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CHECK report for scRNAseq on riesling1

This page was generated on 2021-01-14 15:59:11 -0500 (Thu, 14 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 323/385HostnameOS / ArchINSTALLBUILDCHECK
scRNAseq 2.5.1
Aaron Lun
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/scRNAseq
Branch: master
Last Commit: f6c502b
Last Changed Date: 2021-01-14 00:05:28 -0500 (Thu, 14 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: 2.5.1
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scRNAseq.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings scRNAseq_2.5.1.tar.gz
StartedAt: 2021-01-14 11:41:12 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 12:39:52 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 3519.5 seconds
RetCode: 1
Status:  ERROR  
CheckDir: scRNAseq.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scRNAseq.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings scRNAseq_2.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/scRNAseq.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scRNAseq/DESCRIPTION' ... OK
* this is package 'scRNAseq' version '2.5.1'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... ERROR
Running examples in 'scRNAseq-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BacherTCellData
> ### Title: Obtain the Bacher T cell data
> ### Aliases: BacherTCellData
> 
> ### ** Examples
> 
> sce <- BacherTCellData()
snapshotDate(): 2021-01-14
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
Warning: call dbDisconnect() when finished working with a connection
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
Error in subCsp_cols(x, j, drop = drop) : 
  Cholmod error 'out of memory' at file ../Core/cholmod_memory.c, line 146
Calls: BacherTCellData ... do.call -> <Anonymous> -> <Anonymous> -> subCsp_cols
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
LunSpikeInData             17.93   0.88   21.50
LaMannoBrainData           16.43   0.92   20.14
BacherTCellData            13.10   1.56   15.32
GiladiHSCData              11.98   2.02  112.83
BachMammaryData            11.43   2.04  185.72
StoeckiusHashingData       11.55   1.09   15.97
MessmerESCData              9.60   2.30  302.78
ZilionisLungData            9.83   0.81   13.67
BuettnerESCData             8.62   0.58   10.83
ReprocessedData             8.58   0.55   11.17
RichardTCellData            7.78   0.45   10.88
BaronPancreasData           7.09   0.98    9.19
SegerstolpePancreasData     7.28   0.52    9.65
ZeiselBrainData             7.36   0.40    8.80
NestorowaHSCData            7.04   0.62    9.12
KolodziejczykESCData        7.06   0.54    8.83
AztekinTailData             6.53   0.84    8.19
TasicBrainData              6.44   0.61    8.70
MairPBMCData                6.39   0.39    7.91
KotliarovPBMCData           6.01   0.29    8.39
MacoskoRetinaData           4.72   0.52    7.19
XinPancreasData             4.95   0.24    6.19
UsoskinBrainData            4.81   0.27    5.88
CampbellBrainData           4.46   0.55    6.31
HermannSpermatogenesisData  4.57   0.42    5.87
GrunPancreasData            4.11   0.63    5.39
HuCortexData                4.39   0.34    5.53
ShekharRetinaData           4.17   0.25    5.86
PaulHSCData                 3.85   0.44    5.29
ZhongPrefrontalData         3.45   0.24   52.39
DarmanisBrainData           3.11   0.14    5.89
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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 ERROR, 1 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/scRNAseq.Rcheck/00check.log'
for details.

Installation output

scRNAseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/scRNAseq_2.5.1.tar.gz && rm -rf scRNAseq.buildbin-libdir && mkdir scRNAseq.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scRNAseq.buildbin-libdir scRNAseq_2.5.1.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL scRNAseq_2.5.1.zip && rm scRNAseq_2.5.1.tar.gz scRNAseq_2.5.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 91984  100 91984    0     0   590k      0 --:--:-- --:--:-- --:--:--  590k

install for i386

* installing *source* package 'scRNAseq' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scRNAseq'
    finding HTML links ... done
    AztekinTailData                         html  
REDIRECT:topic	 AztekinTailData -> AztekinTailData.html [ SUCCESS ]
    finding level-2 HTML links ... done

