Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:40:04 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 1968/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Yichen Wang
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the singleCellTK package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/singleCellTK.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: singleCellTK |
Version: 2.13.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singleCellTK_2.13.1.tar.gz |
StartedAt: 2024-03-28 00:10:17 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 00:19:53 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 576.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: singleCellTK.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singleCellTK_2.13.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/singleCellTK.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘singleCellTK/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘singleCellTK’ version ‘2.13.1’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘singleCellTK’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: extdata 1.5Mb shiny 2.9Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 whether startup messages can be suppressed ... 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 ... NOTE checkRd: (-1) dedupRowNames.Rd:10: Lost braces 10 | \item{x}{A matrix like or /linkS4class{SingleCellExperiment} object, on which | ^ checkRd: (-1) dedupRowNames.Rd:14: Lost braces 14 | /linkS4class{SingleCellExperiment} object. When set to \code{TRUE}, will | ^ checkRd: (-1) dedupRowNames.Rd:22: Lost braces 22 | By default, a matrix or /linkS4class{SingleCellExperiment} object | ^ checkRd: (-1) dedupRowNames.Rd:24: Lost braces 24 | When \code{x} is a /linkS4class{SingleCellExperiment} and \code{as.rowData} | ^ checkRd: (-1) runEmptyDrops.Rd:66: Lost braces 66 | provided \\linkS4class{SingleCellExperiment} object. | ^ checkRd: (-1) runSCMerge.Rd:44: Lost braces 44 | construct pseudo-replicates. The length of code{kmeansK} needs to be the same | ^ * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘singleCellTK-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: convertSeuratToSCE > ### Title: convertSeuratToSCE Converts the input seurat object to a sce > ### object > ### Aliases: convertSeuratToSCE > > ### ** Examples > > data(scExample, package = "singleCellTK") > seurat <- convertSCEToSeurat(sce) > sce <- convertSeuratToSCE(seurat) Error in normarg_assays(assays, as.null.if.no.assay = TRUE) : no slot of name "counts" for this object of class "Assay5" Calls: convertSeuratToSCE ... SingleCellExperiment -> SummarizedExperiment -> normarg_assays Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 2. └─singleCellTK:::.updateAssaySCE(...) 3. └─methods::slot(...) ── Error ('test-trajectory.R:7:1'): (code run outside of `test_that()`) ──────── Error in `methods::slot(Seurat::GetAssay(seuratObject, seuratAssaySlot), seuratDataSlot)`: no slot of name "data" for this object of class "Assay5" Backtrace: ▆ 1. └─singleCellTK::runNormalization(...) at test-trajectory.R:7:1 2. └─singleCellTK::runSeuratNormalizeData(...) 3. └─singleCellTK:::.updateAssaySCE(...) 4. └─methods::slot(...) [ FAIL 7 | WARN 22 | SKIP 0 | PASS 143 ] 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: 2 ERRORs, 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/singleCellTK.Rcheck/00check.log’ for details.
singleCellTK.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL singleCellTK ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘singleCellTK’ ... ** using staged installation ** R ** data ** exec ** 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 Warning in fun(libname, pkgname) : Package 'singleCellTK' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'singleCellTK' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package keeps a record of temporary installation path * DONE (singleCellTK)
singleCellTK.Rcheck/tests/spelling.Rout
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 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. > if (requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.222 0.092 0.308
singleCellTK.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 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(singleCellTK) 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 Loading required package: SingleCellExperiment Loading required package: DelayedArray Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Loading required package: S4Arrays Loading required package: abind Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: SparseArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Attaching package: 'singleCellTK' The following object is masked from 'package:BiocGenerics': plotPCA Warning message: In fun(libname, pkgname) : Package 'singleCellTK' is deprecated and will be removed from Bioconductor version 3.20 > > test_check("singleCellTK") Found 2 batches Using null model in ComBat-seq. Adjusting for 0 covariate(s) or covariate level(s) Estimating dispersions Fitting the GLM model Shrinkage off - using GLM estimates for parameters Adjusting the data Found 2 batches Using null model in ComBat-seq. Adjusting for 1 covariate(s) or covariate level(s) Estimating dispersions Fitting the GLM model Shrinkage off - using GLM estimates for parameters Adjusting the data Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Uploading data to Enrichr... Done. Querying HDSigDB_Human_2021... Done. Parsing results... Done. Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================================================================| 100% Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| [ FAIL 7 | WARN 22 | SKIP 0 | PASS 143 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-computeHeatmap.R:8:3'): Testing computeHeatmap.R ─────────────── Error in `methods::slot(Seurat::GetAssay(seuratObject, seuratAssaySlot), seuratDataSlot)`: no slot of name "data" for this object of class "Assay5" Backtrace: ▆ 1. └─singleCellTK::runSeuratNormalizeData(sce) at test-computeHeatmap.R:8:3 2. └─singleCellTK:::.updateAssaySCE(...) 3. └─methods::slot(...) ── Error ('test-dimensionReduction.R:8:1'): (code run outside of `test_that()`) ── Error in `(function (cl, name, valueClass) { ClassDef <- getClass(cl) slotClass <- ClassDef@slots[[name]] if (is.null(slotClass)) stop(gettextf("%s is not a slot in class %s", sQuote(name), dQuote(cl)), domain = NA) if (.identC(slotClass, valueClass)) return(TRUE) ok <- possibleExtends(valueClass, slotClass, ClassDef2 = getClassDef(slotClass, where = .classEnv(ClassDef))) if (isFALSE(ok)) stop(gettextf("assignment of an object of class %s is not valid for @%s in an object of class %s; is(value, \"%s\") is not TRUE", dQuote(valueClass), sQuote(name), dQuote(cl), slotClass), domain = NA) TRUE })(structure("Assay5", package = "SeuratObject"), "counts", structure("dgCMatrix", package = "Matrix"))`: 'counts' is not a slot in class "Assay5" Backtrace: ▆ 1. └─singleCellTK::runFeatureSelection(sce, useAssay = "counts") at test-dimensionReduction.R:8:1 2. ├─base::do.call("runSeuratFindHVG", args = params) 3. └─singleCellTK::runSeuratFindHVG(...) 4. └─singleCellTK:::.addSeuratToMetaDataSCE(inSCE, seuratObject) 5. └─methods (local) `<fn>`(`<chr>`, "counts", `<chr>`) ── Error ('test-featureSelection.R:5:1'): (code run outside of `test_that()`) ── Error in `methods::slot(Seurat::GetAssay(seuratObject, seuratAssaySlot), seuratDataSlot)`: no slot of name "data" for this object of class "Assay5" Backtrace: ▆ 1. └─singleCellTK::runSeuratNormalizeData(sce) at test-featureSelection.R:5:1 2. └─singleCellTK:::.updateAssaySCE(...) 3. └─methods::slot(...) ── Error ('test-misc.R:64:3'): Testing runGSVA ───────────────────────────────── Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').", call = GSVA::gsva(as.matrix(expData(inSCE, useAssay)), gene.Set), old = c("::", "GSVA", "gsva"), new = "gsva()", package = "GSVA"), class = c("defunctError", "error", "condition")))`: error in evaluating the argument 'x' in selecting a method for function 't': Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva'). Backtrace: ▆ 1. ├─singleCellTK::runGSVA(...) at test-misc.R:64:3 2. │ ├─base::t(GSVA::gsva(as.matrix(expData(inSCE, useAssay)), gene.Set)) 3. │ ├─GSVA::gsva(as.matrix(expData(inSCE, useAssay)), gene.Set) 4. │ └─GSVA::gsva(as.matrix(expData(inSCE, useAssay)), gene.Set) 5. │ └─base::.Defunct(new = "gsva()", package = "GSVA", msg = "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').") 6. │ └─base::stop(...) 7. └─base (local) `<fn>`(`<dfnctErr>`) ── Error ('test-pathway.R:36:5'): Testing GSVA ───────────────────────────────── Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').", call = GSVA::gsva(as.matrix(expData(inSCE, useAssay)), gene.Set), old = c("::", "GSVA", "gsva"), new = "gsva()", package = "GSVA"), class = c("defunctError", "error", "condition")))`: error in evaluating the argument 'x' in selecting a method for function 't': Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva'). Backtrace: ▆ 1. ├─singleCellTK::runGSVA(sce, geneSetCollectionName = "GeneSetCollection") at test-pathway.R:36:5 2. │ ├─base::t(GSVA::gsva(as.matrix(expData(inSCE, useAssay)), gene.Set)) 3. │ ├─GSVA::gsva(as.matrix(expData(inSCE, useAssay)), gene.Set) 4. │ └─GSVA::gsva(as.matrix(expData(inSCE, useAssay)), gene.Set) 5. │ └─base::.Defunct(new = "gsva()", package = "GSVA", msg = "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').") 6. │ └─base::stop(...) 7. └─base (local) `<fn>`(`<dfnctErr>`) ── Error ('test-seuratFunctions.R:9:3'): Testing standard seurat workflow ────── Error in `methods::slot(Seurat::GetAssay(seuratObject, seuratAssaySlot), seuratDataSlot)`: no slot of name "data" for this object of class "Assay5" Backtrace: ▆ 1. └─singleCellTK::runSeuratNormalizeData(sce) at test-seuratFunctions.R:9:3 2. └─singleCellTK:::.updateAssaySCE(...) 3. └─methods::slot(...) ── Error ('test-trajectory.R:7:1'): (code run outside of `test_that()`) ──────── Error in `methods::slot(Seurat::GetAssay(seuratObject, seuratAssaySlot), seuratDataSlot)`: no slot of name "data" for this object of class "Assay5" Backtrace: ▆ 1. └─singleCellTK::runNormalization(...) at test-trajectory.R:7:1 2. └─singleCellTK::runSeuratNormalizeData(...) 3. └─singleCellTK:::.updateAssaySCE(...) 4. └─methods::slot(...) [ FAIL 7 | WARN 22 | SKIP 0 | PASS 143 ] Error: Test failures Execution halted
singleCellTK.Rcheck/singleCellTK-Ex.timings
name | user | system | elapsed | |
MitoGenes | 0.002 | 0.003 | 0.006 | |
SEG | 0.002 | 0.002 | 0.004 | |
calcEffectSizes | 0.225 | 0.022 | 0.248 | |
combineSCE | 1.809 | 0.069 | 1.894 | |
computeZScore | 0.268 | 0.011 | 0.282 | |
convertSCEToSeurat | 4.980 | 0.276 | 5.312 | |