Davide Risso
| Snapshot Date: 2020-04-14 09:30:11 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/scRNAseq |
| Branch: RELEASE_3_10 |
| Last Commit: c087c40 |
| Last Changed Date: 2019-11-11 01:02:27 -0400 (Mon, 11 Nov 2019) |
| Back to Build/check report for BioC 3.10 experimental data |
This page was generated on 2020-04-14 17:46:25 -0400 (Tue, 14 Apr 2020).
| Package 327/384 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| scRNAseq 2.0.2 Davide Risso
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |
| Package: scRNAseq |
| Version: 2.0.2 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings scRNAseq_2.0.2.tar.gz |
| StartedAt: 2020-04-14 13:38:15 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 13:49:28 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 672.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scRNAseq.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings scRNAseq_2.0.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-data-experiment/meat/scRNAseq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.0.2’
* 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 ... OK
* 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 contents of ‘data’ directory ... WARNING
Output for data("allen", package = "scRNAseq"):
Warning message:
'data(allen)' is deprecated.
Use ReprocessedAllenData() instead.
Output for data("fluidigm", package = "scRNAseq"):
Warning message:
'data(fluidigm)' is deprecated.
Use ReprocessedFluidigmData() instead.
Output for data("th2", package = "scRNAseq"):
Warning message:
'data(th2)' is deprecated.
Use ReprocessedTh2Data() instead.
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
BachMammaryData 40.144 3.144 48.219
LaMannoBrainData 19.316 0.416 27.450
LunSpikeInData 11.128 0.176 12.617
ReprocessedData 10.820 0.312 13.216
AztekinTailData 8.732 0.244 9.780
BaronPancreasData 8.488 0.304 10.216
SegerstolpePancreasData 7.940 0.432 8.905
XinPancreasData 6.952 0.204 7.733
ZeiselBrainData 6.872 0.224 7.937
NestorowaHSCData 6.472 0.584 8.068
MessmerESCData 6.468 0.296 7.283
CampbellBrainData 6.040 0.220 6.655
MacoskoRetinaData 6.008 0.248 6.583
TasicBrainData 5.720 0.272 6.808
BuettnerESCData 5.696 0.096 6.341
ChenBrainData 5.228 0.188 5.788
ShekharRetinaData 5.188 0.172 5.774
UsoskinBrainData 5.044 0.124 5.692
MuraroPancreasData 4.908 0.196 5.799
RomanovBrainData 4.572 0.188 5.902
RichardTCellData 4.120 0.124 5.560
* 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
See
‘/home/biocbuild/bbs-3.10-data-experiment/meat/scRNAseq.Rcheck/00check.log’
for details.
scRNAseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL scRNAseq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘scRNAseq’ ... ** using staged installation ** R ** data ** 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)
scRNAseq.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 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, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
> test_check("scRNAseq")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 50 | SKIPPED: 0 | WARNINGS: 23 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
227.336 8.832 258.918
scRNAseq.Rcheck/scRNAseq-Ex.timings
| name | user | system | elapsed | |
| AztekinTailData | 8.732 | 0.244 | 9.780 | |
| BachMammaryData | 40.144 | 3.144 | 48.219 | |
| BaronPancreasData | 8.488 | 0.304 | 10.216 | |
| BuettnerESCData | 5.696 | 0.096 | 6.341 | |
| CampbellBrainData | 6.040 | 0.220 | 6.655 | |
| ChenBrainData | 5.228 | 0.188 | 5.788 | |
| GrunHSCData | 2.820 | 0.024 | 3.067 | |
| GrunPancreasData | 2.516 | 0.064 | 2.810 | |
| KolodziejczykESCData | 4.080 | 0.364 | 4.767 | |
| LaMannoBrainData | 19.316 | 0.416 | 27.450 | |
| LawlorPancreasData | 3.556 | 0.072 | 3.964 | |
| LengESCData | 3.632 | 0.072 | 4.338 | |
| LunSpikeInData | 11.128 | 0.176 | 12.617 | |
| MacoskoRetinaData | 6.008 | 0.248 | 6.583 | |
| MarquesBrainData | 4.000 | 0.088 | 4.911 | |
| MessmerESCData | 6.468 | 0.296 | 7.283 | |
| MuraroPancreasData | 4.908 | 0.196 | 5.799 | |
| NestorowaHSCData | 6.472 | 0.584 | 8.068 | |
| ReprocessedData | 10.820 | 0.312 | 13.216 | |
| RichardTCellData | 4.120 | 0.124 | 5.560 | |
| RomanovBrainData | 4.572 | 0.188 | 5.902 | |
| SegerstolpePancreasData | 7.940 | 0.432 | 8.905 | |
| ShekharRetinaData | 5.188 | 0.172 | 5.774 | |
| TasicBrainData | 5.720 | 0.272 | 6.808 | |
| UsoskinBrainData | 5.044 | 0.124 | 5.692 | |
| XinPancreasData | 6.952 | 0.204 | 7.733 | |
| ZeiselBrainData | 6.872 | 0.224 | 7.937 | |