    BachMammaryData                         html  
REDIRECT:topic	 BachMammaryData -> BachMammaryData.html [ SUCCESS ]
    BacherTCellData                         html  
REDIRECT:topic	 BacherTCellData -> BacherTCellData.html [ SUCCESS ]
    BaronPancreasData                       html  
REDIRECT:topic	 BaronPancreasData -> BaronPancreasData.html [ SUCCESS ]
    BuettnerESCData                         html  
REDIRECT:topic	 BuettnerESCData -> BuettnerESCData.html [ SUCCESS ]
    CampbellBrainData                       html  
REDIRECT:topic	 CampbellBrainData -> CampbellBrainData.html [ SUCCESS ]
    ChenBrainData                           html  
REDIRECT:topic	 ChenBrainData -> ChenBrainData.html [ SUCCESS ]
    DarmanisBrainData                       html  
REDIRECT:topic	 DarmanisBrainData -> DarmanisBrainData.html [ SUCCESS ]
    ERCCSpikeInConcentrations               html  
REDIRECT:topic	 ERCCSpikeInConcentrations -> ERCCSpikeInConcentrations.html [ SUCCESS ]
    GiladiHSCData                           html  
REDIRECT:topic	 GiladiHSCData -> GiladiHSCData.html [ SUCCESS ]
    GrunHSCData                             html  
REDIRECT:topic	 GrunHSCData -> GrunHSCData.html [ SUCCESS ]
    GrunPancreasData                        html  
REDIRECT:topic	 GrunPancreasData -> GrunPancreasData.html [ SUCCESS ]
    HermannSpermatogenesisData              html  
REDIRECT:topic	 HermannSpermatogenesisData -> HermannSpermatogenesisData.html [ SUCCESS ]
    HuCortexData                            html  
REDIRECT:topic	 HuCortexData -> HuCortexData.html [ SUCCESS ]
    KolodziejczykESCData                    html  
REDIRECT:topic	 KolodziejczykESCData -> KolodziejczykESCData.html [ SUCCESS ]
    KotliarovPBMCData                       html  
REDIRECT:topic	 KotliarovPBMCData -> KotliarovPBMCData.html [ SUCCESS ]
    LaMannoBrainData                        html  
REDIRECT:topic	 LaMannoBrainData -> LaMannoBrainData.html [ SUCCESS ]
    LawlorPancreasData                      html  
REDIRECT:topic	 LawlorPancreasData -> LawlorPancreasData.html [ SUCCESS ]
    LengESCData                             html  
REDIRECT:topic	 LengESCData -> LengESCData.html [ SUCCESS ]
    LunSpikeInData                          html  
REDIRECT:topic	 LunSpikeInData -> LunSpikeInData.html [ SUCCESS ]
    MacoskoRetinaData                       html  
REDIRECT:topic	 MacoskoRetinaData -> MacoskoRetinaData.html [ SUCCESS ]
    MairPBMCData                            html  
REDIRECT:topic	 MairPBMCData -> MairPBMCData.html [ SUCCESS ]
    MarquesBrainData                        html  
REDIRECT:topic	 MarquesBrainData -> MarquesBrainData.html [ SUCCESS ]
    MessmerESCData                          html  
REDIRECT:topic	 MessmerESCData -> MessmerESCData.html [ SUCCESS ]
    MuraroPancreasData                      html  
REDIRECT:topic	 MuraroPancreasData -> MuraroPancreasData.html [ SUCCESS ]
    NestorowaHSCData                        html  
REDIRECT:topic	 NestorowaHSCData -> NestorowaHSCData.html [ SUCCESS ]
    PaulHSCData                             html  
REDIRECT:topic	 PaulHSCData -> PaulHSCData.html [ SUCCESS ]
    ReprocessedData                         html  
REDIRECT:topic	 ReprocessedAllenData -> ReprocessedData.html [ SUCCESS ]
REDIRECT:topic	 ReprocessedTh2Data -> ReprocessedData.html [ SUCCESS ]
REDIRECT:topic	 ReprocessedFluidigmData -> ReprocessedData.html [ SUCCESS ]
REDIRECT:file	 ReprocessedData.html -> ReprocessedData.html [ SUCCESS ]
    RichardTCellData                        html  
REDIRECT:topic	 RichardTCellData -> RichardTCellData.html [ SUCCESS ]
    RomanovBrainData                        html  
REDIRECT:topic	 RomanovBrainData -> RomanovBrainData.html [ SUCCESS ]
    SegerstolpePancreasData                 html  
REDIRECT:topic	 SegerstolpePancreasData -> SegerstolpePancreasData.html [ SUCCESS ]
    ShekharRetinaData                       html  
REDIRECT:topic	 ShekharRetinaData -> ShekharRetinaData.html [ SUCCESS ]
    StoeckiusHashingData                    html  
REDIRECT:topic	 StoeckiusHashingData -> StoeckiusHashingData.html [ SUCCESS ]
    TasicBrainData                          html  
REDIRECT:topic	 TasicBrainData -> TasicBrainData.html [ SUCCESS ]
    UsoskinBrainData                        html  
REDIRECT:topic	 UsoskinBrainData -> UsoskinBrainData.html [ SUCCESS ]
    WuKidneyData                            html  
REDIRECT:topic	 WuKidneyData -> WuKidneyData.html [ SUCCESS ]
    XinPancreasData                         html  
REDIRECT:topic	 XinPancreasData -> XinPancreasData.html [ SUCCESS ]
    ZeiselBrainData                         html  
REDIRECT:topic	 ZeiselBrainData -> ZeiselBrainData.html [ SUCCESS ]
    ZhongPrefrontalData                     html  
REDIRECT:topic	 ZhongPrefrontalData -> ZhongPrefrontalData.html [ SUCCESS ]
    ZilionisLungData                        html  
REDIRECT:topic	 ZilionisLungData -> ZilionisLungData.html [ SUCCESS ]
    listDatasets                            html  
REDIRECT:topic	 listDatasets -> listDatasets.html [ SUCCESS ]
    scRNAseq-package                        html  
REDIRECT:topic	 scRNAseq-package -> scRNAseq-package.html [ SUCCESS ]
REDIRECT:topic	 scRNAseq -> scRNAseq-package.html [ SUCCESS ]
REDIRECT:topic	 fluidigm -> scRNAseq-package.html [ SUCCESS ]
REDIRECT:topic	 th2 -> scRNAseq-package.html [ SUCCESS ]
REDIRECT:topic	 allen -> scRNAseq-package.html [ SUCCESS ]
** 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

