Back to Build/check report for BioC 3.18 experimental data |
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This page was generated on 2024-04-16 14:51:29 -0400 (Tue, 16 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
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 355/429 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
scRNAseq 2.16.0 (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: 2.16.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings scRNAseq_2.16.0.tar.gz |
StartedAt: 2024-04-16 12:18:10 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 12:43:23 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 1512.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scRNAseq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings scRNAseq_2.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-data-experiment/meat/scRNAseq.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 ‘2.16.0’ * 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 ... NOTE Problems with news in ‘inst/NEWS.Rd’: inst/NEWS.Rd:35: unexpected section header '\section' inst/NEWS.Rd:51: unexpected section header '\section' inst/NEWS.Rd:59: unexpected section header '\section' inst/NEWS.Rd:67: unexpected section header '\section' inst/NEWS.Rd:70: unexpected END_OF_INPUT ' ' * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed HeOrganAtlasData 50.437 10.198 63.496 ZeiselNervousData 36.491 4.526 42.079 BhaduriOrganoidData 34.478 4.000 38.916 BacherTCellData 21.231 3.856 25.523 JessaBrainData 21.069 3.770 25.680 ErnstSpermatogenesisData 19.580 2.409 22.994 GiladiHSCData 16.270 2.902 20.114 LunSpikeInData 15.806 1.911 19.782 LaMannoBrainData 14.332 1.808 17.885 ZhaoImmuneLiverData 14.341 1.700 16.587 StoeckiusHashingData 13.315 1.613 16.490 ZilionisLungData 11.151 1.159 13.007 MessmerESCData 10.077 1.404 12.566 BuettnerESCData 9.894 1.578 12.594 NestorowaHSCData 8.605 1.197 10.506 BunisHSPCData 8.159 0.961 9.768 BachMammaryData 8.014 0.992 10.420 KotliarovPBMCData 7.601 0.803 8.835 SegerstolpePancreasData 7.115 1.004 8.794 ReprocessedData 7.418 0.636 8.746 RichardTCellData 7.109 0.920 8.995 ZeiselBrainData 6.671 0.907 8.293 AztekinTailData 6.782 0.655 7.953 KolodziejczykESCData 6.531 0.781 8.274 TasicBrainData 6.182 0.904 7.690 MairPBMCData 6.057 0.740 7.395 NowakowskiCortexData 5.777 1.017 7.292 BaronPancreasData 6.172 0.569 7.607 CampbellBrainData 6.009 0.593 7.000 MacoskoRetinaData 5.334 0.646 6.429 ShekharRetinaData 5.012 0.523 5.881 LedergorMyelomaData 4.981 0.524 5.865 FletcherOlfactoryData 4.848 0.642 5.926 ChenBrainData 4.699 0.551 5.604 XinPancreasData 4.448 0.573 16.006 UsoskinBrainData 4.323 0.583 15.024 MuraroPancreasData 4.058 0.600 5.002 HuCortexData 4.153 0.399 5.140 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘scRNAseq.Rmd’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.18-data-experiment/meat/scRNAseq.Rcheck/00check.log’ for details.
scRNAseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL scRNAseq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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. > 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, sort, 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 37 | SKIP 0 | PASS 120 ] [ FAIL 0 | WARN 37 | SKIP 0 | PASS 120 ] Warning message: call dbDisconnect() when finished working with a connection > > proc.time() user system elapsed 469.489 56.764 575.080
scRNAseq.Rcheck/scRNAseq-Ex.timings
name | user | system | elapsed | |
AztekinTailData | 6.782 | 0.655 | 7.953 | |
BachMammaryData | 8.014 | 0.992 | 10.420 | |
BacherTCellData | 21.231 | 3.856 | 25.523 | |
BaronPancreasData | 6.172 | 0.569 | 7.607 | |
BhaduriOrganoidData | 34.478 | 4.000 | 38.916 | |
BuettnerESCData | 9.894 | 1.578 | 12.594 | |
BunisHSPCData | 8.159 | 0.961 | 9.768 | |
CampbellBrainData | 6.009 | 0.593 | 7.000 | |
ChenBrainData | 4.699 | 0.551 | 5.604 | |
DarmanisBrainData | 2.940 | 0.400 | 3.715 | |
ERCCSpikeInConcentrations | 1.478 | 0.144 | 1.878 | |
ErnstSpermatogenesisData | 19.580 | 2.409 | 22.994 | |
FletcherOlfactoryData | 4.848 | 0.642 | 5.926 | |
GiladiHSCData | 16.270 | 2.902 | 20.114 | |
GrunHSCData | 1.568 | 0.149 | 1.993 | |
GrunPancreasData | 3.498 | 0.398 | 4.440 | |
HeOrganAtlasData | 50.437 | 10.198 | 63.496 | |
HermannSpermatogenesisData | 4.074 | 0.110 | 4.702 | |
HuCortexData | 4.153 | 0.399 | 5.140 | |
JessaBrainData | 21.069 | 3.770 | 25.680 | |
KolodziejczykESCData | 6.531 | 0.781 | 8.274 | |
KotliarovPBMCData | 7.601 | 0.803 | 8.835 | |
LaMannoBrainData | 14.332 | 1.808 | 17.885 | |
LawlorPancreasData | 3.004 | 0.303 | 3.651 | |
LedergorMyelomaData | 4.981 | 0.524 | 5.865 | |
LengESCData | 2.963 | 0.240 | 3.594 | |
LunSpikeInData | 15.806 | 1.911 | 19.782 | |
MacoskoRetinaData | 5.334 | 0.646 | 6.429 | |
MairPBMCData | 6.057 | 0.740 | 7.395 | |
MarquesBrainData | 3.582 | 0.460 | 4.383 | |
MessmerESCData | 10.077 | 1.404 | 12.566 | |
MuraroPancreasData | 4.058 | 0.600 | 5.002 | |
NestorowaHSCData | 8.605 | 1.197 | 10.506 | |
NowakowskiCortexData | 5.777 | 1.017 | 7.292 | |
PaulHSCData | 3.644 | 0.328 | 4.365 | |
PollenGliaData | 2.498 | 0.181 | 3.072 | |
ReprocessedData | 7.418 | 0.636 | 8.746 | |
RichardTCellData | 7.109 | 0.920 | 8.995 | |
RomanovBrainData | 3.304 | 0.344 | 3.895 | |
SegerstolpePancreasData | 7.115 | 1.004 | 8.794 | |
ShekharRetinaData | 5.012 | 0.523 | 5.881 | |
StoeckiusHashingData | 13.315 | 1.613 | 16.490 | |
TasicBrainData | 6.182 | 0.904 | 7.690 | |
UsoskinBrainData | 4.323 | 0.583 | 15.024 | |
WuKidneyData | 2.578 | 0.448 | 3.284 | |
XinPancreasData | 4.448 | 0.573 | 16.006 | |
ZeiselBrainData | 6.671 | 0.907 | 8.293 | |
ZeiselNervousData | 36.491 | 4.526 | 42.079 | |
ZhaoImmuneLiverData | 14.341 | 1.700 | 16.587 | |
ZhongPrefrontalData | 3.272 | 0.292 | 3.952 | |
ZilionisLungData | 11.151 | 1.159 | 13.007 | |
listDatasets | 0.018 | 0.000 | 0.019 | |