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CHECK report for scRNAseq on malbec2

This page was generated on 2021-01-21 16:01:21 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE scRNAseq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 324/386HostnameOS / ArchINSTALLBUILDCHECK
scRNAseq 2.5.2
Aaron Lun
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/scRNAseq
Branch: master
Last Commit: eb0f489
Last Changed Date: 2021-01-20 02:55:43 -0500 (Wed, 20 Jan 2021)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]YES, new version is higher than in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  ERROR 

Summary

Package: scRNAseq
Version: 2.5.2
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings scRNAseq_2.5.2.tar.gz
StartedAt: 2021-01-21 12:44:55 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 13:40:10 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 3314.2 seconds
RetCode: 0
Status:  OK 
CheckDir: scRNAseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings scRNAseq_2.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/scRNAseq.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scRNAseq/DESCRIPTION’ ... OK
* this is package ‘scRNAseq’ version ‘2.5.2’
* 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
  .git_fetch_output.txt
  .git_merge_output.txt
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 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 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        33.508 10.777 656.540
ZeiselNervousData          33.816  6.755 588.291
LunSpikeInData             26.207  0.413  31.512
LaMannoBrainData           25.107  0.363  30.169
BacherTCellData            22.698  1.964  30.535
BachMammaryData            20.585  2.703 177.596
MessmerESCData             17.482  2.962 151.317
StoeckiusHashingData       18.419  0.713  23.636
GiladiHSCData              17.593  1.504  21.045
BuettnerESCData            14.903  0.565  25.576
BaronPancreasData          12.789  0.378  15.859
ReprocessedData            12.882  0.253  15.129
ZilionisLungData           12.157  0.472  14.068
RichardTCellData           12.339  0.238  15.049
KolodziejczykESCData       11.790  0.366  14.211
NestorowaHSCData           11.014  0.659  14.774
SegerstolpePancreasData    11.237  0.276  14.744
ZeiselBrainData            10.329  0.293  11.936
AztekinTailData            10.184  0.408  12.287
MairPBMCData               10.447  0.134  11.882
TasicBrainData              9.985  0.309  11.685
KotliarovPBMCData           9.372  0.303  10.953
NowakowskiCortexData        7.873  0.665  35.133
XinPancreasData             7.331  0.138   8.315
CampbellBrainData           7.187  0.208   8.273
MacoskoRetinaData           7.121  0.269   9.351
HermannSpermatogenesisData  7.148  0.119   8.238
HuCortexData                6.733  0.286   8.650
GrunPancreasData            6.742  0.153   7.905
ChenBrainData               6.567  0.157   7.294
UsoskinBrainData            6.443  0.123   7.506
ShekharRetinaData           5.967  0.203   6.916
MuraroPancreasData          5.723  0.218   7.069
MarquesBrainData            5.643  0.077   6.499
RomanovBrainData            5.517  0.186   7.312
PaulHSCData                 5.491  0.193   6.476
DarmanisBrainData           5.552  0.088   6.409
LengESCData                 4.890  0.114   6.290
LawlorPancreasData          4.903  0.068   5.843
PollenGliaData              4.778  0.109   9.742
ZhongPrefrontalData         4.316  0.082   5.240
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/scRNAseq.Rcheck/00check.log’
for details.



Installation output

scRNAseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL scRNAseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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)

