Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-27 05:50:37 -0000 (Mon, 27 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6083 |
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 |
To the developers/maintainers of the magpie package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/magpie.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 1091/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
magpie 0.99.8 (landing page) Daoyu Duan
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: magpie |
Version: 0.99.8 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:magpie.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings magpie_0.99.8.tar.gz |
StartedAt: 2023-03-25 05:43:08 -0000 (Sat, 25 Mar 2023) |
EndedAt: 2023-03-25 05:49:21 -0000 (Sat, 25 Mar 2023) |
EllapsedTime: 373.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: magpie.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:magpie.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings magpie_0.99.8.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/magpie.Rcheck’ * using R Under development (unstable) (2023-03-12 r83975) * 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 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘magpie/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘magpie’ version ‘0.99.8’ * 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 ‘magpie’ 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 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 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTest.R’ ERROR Running the tests in ‘tests/runTest.R’ failed. Last 13 lines of output: 1 Test Suite : magpie RUnit Tests - 2 test functions, 1 error, 0 failures ERROR in test_PowerEval: Error in seq.default(1, ncol(Counts), 2) : 'to' must be of length 1 Test files with failing tests test_magpie.R test_PowerEval Error in BiocGenerics:::testPackage("magpie") : unit tests failed for package magpie Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘magpie.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.17-bioc/meat/magpie.Rcheck/00check.log’ for details.
magpie.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL magpie ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘magpie’ ... ** 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 (magpie)
magpie.Rcheck/tests/runTest.Rout.fail
R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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. > BiocGenerics:::testPackage("magpie") Loading required package: Rsamtools Loading required package: GenomeInfoDb 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 Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomicRanges Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: GenomicFeatures Loading required package: AnnotationDbi 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")'. Error in x$.self$finalize() : attempt to apply non-function Merge bumps from different replicates... Estimating parameters... Parameters estimation has finished... KL divergence calculation has finished... Parameters simulation has finished for sequencing depth--1x, 2 Controls, 2 Cases. converting counts to integer mode using pre-existing size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing converting counts to integer mode using pre-existing size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing Timing stopped at: 42.18 4.224 37.71 Error in seq.default(1, ncol(Counts), 2) : 'to' must be of length 1 In addition: Warning messages: 1: call dbDisconnect() when finished working with a connection 2: In aod::betabin(cbind(y, n - y) ~ Pred, ~1, data = dat, link = "logit") : Possible convergence problem. Optimization process code: 10 (see ?optim). 3: In aod::betabin(cbind(y, n - y) ~ Pred, ~1, data = dat, link = "logit") : Possible convergence problem. Optimization process code: 10 (see ?optim). 4: In aod::betabin(cbind(y, n - y) ~ Pred, ~1, data = dat, link = "logit") : Possible convergence problem. Optimization process code: 10 (see ?optim). 5: In aod::betabin(cbind(y, n - y) ~ Pred, ~1, data = dat, link = "logit") : Possible convergence problem. Optimization process code: 10 (see ?optim). 6: In aod::betabin(cbind(y, n - y) ~ Pred, ~1, data = dat, link = "logit") : Possible convergence problem. Optimization process code: 10 (see ?optim). 7: In aod::betabin(cbind(y, n - y) ~ Pred, ~1, data = dat, link = "logit") : Possible convergence problem. Optimization process code: 10 (see ?optim). 8: In aod::betabin(cbind(y, n - y) ~ Pred, ~1, data = dat, link = "logit") : Possible convergence problem. Optimization process code: 10 (see ?optim). 9: In aod::betabin(cbind(y, n - y) ~ Pred, ~1, data = dat, link = "logit") : Possible convergence problem. Optimization process code: 10 (see ?optim). RUNIT TEST PROTOCOL -- Sat Mar 25 05:48:53 2023 *********************************************** Number of test functions: 2 Number of errors: 1 Number of failures: 0 1 Test Suite : magpie RUnit Tests - 2 test functions, 1 error, 0 failures ERROR in test_PowerEval: Error in seq.default(1, ncol(Counts), 2) : 'to' must be of length 1 Test files with failing tests test_magpie.R test_PowerEval Error in BiocGenerics:::testPackage("magpie") : unit tests failed for package magpie Execution halted
magpie.Rcheck/magpie-Ex.timings
name | user | system | elapsed | |
PlotAll | 0.047 | 0.004 | 0.051 | |
PlotRes | 0.008 | 0.000 | 0.008 | |
PlotStrata | 0.01 | 0.00 | 0.01 | |
QuickPower | 0.001 | 0.000 | 0.001 | |
WriteToxlsx | 0.524 | 0.037 | 0.568 | |
WriteToxlsx_strata | 0.046 | 0.012 | 0.058 | |
plotAll_Strata | 0.028 | 0.000 | 0.029 | |
power.test | 0.002 | 0.000 | 0.001 | |
powerEval | 0.001 | 0.000 | 0.000 | |