Lorena Pantano
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/DEGreport |
| Branch: RELEASE_3_10 |
| Last Commit: 31ec410 |
| Last Changed Date: 2019-10-29 13:09:00 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:40:12 -0400 (Wed, 15 Apr 2020).
| Package 427/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DEGreport 1.22.0 Lorena Pantano
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: DEGreport |
| Version: 1.22.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DEGreport_1.22.0.tar.gz |
| StartedAt: 2020-04-15 01:42:09 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:49:56 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 467.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DEGreport.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DEGreport_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/DEGreport.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.22.0’
* 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 ... 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 ... NOTE
.benckmark_cutoff: no visible binding for global variable ‘cutoff’
.benckmark_cutoff: no visible binding for global variable ‘cluster’
.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’
.model: no visible global function definition for ‘lm’
.plot_raw: no visible binding for global variable ‘.x’
.plot_shrunken: no visible binding for global variable ‘.x’
.reduce : <anonymous> : <anonymous>: no visible global function
definition for ‘boxplot’
.reduce_covariates : <anonymous>: no visible binding for global
variable ‘fdr’
.reduce_covariates : <anonymous>: no visible binding for global
variable ‘compare’
.reduce_covariates : <anonymous>: no visible binding for global
variable ‘r’
.reduce_covariates : <anonymous>: no visible binding for global
variable ‘p.value’
.run_cluster_profiler: no visible global function definition for
‘enrichGO’
.run_cluster_profiler: no visible global function definition for
‘simplify’
.select_concensus_genes: no visible global function definition for
‘desc’
.select_concensus_genes: no visible binding for global variable ‘score’
.select_concensus_genes: no visible binding for global variable ‘k’
.select_concensus_genes: no visible binding for global variable
‘itemConsensus’
.summarise_res: no visible binding for global variable ‘gene’
.summarise_res: no visible binding for global variable ‘value_fdr’
.summarise_res: no visible binding for global variable ‘value_fc’
.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’
degCovariates: no visible binding for global variable ‘x’
degCovariates: no visible binding for global variable ‘y’
degCovariates: no visible binding for global variable ‘xend’
degCovariates: no visible binding for global variable ‘yend’
degMA: no visible binding for global variable ‘base_mean’
degMA: no visible binding for global variable ‘log2fc’
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’
degPatterns: no visible global function definition for ‘n’
degPlotCluster: no visible binding for global variable ‘genes’
degPlotCluster: no visible binding for global variable ‘cluster’
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 boxplot cluster comp compare count counts covar
cutoff desc enrichGO fdr gene genes itemConsensus k keys lm
log2FoldChange log2fc logFC max_sd min_median n p.value r ratios
rowMedians score simplify value_fc value_fdr x xend y yend
Consider adding
importFrom("graphics", "boxplot")
importFrom("stats", "lm")
to your NAMESPACE file.
* 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 14.071 0.089 14.271
degPlot 12.082 0.038 12.190
degComps 10.679 0.067 10.812
degMB 10.243 0.091 10.355
degPlotWide 10.220 0.043 13.702
degQC 10.179 0.043 10.300
degVar 9.868 0.070 10.017
degMV 9.468 0.063 9.595
degVB 9.013 0.039 9.135
significants 8.577 0.028 8.687
degMean 8.250 0.043 8.335
degSummary 8.128 0.036 8.224
degColors 7.572 0.099 7.719
DEGSet 7.449 0.213 7.745
degMA 5.031 0.029 5.072
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/DEGreport.Rcheck/00check.log’
for details.
DEGreport.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DEGreport ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘DEGreport’ ... ** 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 (DEGreport)
DEGreport.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-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(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, 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
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, rowsum
> library(DEGreport)
>
> test_check("DEGreport")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 62 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
>
> proc.time()
user system elapsed
55.040 0.933 56.449
DEGreport.Rcheck/DEGreport-Ex.timings
| name | user | system | elapsed | |
| DEGSet | 7.449 | 0.213 | 7.745 | |
| degCheckFactors | 2.109 | 0.095 | 2.209 | |
| degColors | 7.572 | 0.099 | 7.719 | |
| degComps | 10.679 | 0.067 | 10.812 | |
| degCorCov | 0.955 | 0.020 | 0.976 | |
| degCovariates | 2.797 | 0.025 | 2.830 | |
| degFilter | 0.487 | 0.021 | 0.514 | |
| degMA | 5.031 | 0.029 | 5.072 | |
| degMB | 10.243 | 0.091 | 10.355 | |
| degMDS | 1.002 | 0.022 | 1.026 | |
| degMV | 9.468 | 0.063 | 9.595 | |
| degMean | 8.250 | 0.043 | 8.335 | |
| degObj | 0.410 | 0.019 | 0.433 | |
| degPCA | 0.950 | 0.016 | 0.971 | |
| degPatterns | 2.315 | 0.026 | 2.350 | |
| degPlot | 12.082 | 0.038 | 12.190 | |
| degPlotCluster | 3.186 | 0.045 | 3.277 | |
| degPlotWide | 10.220 | 0.043 | 13.702 | |
| degQC | 10.179 | 0.043 | 10.300 | |
| degResults | 14.071 | 0.089 | 14.271 | |
| degSignature | 0.975 | 0.023 | 1.010 | |
| degSummary | 8.128 | 0.036 | 8.224 | |
| degVB | 9.013 | 0.039 | 9.135 | |
| degVar | 9.868 | 0.070 | 10.017 | |
| degVolcano | 3.467 | 0.019 | 3.521 | |
| geom_cor | 0.692 | 0.020 | 0.723 | |
| significants | 8.577 | 0.028 | 8.687 | |