | |
extendMetaData | 0.064 | 0.000 | 0.064 | |
fgsea1 | 0 | 0 | 0 | |
fillNA | 0.002 | 0.000 | 0.002 | |
filterRow | 0.002 | 0.000 | 0.002 | |
getAutoRIF | 0.071 | 0.003 | 2.429 | |
gsAnnotIdList | 0.027 | 0.002 | 0.028 | |
hclust2str | 0.000 | 0.000 | 0.001 | |
multi.t.test | 2.993 | 0.201 | 3.194 | |
nColors | 0 | 0 | 0 | |
normalize.nQuantiles | 0.030 | 0.002 | 0.031 | |
normalize.totsum | 0.013 | 0.000 | 0.013 | |
normalizeColWise | 0.034 | 0.002 | 0.035 | |
normalizeData | 0.035 | 0.002 | 0.037 | |
omicsViewer | 0 | 0 | 0 | |
plot_roc_pr_module | 0.000 | 0.001 | 0.001 | |
plotly_boxplot_module | 0.001 | 0.000 | 0.001 | |
plotly_boxplot_ui | 0.001 | 0.000 | 0.001 | |
plotly_scatter_module | 0.003 | 0.001 | 0.004 | |
plotly_scatter_ui | 0.000 | 0.003 | 0.004 | |
prepOmicsViewer | 2.234 | 0.020 | 2.257 | |
readESVObj | 0.796 | 0.068 | 0.865 | |
read_gmt | 0.04 | 0.00 | 0.04 | |
removeVarQC | 0.017 | 0.000 | 0.017 | |
rowshift | 0.016 | 0.000 | 0.016 | |
saveOmicsViewerDb | 0.086 | 0.002 | 0.088 | |
triselector_module | 0.002 | 0.000 | 0.002 | |
triselector_ui | 0.002 | 0.000 | 0.002 | |