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CHECK report for celldex on malbec2

This page was generated on 2021-01-14 15:58:58 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE celldex PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 50/385HostnameOS / ArchINSTALLBUILDCHECK
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 ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK 

Summary

Package: celldex
Version: 1.1.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:celldex.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings celldex_1.1.0.tar.gz
StartedAt: 2021-01-14 11:49:17 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 12:00:55 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 697.7 seconds
RetCode: 0
Status:  OK 
CheckDir: celldex.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:celldex.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings celldex_1.1.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/celldex.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 ‘celldex/DESCRIPTION’ ... OK
* this is package ‘celldex’ version ‘1.1.0’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
  .github
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 ‘celldex’ 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
DatabaseImmuneCellExpressionData 10.661  0.496  14.105
BlueprintEncodeData               8.296  0.276   9.856
HumanPrimaryCellAtlasData         6.581  0.136   7.739
ImmGenData                        6.251  0.132   7.922
MouseRNAseqData                   5.563  0.111   6.675
MonacoImmuneData                  5.440  0.080   6.293
NovershternHematopoieticData      5.446  0.069   6.498
* 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/celldex.Rcheck/00check.log’
for details.



Installation output

celldex.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘celldex’ ...
** 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 (celldex)

Tests output

celldex.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(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 

Example timings

celldex.Rcheck/celldex-Ex.timings

nameusersystemelapsed
BlueprintEncodeData8.2960.2769.856
DatabaseImmuneCellExpressionData10.661 0.49614.105
HumanPrimaryCellAtlasData6.5810.1367.739
ImmGenData6.2510.1327.922
MonacoImmuneData5.4400.0806.293
MouseRNAseqData5.5630.1116.675
NovershternHematopoieticData5.4460.0696.498