Aaron Lun
| Snapshot Date: 2025-01-07 07:30 -0500 (Tue, 07 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/scRNAseq |
| git_branch: devel |
| git_last_commit: e33f182 |
| git_last_commit_date: 2024-10-29 09:46:12 -0500 (Tue, 29 Oct 2024) |
| Back to Build/check report for BioC 3.21 experimental data |
|
This page was generated on 2025-01-07 15:01 -0500 (Tue, 07 Jan 2025).
| 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" | 4756 |
| 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 355/430 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| scRNAseq 2.21.0 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 24.04.1 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: 2.21.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scRNAseq_2.21.0.tar.gz |
| StartedAt: 2025-01-07 12:37:18 -0500 (Tue, 07 Jan 2025) |
| EndedAt: 2025-01-07 12:52:15 -0500 (Tue, 07 Jan 2025) |
| EllapsedTime: 897.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scRNAseq.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scRNAseq_2.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/scRNAseq.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘scRNAseq/DESCRIPTION’ ... OK
* this is package ‘scRNAseq’ version ‘2.21.0’
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
AztekinTailData.Rd: reducedDims, SingleCellExperiment-class
BachMammaryData.Rd: rowRanges, SingleCellExperiment-class
BacherTCellData.Rd: colData, rowRanges, SingleCellExperiment-class
BaronPancreasData.Rd: rowRanges, SingleCellExperiment-class
BhaduriOrganoidData.Rd: rowRanges, SingleCellExperiment-class
BuettnerESCData.Rd: altExps, rowRanges, SingleCellExperiment-class
BunisHSPCData.Rd: colData, SingleCellExperiment-class
CampbellBrainData.Rd: rowRanges, SingleCellExperiment-class
ChenBrainData.Rd: rowRanges, SingleCellExperiment-class
DarmanisBrainData.Rd: rowRanges, SingleCellExperiment-class
ERCCSpikeInConcentrations.Rd: DataFrame-class
ErnstSpermatogenesisData.Rd: rowRanges, SingleCellExperiment-class
FletcherOlfactoryData.Rd: colData, rowRanges,
SingleCellExperiment-class
GiladiHSCData.Rd: colData, rowRanges, SingleCellExperiment-class
GrunHSCData.Rd: rowRanges, SingleCellExperiment-class
GrunPancreasData.Rd: altExps, rowRanges, SingleCellExperiment-class
HeOrganAtlasData.Rd: rowRanges, SingleCellExperiment-class
HermannSpermatogenesisData.Rd: SingleCellExperiment-class
HuCortexData.Rd: rowRanges, SingleCellExperiment-class
JessaBrainData.Rd: colData, rowRanges, SingleCellExperiment-class
KolodziejczykESCData.Rd: altExps, rowRanges,
SingleCellExperiment-class
KotliarovPBMCData.Rd: rowRanges, SingleCellExperiment-class
LaMannoBrainData.Rd: rowRanges, SingleCellExperiment-class
LawlorPancreasData.Rd: SingleCellExperiment-class
LedergorMyelomaData.Rd: rowRanges, SingleCellExperiment-class
LengESCData.Rd: rowRanges, SingleCellExperiment-class
LunSpikeInData.Rd: altExp, altExps, rowRanges,
SingleCellExperiment-class
MacoskoRetinaData.Rd: rowRanges, SingleCellExperiment-class
MairPBMCData.Rd: rowRanges, SingleCellExperiment-class
MarquesBrainData.Rd: rowRanges, SingleCellExperiment-class
MessmerESCData.Rd: altExps, rowRanges, SingleCellExperiment-class
MuraroPancreasData.Rd: altExps, rowRanges, SingleCellExperiment-class
NestorowaHSCData.Rd: colData, reducedDims, altExps, rowRanges,
SingleCellExperiment-class
NowakowskiCortexData.Rd: rowRanges, SingleCellExperiment-class,
reducedDims
PaulHSCData.Rd: rowRanges, SingleCellExperiment-class
PollenGliaData.Rd: rowRanges, SingleCellExperiment-class
ReprocessedData.Rd: altExps, metadata, rowRanges,
SingleCellExperiment-class
RichardTCellData.Rd: altExps, rowRanges, SingleCellExperiment-class
RomanovBrainData.Rd: altExps, rowRanges, SingleCellExperiment-class
SegerstolpePancreasData.Rd: altExps, rowData, rowRanges,
SingleCellExperiment-class
ShekharRetinaData.Rd: rowRanges, SingleCellExperiment-class
StoeckiusHashingData.Rd: rowRanges, SingleCellExperiment-class
TasicBrainData.Rd: altExps, rowRanges, SingleCellExperiment-class
UsoskinBrainData.Rd: rowRanges, SingleCellExperiment-class
WuKidneyData.Rd: rowRanges, SingleCellExperiment-class
XinPancreasData.Rd: rowRanges, SingleCellExperiment-class
ZeiselBrainData.Rd: altExps, rowRanges, SingleCellExperiment-class
ZeiselNervousData.Rd: rowRanges, SingleCellExperiment-class
ZhaoImmuneLiverData.Rd: rowRanges, colData,
SingleCellExperiment-class
ZhongPrefrontalData.Rd: rowRanges, SingleCellExperiment-class
ZilionisLungData.Rd: rowRanges, colData, reducedDim,
SingleCellExperiment-class
countErccMolecules.Rd: DataFrame-class
fetchDataset.Rd: ReloadedArray-class, dgCMatrix-class, readObject,
SummarizedExperiment-class, uploadDirectory
listDatasets.Rd: DataFrame-class
polishDataset.Rd: SummarizedExperiment-class,
SingleCellExperiment-class, altExp
saveDataset.Rd: SummarizedExperiment-class, fetchMetadataSchema,
uploadDirectory
searchDatasets.Rd: gypsum.search.clause, fetchMetadataDatabase,
DataFrame-class, translateTextQuery
surveyDatasets.Rd: fetchMetadataDatabase, DataFrame-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 23.626 8.535 32.464
BacherTCellData 17.461 5.419 24.041
ZeiselNervousData 15.358 6.089 23.028
HeOrganAtlasData 13.065 7.432 21.160
ErnstSpermatogenesisData 10.299 4.183 15.720
JessaBrainData 9.216 4.521 14.959
StoeckiusHashingData 9.095 1.686 13.956
BachMammaryData 7.089 1.354 9.421
LunSpikeInData 6.540 1.376 8.386
GiladiHSCData 4.935 2.747 8.278
AztekinTailData 6.552 0.691 7.456
ZhaoImmuneLiverData 4.655 2.336 7.721
NestorowaHSCData 4.376 1.081 5.858
ZilionisLungData 3.960 1.159 5.529
KolodziejczykESCData 3.435 1.257 5.017
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-data-experiment/meat/scRNAseq.Rcheck/00check.log’
for details.
scRNAseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL scRNAseq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
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
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
> 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
277.545 45.332 340.909
scRNAseq.Rcheck/scRNAseq-Ex.timings
| name | user | system | elapsed | |
| AztekinTailData | 6.552 | 0.691 | 7.456 | |
| BachMammaryData | 7.089 | 1.354 | 9.421 | |
| BacherTCellData | 17.461 | 5.419 | 24.041 | |
| BaronPancreasData | 0.980 | 0.163 | 1.179 | |
| BhaduriOrganoidData | 23.626 | 8.535 | 32.464 | |
| BuettnerESCData | 3.200 | 0.737 | 4.173 | |
| BunisHSPCData | 1.030 | 0.490 | 1.643 | |
| CampbellBrainData | 1.862 | 0.943 | 3.072 | |
| ChenBrainData | 0.938 | 0.480 | 1.543 | |
| DarmanisBrainData | 0.252 | 0.056 | 0.314 | |
| ERCCSpikeInConcentrations | 0.019 | 0.002 | 0.022 | |
| ErnstSpermatogenesisData | 10.299 | 4.183 | 15.720 | |
| FletcherOlfactoryData | 0.673 | 0.110 | 0.796 | |
| GiladiHSCData | 4.935 | 2.747 | 8.278 | |
| GrunHSCData | 0.233 | 0.054 | 0.292 | |
| GrunPancreasData | 0.510 | 0.124 | 0.646 | |
| HeOrganAtlasData | 13.065 | 7.432 | 21.160 | |
| HermannSpermatogenesisData | 0.806 | 0.123 | 0.955 | |
| HuCortexData | 0.503 | 0.103 | 0.662 | |
| JessaBrainData | 9.216 | 4.521 | 14.959 | |
| KolodziejczykESCData | 3.435 | 1.257 | 5.017 | |
| KotliarovPBMCData | 2.271 | 0.777 | 3.328 | |
| LaMannoBrainData | 1.624 | 0.380 | 2.116 | |
| LawlorPancreasData | 0.796 | 0.133 | 0.931 | |
| LedergorMyelomaData | 1.389 | 0.373 | 1.957 | |
| LengESCData | 0.497 | 0.104 | 0.604 | |
| LunSpikeInData | 6.540 | 1.376 | 8.386 | |
| MacoskoRetinaData | 1.762 | 0.629 | 2.625 | |
| MairPBMCData | 0.570 | 0.161 | 0.739 | |
| MarquesBrainData | 0.652 | 0.154 | 0.880 | |
| MessmerESCData | 3.886 | 0.842 | 4.982 | |
| MuraroPancreasData | 0.905 | 0.234 | 1.159 | |
| NestorowaHSCData | 4.376 | 1.081 | 5.858 | |
| NowakowskiCortexData | 1.520 | 0.314 | 1.856 | |
| PaulHSCData | 2.790 | 0.373 | 3.334 | |
| PollenGliaData | 0.215 | 0.030 | 0.247 | |
| ReprocessedData | 1.978 | 0.294 | 2.278 | |
| RichardTCellData | 3.121 | 0.663 | 4.018 | |
| RomanovBrainData | 0.477 | 0.133 | 0.629 | |
| SegerstolpePancreasData | 1.162 | 0.391 | 1.653 | |
| ShekharRetinaData | 2.104 | 0.653 | 2.970 | |
| StoeckiusHashingData | 9.095 | 1.686 | 13.956 | |
| TasicBrainData | 1.678 | 0.368 | 2.050 | |
| UsoskinBrainData | 0.520 | 0.111 | 0.643 | |
| WuKidneyData | 0.373 | 0.067 | 0.456 | |
| XinPancreasData | 0.983 | 0.251 | 1.250 | |
| ZeiselBrainData | 0.914 | 0.234 | 1.173 | |
| ZeiselNervousData | 15.358 | 6.089 | 23.028 | |
| ZhaoImmuneLiverData | 4.655 | 2.336 | 7.721 | |
| ZhongPrefrontalData | 0.805 | 0.366 | 1.238 | |
| ZilionisLungData | 3.960 | 1.159 | 5.529 | |
| countErccMolecules | 0.033 | 0.003 | 0.036 | |
| fetchDataset | 0.418 | 0.016 | 0.434 | |
| listDatasets | 0.009 | 0.001 | 0.011 | |
| listVersions | 0.073 | 0.008 | 0.578 | |
| polishDataset | 0.121 | 0.012 | 0.134 | |
| saveDataset | 0.843 | 0.157 | 0.941 | |
| searchDatasets | 1.323 | 0.123 | 1.582 | |
| surveyDatasets | 0.832 | 0.024 | 0.855 | |