Subhadeep Das
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/OMICsPCA |
| Branch: RELEASE_3_8 |
| Last Commit: f1cf3f0 |
| Last Changed Date: 2019-01-04 13:42:15 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:53:48 -0400 (Tue, 16 Apr 2019).
| Package 1085/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| OMICsPCA 1.0.1 Subhadeep Das
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: OMICsPCA |
| Version: 1.0.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:OMICsPCA.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings OMICsPCA_1.0.1.tar.gz |
| StartedAt: 2019-04-16 01:51:50 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:57:50 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 360.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OMICsPCA.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:OMICsPCA.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings OMICsPCA_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/OMICsPCA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OMICsPCA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OMICsPCA’ version ‘1.0.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OMICsPCA’ 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 or elapsed time > 5s
user system elapsed
analyse_individuals 7.944 0.468 8.771
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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: OK
OMICsPCA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL OMICsPCA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘OMICsPCA’ ... ** 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 * DONE (OMICsPCA)
OMICsPCA.Rcheck/tests/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(OMICsPCAdata)
> BiocGenerics:::testPackage("OMICsPCA")
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
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
Attaching package: 'OMICsPCA'
The following object is masked from 'package:GenomicRanges':
intersect
The following object is masked from 'package:GenomeInfoDb':
intersect
The following object is masked from 'package:IRanges':
intersect
The following object is masked from 'package:S4Vectors':
intersect
The following object is masked from 'package:BiocGenerics':
intersect
The following object is masked from 'package:base':
intersect
[1] "Running intersect... This may take some time"
[1] "Merging cell lines... This may take some time"
[1] "Total time taken is: 0.877640962600708"
[1] "time taken to run intersect() is: 0.64716911315918"
[1] "time taken to run merge_cells() is: 0.230471849441528"
RUNIT TEST PROTOCOL -- Tue Apr 16 01:57:41 2019
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
OMICsPCA RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
16.536 0.676 16.746
OMICsPCA.Rcheck/OMICsPCA-Ex.timings
| name | user | system | elapsed | |
| analyse_individuals | 7.944 | 0.468 | 8.771 | |
| analyse_integrated_individuals | 2.728 | 0.192 | 2.935 | |
| analyse_integrated_variables | 1.372 | 0.076 | 1.453 | |
| analyse_variables | 0.680 | 0.004 | 0.685 | |
| chart_correlation | 0.024 | 0.000 | 0.025 | |
| cluster | 1.976 | 0.004 | 1.985 | |
| cluster_boxplot | 0.668 | 0.000 | 0.687 | |
| cluster_parameters | 1.844 | 0.056 | 1.903 | |
| create_group | 0.748 | 0.024 | 0.771 | |
| descriptor | 1.288 | 0.000 | 1.290 | |
| extract | 1.380 | 0.072 | 1.453 | |
| extract_assay | 1.716 | 0.264 | 1.985 | |
| integrate_pca | 2.400 | 0.108 | 2.511 | |
| integrate_variables | 0.196 | 0.000 | 0.197 | |
| intersect | 1.112 | 0.000 | 0.686 | |
| merge_cells | 0.860 | 0.000 | 0.358 | |
| plot_density | 0.536 | 0.004 | 0.540 | |
| plot_density_3D | 0.400 | 0.000 | 0.403 | |
| plot_integrated_density | 2.256 | 0.052 | 2.311 | |
| plot_integrated_density_3D | 2.976 | 0.056 | 3.036 | |
| prepare_dataset | 0.812 | 0.000 | 0.336 | |