This page was generated on 2021-01-14 15:58:58 -0500 (Thu, 14 Jan 2021).
celldex 1.1.0 Aaron Lun
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021) |
URL: https://git.bioconductor.org/packages/celldex |
Branch: master |
Last Commit: e3fabad |
Last Changed Date: 2020-10-27 10:32:01 -0500 (Tue, 27 Oct 2020) |
| malbec2 | Linux (Ubuntu 20.04.1 LTS) / x86_64 | OK | OK | [ OK ] |  |
riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | |
R Under development (unstable) (2021-01-05 r79797) -- "Unsuffered Consequences"
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> library(testthat)
> library(celldex)
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("celldex")
══ Warnings ════════════════════════════════════════════════════════════════════
── Warning (test-datasets.R:5:5): Ensembl coercion works for all datasets ──────
Unable to map 532 of 19859 requested IDs.
Backtrace:
1. testthat::expect_error(...) test-datasets.R:5:4
6. celldex::BlueprintEncodeData(ensembl = TRUE)
7. celldex:::.convert_to_ensembl(se, "Hs", ensembl)
9. ensembldb::mapIds(...)
10. ensembldb:::.mapIds(...)
── Warning (test-datasets.R:7:5): Ensembl coercion works for all datasets ──────
Unable to map 18129 of 48043 requested IDs.
Backtrace:
1. testthat::expect_error(...) test-datasets.R:7:4
6. celldex::DatabaseImmuneCellExpressionData(ensembl = TRUE)
7. celldex:::.convert_to_ensembl(se, "Hs", ensembl)
9. ensembldb::mapIds(...)
10. ensembldb:::.mapIds(...)
── Warning (test-datasets.R:9:5): Ensembl coercion works for all datasets ──────
Unable to map 1470 of 19363 requested IDs.
Backtrace:
1. testthat::expect_error(...) test-datasets.R:9:4
6. celldex::HumanPrimaryCellAtlasData(ensembl = TRUE)
7. celldex:::.convert_to_ensembl(se, "Hs", ensembl)
9. ensembldb::mapIds(...)
10. ensembldb:::.mapIds(...)
── Warning (test-datasets.R:11:5): Ensembl coercion works for all datasets ─────
Unable to map 782 of 22134 requested IDs.
Backtrace:
1. testthat::expect_error(X <- ImmGenData(ensembl = TRUE), NA) test-datasets.R:11:4
6. celldex::ImmGenData(ensembl = TRUE)
7. celldex:::.convert_to_ensembl(se, "Mm", ensembl)
9. ensembldb::mapIds(...)
10. ensembldb:::.mapIds(...)
── Warning (test-datasets.R:15:5): Ensembl coercion works for all datasets ─────
Unable to map 2180 of 21214 requested IDs.
Backtrace:
1. testthat::expect_error(...) test-datasets.R:15:4
6. celldex::MouseRNAseqData(ensembl = TRUE)
7. celldex:::.convert_to_ensembl(se, "Mm", ensembl)
9. ensembldb::mapIds(...)
10. ensembldb:::.mapIds(...)
── Warning (test-datasets.R:17:5): Ensembl coercion works for all datasets ─────
Unable to map 3426 of 13276 requested IDs.
Backtrace:
1. testthat::expect_error(...) test-datasets.R:17:4
6. celldex::NovershternHematopoieticData(ensembl = TRUE)
7. celldex:::.convert_to_ensembl(se, "Hs", ensembl)
9. ensembldb::mapIds(...)
10. ensembldb:::.mapIds(...)
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 14 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
141.761 8.087 505.407