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 12:12:58 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OMICsPCA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OMICsPCA_1.0.1.tar.gz |
| StartedAt: 2019-04-16 01:40:30 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:47:04 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 393.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: OMICsPCA.Rcheck |
| Warnings: 1 |
##############################################################################
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OMICsPCA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OMICsPCA_1.0.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/OMICsPCA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ... WARNING
Found the following significant warnings:
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/OMICsPCA.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 ... 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 8.432 0.909 9.417
* 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: 1 WARNING
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/OMICsPCA.Rcheck/00check.log’
for details.
OMICsPCA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL OMICsPCA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘OMICsPCA’ ... ** R ** inst ** byte-compile and prepare package for lazy loading Warning in rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning in rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE * 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-apple-darwin15.6.0 (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: 1.0826199054718"
[1] "time taken to run intersect() is: 0.719927787780762"
[1] "time taken to run merge_cells() is: 0.36269211769104"
RUNIT TEST PROTOCOL -- Tue Apr 16 01:46:59 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
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
>
> proc.time()
user system elapsed
21.237 1.383 24.364
OMICsPCA.Rcheck/OMICsPCA-Ex.timings
| name | user | system | elapsed | |
| analyse_individuals | 8.432 | 0.909 | 9.417 | |
| analyse_integrated_individuals | 2.485 | 0.414 | 2.916 | |
| analyse_integrated_variables | 1.586 | 0.409 | 2.015 | |
| analyse_variables | 0.922 | 0.170 | 1.105 | |
| chart_correlation | 0.028 | 0.004 | 0.033 | |
| cluster | 2.219 | 0.468 | 2.696 | |
| cluster_boxplot | 0.831 | 0.016 | 0.856 | |
| cluster_parameters | 1.918 | 0.592 | 2.533 | |
| create_group | 0.831 | 0.190 | 1.029 | |
| descriptor | 1.483 | 0.132 | 1.624 | |
| extract | 1.293 | 0.329 | 1.635 | |
| extract_assay | 3.647 | 0.852 | 4.556 | |
| integrate_pca | 2.196 | 0.504 | 2.726 | |
| integrate_variables | 0.280 | 0.086 | 0.368 | |
| intersect | 0.826 | 0.561 | 0.544 | |
| merge_cells | 0.852 | 1.218 | 0.268 | |
| plot_density | 1.149 | 0.989 | 0.901 | |
| plot_density_3D | 0.363 | 0.044 | 0.411 | |
| plot_integrated_density | 2.199 | 0.387 | 2.608 | |
| plot_integrated_density_3D | 3.223 | 0.481 | 3.731 | |
| prepare_dataset | 0.529 | 0.313 | 0.253 | |