Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:19 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the peco package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/peco.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1448/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
peco 1.11.0 (landing page) Chiaowen Joyce Hsiao
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: peco |
Version: 1.11.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:peco.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings peco_1.11.0.tar.gz |
StartedAt: 2023-02-07 11:02:18 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 11:13:11 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 653.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: peco.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:peco.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings peco_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/peco.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘peco/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘peco’ version ‘1.11.0’ * 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 ‘peco’ 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 R 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 ... ERROR Running examples in ‘peco-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cycle_npreg_outsample > ### Title: Predict test-sample ordering using training labels (no update) > ### Aliases: cycle_npreg_outsample > > ### ** Examples > > # import data > library(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, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: ‘S4Vectors’ 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 > data(sce_top101genes) > > # select top 5 cyclic genes > sce_top5 <- sce_top101genes[order(rowData(sce_top101genes)$pve_fucci, + decreasing=TRUE)[1:5],] > > # Select samples from NA18511 for our prediction example > coldata <- colData(sce_top5) > which_samples_train <- rownames(coldata)[coldata$chip_id != "NA18511"] > which_samples_predict <- rownames(coldata)[coldata$chip_id == "NA18511"] > > # learning cyclic functions of the genes using our training data > sce_top5 <- data_transform_quantile(sce_top5) computing on 2 cores > expr_quant <- assay(sce_top5, "cpm_quantNormed") > Y_train <- expr_quant[, colnames(expr_quant) %in% which_samples_train] > theta_train <- + coldata$theta_shifted[rownames(coldata) %in% which_samples_train] > names(theta_train) <- + rownames(coldata)[rownames(coldata) %in% which_samples_train] > > # obtain cyclic function estimates > model_5genes_train <- cycle_npreg_insample(Y = Y_train, + theta = theta_train, + polyorder=2, + ncores=2, + method.trend="trendfilter") computing on 2 cores > > # predict cell cycle > model_5genes_predict <- cycle_npreg_outsample( + Y_test=sce_top5[,colnames(sce_top5) %in% which_samples_predict], + sigma_est=model_5genes_train$sigma_est, + funs_est=model_5genes_train$funs_est, + method.trend="trendfilter", + ncores=2, + get_trend_estimates=FALSE) > > # estimate cyclic gene expression levels given cell cycle for each gene > predict_cyclic <- + fit_cyclical_many(Y=assay(model_5genes_predict$Y,"cpm_quantNormed"), + theta=colData(model_5genes_predict$Y)$cellcycle_peco) computing on 2 cores Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘vignette.Rmd’ using rmarkdown Quitting from lines 121-143 (vignette.Rmd) Error: processing vignette 'vignette.Rmd' failed with diagnostics: error reading from connection --- failed re-building ‘vignette.Rmd’ SUMMARY: processing the following file failed: ‘vignette.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs See ‘/home/biocbuild/bbs-3.17-bioc/meat/peco.Rcheck/00check.log’ for details.
peco.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL peco ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘peco’ ... ** using staged installation ** R ** data ** 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 (peco)
peco.Rcheck/peco-Ex.timings
name | user | system | elapsed | |
circ_dist | 0.019 | 0.000 | 0.019 | |
cycle_npreg_insample | 0 | 0 | 0 | |