Back to Build/check report for BioC 3.15 experimental data
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This page was generated on 2022-10-13 14:50:05 -0400 (Thu, 13 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4383
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for imcdatasets on nebbiolo1


To the developers/maintainers of the imcdatasets package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 189/410HostnameOS / ArchINSTALLBUILDCHECK
imcdatasets 1.4.1  (landing page)
Nicolas Damond
Snapshot Date: 2022-10-13 07:30:02 -0400 (Thu, 13 Oct 2022)
git_url: https://git.bioconductor.org/packages/imcdatasets
git_branch: RELEASE_3_15
git_last_commit: 9b0d63d
git_last_commit_date: 2022-06-29 12:29:51 -0400 (Wed, 29 Jun 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: imcdatasets
Version: 1.4.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:imcdatasets.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings imcdatasets_1.4.1.tar.gz
StartedAt: 2022-10-13 11:27:08 -0400 (Thu, 13 Oct 2022)
EndedAt: 2022-10-13 11:42:41 -0400 (Thu, 13 Oct 2022)
EllapsedTime: 933.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: imcdatasets.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:imcdatasets.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings imcdatasets_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-data-experiment/meat/imcdatasets.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘imcdatasets/DESCRIPTION’ ... OK
* this is package ‘imcdatasets’ version ‘1.4.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘imcdatasets’ can be installed ... WARNING
Found the following significant warnings:
  Warning: The .onLoad functions will be deprecated, please use the wrapper 
See ‘/home/biocbuild/bbs-3.15-data-experiment/meat/imcdatasets.Rcheck/00install.out’ for details.
* 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 ... NOTE
Warning: The .onLoad functions will be deprecated, please use the wrapper 
    functions instead (e.g. 'JacksonFischer2020Data(data_type = 'sce')'
    rather than 'JacksonFischer2020_sce()'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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
JacksonFischer2020         75.328 10.614  87.027
JacksonFischer2020Data     71.516 10.184  82.861
ZanotelliSpheroids2020     70.618 10.988  82.803
ZanotelliSpheroids2020Data 70.203  9.783  81.113
DamondPancreas2019         53.940  6.578  61.782
DamondPancreas2019Data     40.372  5.588  47.046
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-data-experiment/meat/imcdatasets.Rcheck/00check.log’
for details.



Installation output

imcdatasets.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL imcdatasets
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘imcdatasets’ ...
** 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
Warning: The .onLoad functions will be deprecated, please use the wrapper 
    functions instead (e.g. 'JacksonFischer2020Data(data_type = 'sce')'
    rather than 'JacksonFischer2020_sce()'
snapshotDate(): 2022-04-26
** testing if installed package can be loaded from final location
Warning: The .onLoad functions will be deprecated, please use the wrapper 
    functions instead (e.g. 'JacksonFischer2020Data(data_type = 'sce')'
    rather than 'JacksonFischer2020_sce()'
snapshotDate(): 2022-04-26
** testing if installed package keeps a record of temporary installation path
* DONE (imcdatasets)

Tests output

imcdatasets.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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(imcdatasets)
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

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, 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

Loading required package: cytomapper
Loading required package: EBImage

Attaching package: 'EBImage'

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

    resize

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

    channel

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

    resize, tile

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

    resize, tile


Attaching package: 'cytomapper'

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

    channelNames, channelNames<-

snapshotDate(): 2022-04-26
Warning message:
The .onLoad functions will be deprecated, please use the wrapper 
    functions instead (e.g. 'JacksonFischer2020Data(data_type = 'sce')'
    rather than 'JacksonFischer2020_sce()' 
> test_check("imcdatasets")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
211.475  26.826 242.337 

Example timings

imcdatasets.Rcheck/imcdatasets-Ex.timings

nameusersystemelapsed
DamondPancreas201953.940 6.57861.782
DamondPancreas2019Data40.372 5.58847.046
JacksonFischer202075.32810.61487.027
JacksonFischer2020Data71.51610.18482.861
ZanotelliSpheroids202070.61810.98882.803
ZanotelliSpheroids2020Data70.203 9.78381.113
listDatasets0.0120.0000.012