Lorena Pantano
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/DEGreport |
| Branch: RELEASE_3_7 |
| Last Commit: bfe4ccb |
| Last Changed Date: 2018-04-30 10:35:33 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:26:17 -0400 (Wed, 17 Oct 2018).
| Package 363/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DEGreport 1.16.0 Lorena Pantano
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DEGreport |
| Version: 1.16.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings DEGreport_1.16.0.tar.gz |
| StartedAt: 2018-10-15 23:43:54 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 23:47:50 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 236.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DEGreport.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings DEGreport_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/DEGreport.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEGreport/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DEGreport’ version ‘1.16.0’
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
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 ‘DEGreport’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘knitr’
A package should be listed in only one of these fields.
* 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 ... NOTE
.convertIDs: no visible global function definition for ‘keys’
.generate_scatter_plot: no visible binding for global variable
‘compare’
.generate_scatter_plot: no visible binding for global variable ‘covar’
.get_counts: no visible global function definition for ‘counts’
.plotMA: no visible binding for global variable ‘base_mean’
.plotMA: no visible binding for global variable ‘log2fc’
.plot_raw: no visible binding for global variable ‘.x’
.plot_shrunken: no visible binding for global variable ‘.x’
.run_cluster_profiler: no visible global function definition for
‘enrichGO’
.run_cluster_profiler: no visible global function definition for
‘simplify’
.table_w_fc: no visible binding for global variable ‘comp’
.table_w_fc: no visible binding for global variable ‘log2FoldChange’
degCheckFactors: no visible binding for global variable ‘ratios’
degCorCov: no visible binding for global variable ‘compare’
degMV: no visible binding for global variable ‘min_median’
degMV: no visible binding for global variable ‘max_sd’
degPatterns: no visible global function definition for ‘rowMedians’
degPatterns: no visible binding for global variable ‘genes’
degPlotWide : <anonymous>: no visible binding for global variable
‘count’
significants,TopTags: no visible binding for global variable ‘FDR’
significants,TopTags: no visible binding for global variable ‘logFC’
significants,list : <anonymous>: no visible binding for global variable
‘gene’
Undefined global functions or variables:
.x FDR base_mean comp compare count counts covar enrichGO gene genes
keys log2FoldChange log2fc logFC max_sd min_median ratios rowMedians
simplify
* 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 ... OK
* 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
degResults 6.084 0.016 6.106
degPlot 5.272 0.004 5.279
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/DEGreport.Rcheck/00check.log’
for details.
DEGreport.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL DEGreport ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘DEGreport’ ... ** 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 * DONE (DEGreport)
DEGreport.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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(edgeR)
Loading required package: limma
> library(DESeq2)
Loading required package: S4Vectors
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 object is masked from 'package:limma':
plotMA
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
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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
> library(DEGreport)
Loading required package: quantreg
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
>
> test_check("DEGreport")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 56 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
21.284 0.376 21.674
DEGreport.Rcheck/DEGreport-Ex.timings
| name | user | system | elapsed | |
| DEGSet | 3.688 | 0.068 | 3.759 | |
| degCheckFactors | 1.392 | 0.004 | 1.528 | |
| degComps | 4.904 | 0.012 | 4.921 | |
| degCorCov | 0.956 | 0.012 | 0.971 | |
| degCovariates | 2.204 | 0.008 | 2.213 | |
| degFilter | 0.304 | 0.000 | 0.306 | |
| degMB | 2.928 | 0.000 | 2.928 | |
| degMDS | 0.6 | 0.0 | 0.6 | |
| degMV | 2.960 | 0.004 | 2.969 | |
| degMean | 3.692 | 0.004 | 3.698 | |
| degObj | 0.304 | 0.012 | 0.316 | |
| degPCA | 0.648 | 0.000 | 0.650 | |
| degPatterns | 1.016 | 0.000 | 1.017 | |
| degPlot | 5.272 | 0.004 | 5.279 | |
| degPlotWide | 2.748 | 0.000 | 2.749 | |
| degQC | 4.360 | 0.008 | 4.371 | |
| degResults | 6.084 | 0.016 | 6.106 | |
| degSignature | 0.664 | 0.000 | 0.672 | |
| degSummary | 2.444 | 0.024 | 2.472 | |
| degVB | 3.104 | 0.012 | 3.119 | |
| degVar | 3.124 | 0.000 | 3.127 | |
| degVolcano | 1.876 | 0.000 | 1.876 | |
| geom_cor | 0.508 | 0.000 | 0.507 | |
| plotMA | 2.268 | 0.000 | 2.270 | |
| significants | 4.360 | 0.000 | 4.365 | |