| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:26 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the DEGreport package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 490/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DEGreport 1.35.0 (landing page) Lorena Pantano
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
| Package: DEGreport |
| Version: 1.35.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DEGreport.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings DEGreport_1.35.0.tar.gz |
| StartedAt: 2022-12-28 23:05:30 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 23:10:12 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 282.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DEGreport.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DEGreport.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings DEGreport_1.35.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/DEGreport.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DEGreport/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DEGreport' version '1.35.0'
* 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 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'
.correct_fdr: no visible global function definition for 'fdrtool'
.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'
.process: no visible binding for global variable 'genes'
.process: no visible binding for global variable 'cluster'
.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 global function definition for 'matches'
.summarise_res: no visible binding for global variable 'comparison'
.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'
degCovariates: no visible binding for global variable 'pvalue'
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'
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 global function definition
for 'matches'
Undefined global functions or variables:
.x FDR base_mean boxplot cluster comp compare comparison count counts
covar cutoff desc enrichGO fdr fdrtool gene genes itemConsensus k
keys lm log2FoldChange log2fc logFC matches max_sd min_median p.value
pvalue 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 ... WARNING
checkRd: (7) DEGreport-deprecated.Rd:35: Invalid email address: @jnhutchinson
checkRd: (7) DEGreport-deprecated.Rd:36: Invalid email address: @vbarrera
checkRd: (7) DEGreport-deprecated.Rd:37: Invalid email address: @marypiper
checkRd: (7) DEGreport-deprecated.Rd:38: Invalid email address: @rkhetani
checkRd: (7) DEGreport-deprecated.Rd:41: Invalid email address: @roryk
checkRd: (7) DEGreport-deprecated.Rd:42: Invalid email address: @mjsteinbaugh
* 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 (user + system) or elapsed time > 5s
user system elapsed
degResults 5.67 0.08 5.75
degPlot 5.32 0.10 5.42
* 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: 1 WARNING, 2 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/DEGreport.Rcheck/00check.log'
for details.
DEGreport.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL DEGreport ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Attaching package: 'BiocGenerics'
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, aperm, 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.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
> library(DEGreport)
>
> test_check("DEGreport")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 64 ]
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 64 ]
>
> proc.time()
user system elapsed
29.20 1.00 30.35
DEGreport.Rcheck/DEGreport-Ex.timings
| name | user | system | elapsed | |
| DEGSet | 4.10 | 0.13 | 4.22 | |
| degCheckFactors | 1.18 | 0.07 | 1.25 | |
| degColors | 3.73 | 0.04 | 3.78 | |
| degComps | 4.69 | 0.05 | 4.74 | |
| degCorCov | 0.52 | 0.05 | 0.56 | |
| degCovariates | 1.42 | 0.03 | 1.45 | |
| degDefault | 2.61 | 0.03 | 2.64 | |
| degFilter | 0.24 | 0.03 | 0.26 | |
| degMA | 2.48 | 0.05 | 2.55 | |
| degMB | 4.38 | 0.05 | 4.42 | |
| degMDS | 0.56 | 0.01 | 0.58 | |
| degMV | 3.82 | 0.17 | 4.09 | |
| degMean | 4.08 | 0.07 | 4.14 | |
| degObj | 0.30 | 0.01 | 0.31 | |
| degPCA | 0.59 | 0.00 | 0.60 | |
| degPatterns | 1.46 | 0.09 | 1.54 | |
| degPlot | 5.32 | 0.10 | 5.42 | |
| degPlotCluster | 1.89 | 0.09 | 1.98 | |
| degPlotWide | 3.45 | 0.00 | 3.45 | |
| degQC | 4.36 | 0.08 | 4.44 | |
| degResults | 5.67 | 0.08 | 5.75 | |
| degSignature | 0.55 | 0.00 | 0.55 | |
| degSummary | 3.64 | 0.11 | 3.75 | |
| degVB | 3.54 | 0.04 | 3.60 | |
| degVar | 3.79 | 0.05 | 3.83 | |
| degVolcano | 1.82 | 0.05 | 1.87 | |
| geom_cor | 0.61 | 0.05 | 0.67 | |
| significants | 4.33 | 0.03 | 4.36 | |