Tests output

scRNAseq.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-01-05 r79797) -- "Unsuffered Consequences"
Copyright (C) 2021 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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 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")
══ Warnings ════════════════════════════════════════════════════════════════════
── Warning (test-loading.R:11:5): BaronPancreasData works ──────────────────────
Unable to map 1280 of 20125 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(BaronPancreasData(ensembl = TRUE)) test-loading.R:11:4
 5. scRNAseq::BaronPancreasData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:12:5): BaronPancreasData works ──────────────────────
Unable to map 962 of 14878 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(BaronPancreasData("mouse", ensembl = TRUE)) test-loading.R:12:4
 5. scRNAseq::BaronPancreasData("mouse", ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:25:5): CampbellBrainData works ──────────────────────
Unable to map 2084 of 26774 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(CampbellBrainData(ensembl = TRUE)) test-loading.R:25:4
 5. scRNAseq::CampbellBrainData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:29:5): ChenBrainData works ──────────────────────────
Unable to map 2432 of 23284 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(ChenBrainData(ensembl = TRUE)) test-loading.R:29:4
 5. scRNAseq::ChenBrainData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:33:5): GrunHSCData works ────────────────────────────
Unable to map 1655 of 23536 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(GrunHSCData(ensembl = TRUE)) test-loading.R:33:4
 5. scRNAseq::GrunHSCData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:37:5): GrunPancreasData works ───────────────────────
Unable to map 2250 of 20064 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(GrunPancreasData(ensembl = TRUE)) test-loading.R:37:4
 5. scRNAseq::GrunPancreasData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:54:5): LaMannoBrainData works ───────────────────────
Unable to map 2778 of 18538 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(LaMannoBrainData(ensembl = TRUE, "human-es")) test-loading.R:54:4
 5. scRNAseq::LaMannoBrainData(ensembl = TRUE, "human-es")
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:55:5): LaMannoBrainData works ───────────────────────
Unable to map 2972 of 19530 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(LaMannoBrainData(ensembl = TRUE, "human-embryo")) test-loading.R:55:4
 5. scRNAseq::LaMannoBrainData(ensembl = TRUE, "human-embryo")
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:56:5): LaMannoBrainData works ───────────────────────
Unable to map 1904 of 14725 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(LaMannoBrainData(ensembl = TRUE, "human-ips")) test-loading.R:56:4
 5. scRNAseq::LaMannoBrainData(ensembl = TRUE, "human-ips")
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:57:5): LaMannoBrainData works ───────────────────────
Unable to map 1333 of 18219 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(LaMannoBrainData(ensembl = TRUE, "mouse-adult")) test-loading.R:57:4
 5. scRNAseq::LaMannoBrainData(ensembl = TRUE, "mouse-adult")
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:58:5): LaMannoBrainData works ───────────────────────
Unable to map 2692 of 24377 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(LaMannoBrainData(ensembl = TRUE, "mouse-embryo")) test-loading.R:58:4
 5. scRNAseq::LaMannoBrainData(ensembl = TRUE, "mouse-embryo")
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:78:5): MarquesBrainData works ───────────────────────
Unable to map 1561 of 23556 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(MarquesBrainData(ensembl = TRUE)) test-loading.R:78:4
 5. scRNAseq::MarquesBrainData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:82:5): MuraroPancreasData works ─────────────────────
Unable to map 2110 of 19059 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(MuraroPancreasData(ensembl = TRUE)) test-loading.R:82:4
 5. scRNAseq::MuraroPancreasData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:90:5): PaulHSCData works ────────────────────────────
Unable to map 7705 of 25188 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(PaulHSCData(ensembl = TRUE)) test-loading.R:90:4
 5. scRNAseq::PaulHSCData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:95:5): Reprocessed*Data works ───────────────────────
Unable to map 812 of 20816 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(...) test-loading.R:95:4
 5. scRNAseq::ReprocessedAllenData(assays = "tophat_counts", ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:96:5): Reprocessed*Data works ───────────────────────
Unable to map 812 of 20816 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(...) test-loading.R:96:4
 5. scRNAseq::ReprocessedTh2Data(assays = "tophat_counts", ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:97:5): Reprocessed*Data works ───────────────────────
Unable to map 1004 of 26255 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(...) test-loading.R:97:4
 5. scRNAseq::ReprocessedFluidigmData(assays = "tophat_counts", ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:101:5): RomanovBrainData works ──────────────────────
Unable to map 2692 of 24341 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(RomanovBrainData(ensembl = TRUE)) test-loading.R:101:4
 5. scRNAseq::RomanovBrainData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:105:5): SegerstolpePancreasData works ───────────────
Unable to map 3305 of 26179 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(SegerstolpePancreasData(ensembl = TRUE)) test-loading.R:105:4
 5. scRNAseq::SegerstolpePancreasData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:109:5): ShekharRetinaData works ─────────────────────
Unable to map 1957 of 24904 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(ShekharRetinaData(ensembl = TRUE)) test-loading.R:109:4
 5. scRNAseq::ShekharRetinaData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:113:5): TasicBrainData works ────────────────────────
Unable to map 3139 of 24058 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(TasicBrainData(ensembl = TRUE)) test-loading.R:113:4
 5. scRNAseq::TasicBrainData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:117:5): UsoskinBrainData works ──────────────────────
Unable to map 4768 of 25334 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(UsoskinBrainData(ensembl = TRUE)) test-loading.R:117:4
 5. scRNAseq::UsoskinBrainData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:121:5): XinPancreasData works ───────────────────────
Unable to map 20194 of 39851 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(XinPancreasData(ensembl = TRUE)) test-loading.R:121:4
 5. scRNAseq::XinPancreasData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:125:5): ZeiselBrainData works ───────────────────────
Unable to map 1565 of 20006 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(ZeiselBrainData(ensembl = TRUE)) test-loading.R:125:4
 5. scRNAseq::ZeiselBrainData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:129:5): ZilionisBrianData works ─────────────────────
Unable to map 1467 of 41861 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(ZilionisLungData(ensembl = TRUE)) test-loading.R:129:4
 5. scRNAseq::ZilionisLungData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:131:5): ZilionisBrianData works ─────────────────────
Unable to map 1663 of 28205 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(ZilionisLungData("mouse", ensembl = TRUE)) test-loading.R:131:4
 5. scRNAseq::ZilionisLungData("mouse", ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:139:5): StoeckiusHashingData works ──────────────────
Unable to map 8324 of 27679 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(StoeckiusHashingData(ensembl = TRUE)) test-loading.R:139:4
 5. scRNAseq::StoeckiusHashingData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:139:5): StoeckiusHashingData works ──────────────────
Unable to map 778 of 13220 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(StoeckiusHashingData(ensembl = TRUE)) test-loading.R:139:4
 5. scRNAseq::StoeckiusHashingData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:147:5): StoeckiusHashingData works ──────────────────
Unable to map 8324 of 27679 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(...) test-loading.R:147:4
 5. scRNAseq::StoeckiusHashingData(mode = c("hto", "human"), ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:150:5): StoeckiusHashingData works ──────────────────
Unable to map 778 of 13220 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(...) test-loading.R:150:4
 5. scRNAseq::StoeckiusHashingData(mode = c("adt1", "mouse"), ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:156:5): StoeckiusHashingData works ──────────────────
Unable to map 7096 of 25339 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(StoeckiusHashingData(type = "mixed", ensembl = TRUE)) test-loading.R:156:4
 5. scRNAseq::StoeckiusHashingData(type = "mixed", ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:160:5): MairPBMCData works ──────────────────────────
Unable to map 16 of 499 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(MairPBMCData(ensembl = TRUE)) test-loading.R:160:4
 5. scRNAseq::MairPBMCData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:162:5): MairPBMCData works ──────────────────────────
Unable to map 16 of 499 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(MairPBMCData(mode = c("adt", "rna"), ensembl = TRUE)) test-loading.R:162:4
 5. scRNAseq::MairPBMCData(mode = c("adt", "rna"), ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:168:5): KotliarovPBMCData works ─────────────────────
Unable to map 11979 of 32738 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(KotliarovPBMCData(ensembl = TRUE)) test-loading.R:168:4
 5. scRNAseq::KotliarovPBMCData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:170:5): KotliarovPBMCData works ─────────────────────
Unable to map 11979 of 32738 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(KotliarovPBMCData(mode = c("adt", "rna"), ensembl = TRUE)) test-loading.R:170:4
 5. scRNAseq::KotliarovPBMCData(mode = c("adt", "rna"), ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:178:5): HuCortexData works ──────────────────────────
Unable to map 837 of 19060 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(HuCortexData(ensembl = TRUE)) test-loading.R:178:4
 5. scRNAseq::HuCortexData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)
── Warning (test-loading.R:186:5): WuKidneyData works ──────────────────────────
Unable to map 191 of 18249 requested IDs.
Backtrace:
 1. scRNAseq:::CHECK(WuKidneyData(ensembl = TRUE)) test-loading.R:186:4
 5. scRNAseq::WuKidneyData(ensembl = TRUE)
 6. scRNAseq:::.convert_to_ensembl(...)
 8. ensembldb::mapIds(edb, keys = symbols, keytype = keytype, column = "GENEID")
 9. ensembldb:::.mapIds(...)

