Back to Build/check report for BioC 3.20 experimental data |
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This page was generated on 2024-06-20 14:51 -0400 (Thu, 20 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4687 |
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 350/425 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
scRNAseq 2.19.0 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||
To the developers/maintainers of the scRNAseq package: - 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: scRNAseq |
Version: 2.19.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scRNAseq_2.19.0.tar.gz |
StartedAt: 2024-06-20 12:01:24 -0400 (Thu, 20 Jun 2024) |
EndedAt: 2024-06-20 12:22:38 -0400 (Thu, 20 Jun 2024) |
EllapsedTime: 1274.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scRNAseq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scRNAseq_2.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/scRNAseq.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘scRNAseq/DESCRIPTION’ ... OK * this is package ‘scRNAseq’ version ‘2.19.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘scRNAseq’ 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed BhaduriOrganoidData 61.979 8.885 73.321 ZeiselNervousData 53.376 10.345 64.258 JessaBrainData 35.682 5.324 41.464 BacherTCellData 34.231 5.895 40.251 ErnstSpermatogenesisData 27.369 5.725 33.563 HeOrganAtlasData 24.879 7.446 32.523 ZhaoImmuneLiverData 20.446 4.896 25.431 GiladiHSCData 14.999 3.658 18.733 ZilionisLungData 15.876 2.238 18.278 StoeckiusHashingData 12.007 1.686 24.676 AztekinTailData 9.266 0.803 10.100 KotliarovPBMCData 8.022 1.960 10.041 BachMammaryData 7.898 0.552 9.708 PaulHSCData 6.026 1.936 7.977 NestorowaHSCData 6.673 1.140 8.117 LunSpikeInData 6.822 0.710 8.145 ShekharRetinaData 6.254 1.152 7.484 CampbellBrainData 5.681 1.445 7.162 MacoskoRetinaData 5.441 1.177 6.655 MessmerESCData 5.216 0.790 6.303 ChenBrainData 4.010 1.829 5.857 LedergorMyelomaData 4.301 0.700 5.060 * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.20-data-experiment/meat/scRNAseq.Rcheck/00check.log’ for details.
scRNAseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL scRNAseq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘scRNAseq’ ... ** using staged installation ** R ** 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 (scRNAseq)
scRNAseq.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" Copyright (C) 2024 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. > library(testthat) > library(scRNAseq) Loading required package: 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, 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 > test_check("scRNAseq") [ FAIL 0 | WARN 35 | SKIP 1 | PASS 176 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • is.null(gh_token) is TRUE (1): 'test-uploadDirectory.R:59:5' [ FAIL 0 | WARN 35 | SKIP 1 | PASS 176 ] Warning message: call dbDisconnect() when finished working with a connection > > proc.time() user system elapsed 377.341 53.951 452.145
scRNAseq.Rcheck/scRNAseq-Ex.timings
name | user | system | elapsed | |
AztekinTailData | 9.266 | 0.803 | 10.100 | |
BachMammaryData | 7.898 | 0.552 | 9.708 | |
BacherTCellData | 34.231 | 5.895 | 40.251 | |
BaronPancreasData | 2.620 | 0.520 | 3.147 | |
BhaduriOrganoidData | 61.979 | 8.885 | 73.321 | |
BuettnerESCData | 3.550 | 0.352 | 4.355 | |
BunisHSPCData | 2.838 | 0.537 | 3.402 | |
CampbellBrainData | 5.681 | 1.445 | 7.162 | |
ChenBrainData | 4.010 | 1.829 | 5.857 | |
DarmanisBrainData | 0.460 | 0.064 | 0.530 | |
ERCCSpikeInConcentrations | 0.020 | 0.000 | 0.022 | |
ErnstSpermatogenesisData | 27.369 | 5.725 | 33.563 | |
FletcherOlfactoryData | 1.130 | 0.151 | 1.289 | |
GiladiHSCData | 14.999 | 3.658 | 18.733 | |
GrunHSCData | 0.422 | 0.023 | 0.450 | |
GrunPancreasData | 1.017 | 0.176 | 1.204 | |
HeOrganAtlasData | 24.879 | 7.446 | 32.523 | |
HermannSpermatogenesisData | 1.708 | 0.164 | 1.886 | |
HuCortexData | 1.357 | 0.311 | 1.679 | |
JessaBrainData | 35.682 | 5.324 | 41.464 | |
KolodziejczykESCData | 3.975 | 0.320 | 4.618 | |
KotliarovPBMCData | 8.022 | 1.960 | 10.041 | |
LaMannoBrainData | 3.194 | 0.364 | 3.584 | |
LawlorPancreasData | 0.836 | 0.094 | 0.957 | |
LedergorMyelomaData | 4.301 | 0.700 | 5.060 | |
LengESCData | 0.568 | 0.209 | 0.818 | |
LunSpikeInData | 6.822 | 0.710 | 8.145 | |
MacoskoRetinaData | 5.441 | 1.177 | 6.655 | |
MairPBMCData | 0.886 | 0.238 | 1.134 | |
MarquesBrainData | 1.745 | 0.364 | 2.123 | |
MessmerESCData | 5.216 | 0.790 | 6.303 | |
MuraroPancreasData | 2.149 | 0.420 | 2.582 | |
NestorowaHSCData | 6.673 | 1.140 | 8.117 | |
NowakowskiCortexData | 3.230 | 0.517 | 3.762 | |
PaulHSCData | 6.026 | 1.936 | 7.977 | |
PollenGliaData | 0.405 | 0.032 | 0.439 | |
ReprocessedData | 2.345 | 0.217 | 2.640 | |
RichardTCellData | 3.500 | 0.276 | 4.070 | |
RomanovBrainData | 1.353 | 0.205 | 1.566 | |
SegerstolpePancreasData | 2.705 | 0.468 | 3.190 | |
ShekharRetinaData | 6.254 | 1.152 | 7.484 | |
StoeckiusHashingData | 12.007 | 1.686 | 24.676 | |
TasicBrainData | 2.059 | 0.348 | 2.495 | |
UsoskinBrainData | 0.770 | 0.092 | 0.868 | |
WuKidneyData | 1.299 | 0.060 | 1.366 | |
XinPancreasData | 1.650 | 0.275 | 1.933 | |
ZeiselBrainData | 2.234 | 0.352 | 2.598 | |
ZeiselNervousData | 53.376 | 10.345 | 64.258 | |
ZhaoImmuneLiverData | 20.446 | 4.896 | 25.431 | |
ZhongPrefrontalData | 1.471 | 0.185 | 1.665 | |
ZilionisLungData | 15.876 | 2.238 | 18.278 | |
countErccMolecules | 0.033 | 0.000 | 0.034 | |
fetchDataset | 0.732 | 0.012 | 0.744 | |
listDatasets | 0.011 | 0.000 | 0.011 | |
listVersions | 0.086 | 0.008 | 0.842 | |
polishDataset | 0.198 | 0.004 | 0.202 | |
saveDataset | 0.993 | 0.020 | 0.956 | |
searchDatasets | 1.160 | 0.027 | 1.393 | |
surveyDatasets | 0.880 | 0.100 | 0.979 | |