Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-19 11:41 -0400 (Wed, 19 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4742 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
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 1909/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scQTLtools 0.99.11 (landing page) Xiaofeng Wu
| 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 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the scQTLtools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scQTLtools.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: scQTLtools |
Version: 0.99.11 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scQTLtools.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scQTLtools_0.99.11.tar.gz |
StartedAt: 2025-03-19 02:12:58 -0400 (Wed, 19 Mar 2025) |
EndedAt: 2025-03-19 02:22:10 -0400 (Wed, 19 Mar 2025) |
EllapsedTime: 551.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scQTLtools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scQTLtools.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scQTLtools_0.99.11.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scQTLtools.Rcheck’ * using R Under development (unstable) (2025-03-13 r87965) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘scQTLtools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scQTLtools’ version ‘0.99.11’ * 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 ‘scQTLtools’ 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 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 zinbModel 48.103 0.442 48.569 DESeq_normalize 8.518 0.848 9.366 callQTL 5.570 0.486 21.974 createGeneLoc 2.314 0.105 16.175 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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
scQTLtools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL scQTLtools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘scQTLtools’ ... ** this is package ‘scQTLtools’ version ‘0.99.11’ ** 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 (scQTLtools)
scQTLtools.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" Copyright (C) 2025 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(scQTLtools) > > test_check("scQTLtools") Normalization completed using method: logNormalize Dimensions of normalized data:84 2705 Start the sc-eQTLs calling. Matrix: 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| Start the sc-eQTLs calling. Matrix: 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| Start the sc-eQTLs calling. Matrix: 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| Start the sc-eQTLs calling. Matrix: 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| Finished! Start the sc-eQTLs calling. Matrix: 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| Finished! Start the sc-eQTLs calling. Matrix: 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| Finished! Start the sc-eQTLs calling. Matrix: 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| Finished! Start the sc-eQTLs calling. Matrix: 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| Finished! Start the sc-eQTLs calling. Matrix: 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| Finished! Start the sc-eQTLs calling. Matrix: 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| Finished! 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 Loading required package: generics 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 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 No Normalized counts found named 'normcounts', you can achieve data normalization with `normalizeGene()`, or check if it is has been renamed. Normalization completed using method: logNormalize Dimensions of normalized data:84 2705 Attaching package: 'limma' The following object is masked from 'package:DESeq2': plotMA The following object is masked from 'package:BiocGenerics': plotMA Normalization completed using method: logNormalize Dimensions of normalized data:84 2705 Normalization completed using method: CPM Dimensions of normalized data:84 2705 Normalization completed using method: TPM Dimensions of normalized data:84 2705 converting counts to integer mode estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing Normalization completed using method: DESeq Dimensions of normalized data:84 2705 Normalization completed using method: limma Dimensions of normalized data:84 2705 Normalization completed using method: logNormalize Dimensions of normalized data:84 2705 Normalization completed using method: logNormalize Dimensions of normalized data:84 2705 Start the sc-eQTLs calling. Matrix: 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| Finished! Normalization completed using method: logNormalize Dimensions of normalized data:74 500 Start the sc-eQTLs calling. CMP: 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| GMP: 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| Finished! [ FAIL 0 | WARN 0 | SKIP 0 | PASS 54 ] > > proc.time() user system elapsed 104.803 1.356 109.154
scQTLtools.Rcheck/scQTLtools-Ex.timings
name | user | system | elapsed | |
CPM_normalize | 0.938 | 0.718 | 1.656 | |
DESeq_normalize | 8.518 | 0.848 | 9.366 | |
TPM_normalize | 0.945 | 0.658 | 1.602 | |
adjust_pvalues | 0.001 | 0.001 | 0.002 | |
buildZINB | 0.244 | 0.032 | 0.277 | |
callQTL | 5.570 | 0.486 | 21.974 | |
checkSNPList | 0.146 | 0.002 | 0.148 | |
createGeneLoc | 2.314 | 0.105 | 16.175 | |
createQTLObject | 1.527 | 0.186 | 1.714 | |
createSNPsLoc | 1.884 | 0.094 | 4.609 | |
draw_QTLplot | 0.385 | 0.008 | 0.393 | |
draw_boxplot | 0.173 | 0.011 | 0.186 | |
draw_histplot | 0.251 | 0.009 | 0.260 | |
draw_violinplot | 0.149 | 0.000 | 0.148 | |
filterGeneSNP | 1.810 | 0.146 | 1.956 | |
filter_by_abs_b | 0.003 | 0.000 | 0.002 | |
get_cell_groups | 1.435 | 0.060 | 1.496 | |
get_counts | 0.035 | 0.001 | 0.036 | |
get_filter_data | 0.096 | 0.219 | 0.315 | |
get_model_info | 0.035 | 0.003 | 0.037 | |
get_raw_data | 0.309 | 1.290 | 1.598 | |
get_result_info | 0.037 | 0.000 | 0.037 | |
initialize_progress_bar | 0.013 | 0.000 | 2.015 | |
limma_normalize | 0.528 | 0.689 | 1.217 | |
linearModel | 2.378 | 0.006 | 2.385 | |
load_biclassify_info | 0.037 | 0.000 | 0.037 | |
load_group_info | 0.039 | 0.004 | 0.043 | |
load_species_info | 0.035 | 0.001 | 0.035 | |
log_normalize | 0.946 | 0.686 | 1.632 | |
normalizeGene | 0.039 | 0.001 | 0.039 | |
plots_theme_opts | 0.111 | 0.001 | 0.111 | |
poissonModel | 3.757 | 0.047 | 3.804 | |
process_matrix | 0.001 | 0.000 | 0.001 | |
remove_outliers | 0.002 | 0.000 | 0.002 | |
set_filter_data-eQTLObject-method | 0.037 | 0.010 | 0.047 | |
set_filter_data | 0.035 | 0.001 | 0.036 | |
set_model_info-eQTLObject-method | 0.037 | 0.000 | 0.037 | |
set_model_info | 0.035 | 0.000 | 0.036 | |
set_raw_data-eQTLObject-method | 0.035 | 0.002 | 0.036 | |
set_raw_data | 0.034 | 0.002 | 0.036 | |
set_result_info-eQTLObject-method | 0.037 | 0.000 | 0.037 | |
set_result_info | 0.037 | 0.000 | 0.037 | |
show-eQTLObject-method | 0.034 | 0.002 | 0.037 | |
testEQTL | 0.071 | 0.002 | 0.073 | |
testGene | 0.033 | 0.000 | 0.033 | |
testSNP | 0.183 | 0.001 | 0.184 | |
testSNP2 | 0.005 | 0.001 | 0.005 | |
testSeurat | 0.2 | 0.0 | 0.2 | |
visualizeQTL | 2.887 | 0.023 | 2.910 | |
zinbModel | 48.103 | 0.442 | 48.569 | |