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 11:47 -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 2106/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TCC 1.47.0 (landing page) Jianqiang Sun
| 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 TCC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TCC.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: TCC |
Version: 1.47.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:TCC.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TCC_1.47.0.tar.gz |
StartedAt: 2024-12-24 11:58:42 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 12:05:12 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 389.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TCC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:TCC.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TCC_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/TCC.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TCC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TCC’ version ‘1.47.0’ * 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 ‘TCC’ 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 ... NOTE checkRd: (-1) calcNormFactors.Rd:84: Lost braces 84 | {the \eqn{STEP1 - (STEP2 - STEP3)_{n}} pipeline}.} | ^ checkRd: (-1) hypoData.Rd:19: Lost braces; missing escapes or markup? 19 | i.e., {G1_rep1, G1_rep2, G1_rep3} vs. {G2_rep1, G2_rep2, G2_rep3}. | ^ checkRd: (-1) hypoData.Rd:19: Lost braces; missing escapes or markup? 19 | i.e., {G1_rep1, G1_rep2, G1_rep3} vs. {G2_rep1, G2_rep2, G2_rep3}. | ^ checkRd: (-1) hypoData_mg.Rd:19: Lost braces; missing escapes or markup? 19 | i.e., {G1_rep1, G1_rep2, G1_rep3} vs. {G2_rep1, G2_rep2, G2_rep3} vs. | ^ checkRd: (-1) hypoData_mg.Rd:19: Lost braces; missing escapes or markup? 19 | i.e., {G1_rep1, G1_rep2, G1_rep3} vs. {G2_rep1, G2_rep2, G2_rep3} vs. | ^ checkRd: (-1) hypoData_mg.Rd:20: Lost braces; missing escapes or markup? 20 | {G3_rep1, G3_rep2, G3_rep3}. | ^ * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed TCC-class 8.733 0.175 9.214 simulateReadCounts 8.205 0.048 8.422 plot.TCC 6.523 0.064 6.762 plotFCPseudocolor 5.316 0.052 5.476 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * 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 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/TCC.Rcheck/00check.log’ for details.
TCC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL TCC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘TCC’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘calcNormFactors’ in package ‘TCC’ ** 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 (TCC)
TCC.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > BiocGenerics:::testPackage("TCC") Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname 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 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 Attaching package: 'limma' The following object is masked from 'package:DESeq2': plotMA The following object is masked from 'package:BiocGenerics': plotMA Attaching package: 'TCC' The following object is masked from 'package:edgeR': calcNormFactors TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 1 ) TCC::INFO: Done. TCC::INFO: Generating simulation data under NB distribution ... TCC::INFO: (genesizes : 1000 ) TCC::INFO: (replicates : 3, 3 ) TCC::INFO: (PDEG : 0.16, 0.04 ) TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : tmm - [ deseq2 - tmm ] X 1 ) TCC::INFO: Done. TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq2 - deseq2 ] X 1 ) TCC::INFO: Done. TCC::INFO: Identifying DE genes using deseq2 ... TCC::INFO: Done. [1] 0.896225 TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 1 ) TCC::INFO: Done. TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : deseq2 - [ edger - deseq2 ] X 1 ) TCC::INFO: Done. TCC::INFO: Identifying DE genes using edger ... TCC::INFO: Done. [1] 0.9007156 TCC::INFO: Generating simulation data under NB distribution ... TCC::INFO: (genesizes : 1000 ) TCC::INFO: (samples : 8 ) TCC::INFO: (factors : 2 ) TCC::INFO: (PDEG : 0.1 ) TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : tmm - [ deseq2 - tmm ] X 1 ) TCC::INFO: Done. TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq2 - deseq2 ] X 1 ) TCC::INFO: Done. TCC::INFO: Identifying DE genes using deseq2 ... TCC::INFO: Done. [1] 0.8928111 TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 1 ) TCC::INFO: Done. TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : deseq2 - [ edger - deseq2 ] X 1 ) TCC::INFO: Done. TCC::INFO: Identifying DE genes using edger ... TCC::INFO: Done. [1] 0.9340333 TCC::INFO: Generating simulation data under NB distribution ... TCC::INFO: (genesizes : 1000 ) TCC::INFO: (replicates : 3, 3, 3 ) TCC::INFO: (PDEG : 0.12, 0.04, 0.04 ) TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : tmm - [ deseq2 - tmm ] X 1 ) TCC::INFO: Done. TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq2 - deseq2 ] X 1 ) TCC::INFO: Done. TCC::INFO: Identifying DE genes using deseq2 ... TCC::INFO: Done. [1] 0.8929125 TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 1 ) TCC::INFO: Done. TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : deseq2 - [ edger - deseq2 ] X 1 ) TCC::INFO: Done. TCC::INFO: Identifying DE genes using edger ... TCC::INFO: Done. [1] 0.9133687 TCC::INFO: Generating simulation data under NB distribution ... TCC::INFO: (genesizes : 1000 ) TCC::INFO: (samples : 12 ) TCC::INFO: (factors : 2 ) TCC::INFO: (PDEG : 0.1 ) TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : tmm - [ deseq2 - tmm ] X 1 ) TCC::INFO: Done. TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : deseq2 - [ deseq2 - deseq2 ] X 1 ) TCC::INFO: Done. TCC::INFO: Identifying DE genes using deseq2 ... TCC::INFO: Done. [1] 0.9189482 TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 1 ) TCC::INFO: Done. TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : deseq2 - [ edger - deseq2 ] X 1 ) TCC::INFO: Done. TCC::INFO: Identifying DE genes using edger ... TCC::INFO: Done. [1] 0.7196718 TCC::INFO: Calculating normalization factors using tmm ... TCC::INFO: Done. TCC::INFO: Identifying DE genes using edger ... TCC::INFO: Done. TCC::INFO: Calculating normalization factors using tmm ... TCC::INFO: Done. TCC::INFO: Identifying DE genes using edger ... TCC::INFO: Done. TCC::INFO: Generating simulation data under NB distribution ... TCC::INFO: (genesizes : 1000 ) TCC::INFO: (replicates : 3, 3 ) TCC::INFO: (PDEG : 0.18, 0.02 ) TCC::INFO: Generating simulation data under NB distribution ... TCC::INFO: (genesizes : 1000 ) TCC::INFO: (replicates : 3, 3, 3 ) TCC::INFO: (PDEG : 0.18, 0.01, 0.01 ) RUNIT TEST PROTOCOL -- Tue Dec 24 12:05:05 2024 *********************************************** Number of test functions: 6 Number of errors: 0 Number of failures: 0 1 Test Suite : TCC RUnit Tests - 6 test functions, 0 errors, 0 failures Number of test functions: 6 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 82.846 1.079 100.214
TCC.Rcheck/TCC-Ex.timings
name | user | system | elapsed | |
ROKU | 0.011 | 0.000 | 0.012 | |
TCC-class | 8.733 | 0.175 | 9.214 | |
TCC | 0.005 | 0.004 | 0.010 | |
WAD | 0.199 | 0.012 | 0.211 | |
arab | 0.036 | 0.000 | 0.036 | |
calcAUCValue | 3.276 | 0.032 | 3.429 | |
calcNormFactors | 1.771 | 0.008 | 1.794 | |
clusterSample | 0.260 | 0.000 | 0.396 | |
estimateDE | 0.823 | 0.000 | 0.824 | |
filterLowCountGenes | 0.023 | 0.000 | 0.023 | |
getNormalizedData | 0.439 | 0.000 | 0.441 | |
getResult | 0.823 | 0.024 | 0.858 | |
hypoData | 3.171 | 0.102 | 3.624 | |
hypoData_mg | 2.496 | 0.000 | 2.517 | |
hypoData_ts | 0.000 | 0.002 | 0.001 | |
makeFCMatrix | 0.001 | 0.002 | 0.003 | |
nakai | 0.031 | 0.008 | 0.040 | |
plot.TCC | 6.523 | 0.064 | 6.762 | |
plotFCPseudocolor | 5.316 | 0.052 | 5.476 | |
simulateReadCounts | 8.205 | 0.048 | 8.422 | |