[ FAIL 0 | WARN 37 | SKIP 0 | PASS 118 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
    user   system  elapsed 
 593.695   28.611 1009.836 

Example timings

scRNAseq.Rcheck/scRNAseq-Ex.timings

nameusersystemelapsed
AztekinTailData10.184 0.40812.287
BachMammaryData 20.585 2.703177.596
BacherTCellData22.698 1.96430.535
BaronPancreasData12.789 0.37815.859
BhaduriOrganoidData 33.508 10.777656.540
BuettnerESCData14.903 0.56525.576
CampbellBrainData7.1870.2088.273
ChenBrainData6.5670.1577.294
DarmanisBrainData5.5520.0886.409
ERCCSpikeInConcentrations2.9570.0193.472
GiladiHSCData17.593 1.50421.045
GrunHSCData2.8170.0283.610
GrunPancreasData6.7420.1537.905
HermannSpermatogenesisData7.1480.1198.238
HuCortexData6.7330.2868.650
KolodziejczykESCData11.790 0.36614.211
KotliarovPBMCData 9.372 0.30310.953
LaMannoBrainData25.107 0.36330.169
LawlorPancreasData4.9030.0685.843
LengESCData4.8900.1146.290
LunSpikeInData26.207 0.41331.512
MacoskoRetinaData7.1210.2699.351
MairPBMCData10.447 0.13411.882
MarquesBrainData5.6430.0776.499
MessmerESCData 17.482 2.962151.317
MuraroPancreasData5.7230.2187.069
NestorowaHSCData11.014 0.65914.774
NowakowskiCortexData 7.873 0.66535.133
PaulHSCData5.4910.1936.476
PollenGliaData4.7780.1099.742
ReprocessedData12.882 0.25315.129
RichardTCellData12.339 0.23815.049
RomanovBrainData5.5170.1867.312
SegerstolpePancreasData11.237 0.27614.744
ShekharRetinaData5.9670.2036.916
StoeckiusHashingData18.419 0.71323.636
TasicBrainData 9.985 0.30911.685
UsoskinBrainData6.4430.1237.506
WuKidneyData3.0610.0313.786
XinPancreasData7.3310.1388.315
ZeiselBrainData10.329 0.29311.936
ZeiselNervousData 33.816 6.755588.291
ZhongPrefrontalData4.3160.0825.240
ZilionisLungData12.157 0.47214.068
listDatasets0.0140.0000.027