Subhadeep Das
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/OMICsPCA |
| Branch: RELEASE_3_9 |
| Last Commit: 093d3ff |
| Last Changed Date: 2019-05-02 11:54:13 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:03:23 -0400 (Wed, 16 Oct 2019).
| Package 1134/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| OMICsPCA 1.2.0 Subhadeep Das
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: OMICsPCA |
| Version: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2019-10-16 05:13:45 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:23:05 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 559.9 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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/OMICsPCA.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.2.0’
* 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 ... 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-3.9-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 10.065 1.684 11.771
extract_assay 5.069 2.058 12.072
* 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-3.9-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/3.6/Resources/library’ * installing *source* package ‘OMICsPCA’ ... ** using staged installation ** 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 from temporary location Warning in rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE ** testing if installed package can be loaded from final location Warning in rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE ** testing if installed package keeps a record of temporary installation path * DONE (OMICsPCA)
OMICsPCA.Rcheck/tests/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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, 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
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, rowsum
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: 1.50633597373962"
[1] "time taken to run intersect() is: 1.1120719909668"
[1] "time taken to run merge_cells() is: 0.394263982772827"
RUNIT TEST PROTOCOL -- Wed Oct 16 05:22:56 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
25.731 2.545 36.599
OMICsPCA.Rcheck/OMICsPCA-Ex.timings
| name | user | system | elapsed | |
| analyse_individuals | 10.065 | 1.684 | 11.771 | |
| analyse_integrated_individuals | 3.103 | 0.981 | 4.087 | |
| analyse_integrated_variables | 2.127 | 0.613 | 2.741 | |
| analyse_variables | 1.410 | 0.240 | 1.649 | |
| chart_correlation | 0.047 | 0.003 | 0.050 | |
| cluster | 1.907 | 0.773 | 2.686 | |
| cluster_boxplot | 1.098 | 0.012 | 1.110 | |
| cluster_parameters | 2.938 | 1.045 | 3.984 | |
| create_group | 1.116 | 0.380 | 1.497 | |
| descriptor | 1.603 | 0.247 | 1.851 | |
| extract | 3.032 | 0.793 | 4.942 | |
| extract_assay | 5.069 | 2.058 | 12.072 | |
| integrate_pca | 1.849 | 0.706 | 3.461 | |
| integrate_variables | 0.455 | 0.171 | 0.626 | |
| intersect | 0.945 | 0.248 | 0.716 | |
| merge_cells | 2.370 | 0.267 | 0.381 | |
| plot_density | 1.290 | 0.508 | 1.267 | |
| plot_density_3D | 0.407 | 0.085 | 0.491 | |
| plot_integrated_density | 2.737 | 0.592 | 3.331 | |
| plot_integrated_density_3D | 2.573 | 0.574 | 3.150 | |
| prepare_dataset | 1.544 | 0.137 | 0.372 | |