install for x64

* installing *source* package 'scRNAseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scRNAseq' as scRNAseq_2.5.1.zip
* DONE (scRNAseq)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'scRNAseq' successfully unpacked and MD5 sums checked

Tests output

scRNAseq.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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")
== Skipped tests ===============================================================
* On Windows (1)

== 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: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 36 | SKIP 1 | PASS 112 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 394.01   34.18 1151.34

scRNAseq.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
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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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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")
== Skipped tests ===============================================================
* On Windows (1)

== 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: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 36 | SKIP 1 | PASS 112 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 401.78   35.89  816.42

Example timings

scRNAseq.Rcheck/examples_i386/scRNAseq-Ex.timings

nameusersystemelapsed
AztekinTailData7.390.809.92
BachMammaryData 11.60 2.31153.38

scRNAseq.Rcheck/examples_x64/scRNAseq-Ex.timings

nameusersystemelapsed
AztekinTailData6.530.848.19
BachMammaryData 11.43 2.04185.72
BacherTCellData13.10 1.5615.32
BaronPancreasData7.090.989.19
BuettnerESCData 8.62 0.5810.83
CampbellBrainData4.460.556.31
ChenBrainData3.760.404.95
DarmanisBrainData3.110.145.89
ERCCSpikeInConcentrations1.770.082.16
GiladiHSCData 11.98 2.02112.83
GrunHSCData1.890.152.38
GrunPancreasData4.110.635.39
HermannSpermatogenesisData4.570.425.87
HuCortexData4.390.345.53
KolodziejczykESCData7.060.548.83
KotliarovPBMCData6.010.298.39
LaMannoBrainData16.43 0.9220.14
LawlorPancreasData3.460.364.66
LengESCData3.250.144.22
LunSpikeInData17.93 0.8821.50
MacoskoRetinaData4.720.527.19
MairPBMCData6.390.397.91
MarquesBrainData3.320.264.44
MessmerESCData 9.60 2.30302.78
MuraroPancreasData3.750.284.88
NestorowaHSCData7.040.629.12
PaulHSCData3.850.445.29
ReprocessedData 8.58 0.5511.17
RichardTCellData 7.78 0.4510.88
RomanovBrainData3.410.254.58
SegerstolpePancreasData7.280.529.65
ShekharRetinaData4.170.255.86
StoeckiusHashingData11.55 1.0915.97
TasicBrainData6.440.618.70
UsoskinBrainData4.810.275.88
WuKidneyData2.140.122.66
XinPancreasData4.950.246.19
ZeiselBrainData7.360.408.80
ZhongPrefrontalData 3.45 0.2452.39
ZilionisLungData 9.83 0.8113.67
listDatasets0.020.000.01