Lorena Pantano
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/DEGreport |
| Branch: RELEASE_3_12 |
| Last Commit: 18aeb4f |
| Last Changed Date: 2020-10-27 10:57:10 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:30:39 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the DEGreport package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 447/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DEGreport 1.26.0 (landing page) Lorena Pantano
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: DEGreport |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEGreport.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DEGreport_1.26.0.tar.gz |
| StartedAt: 2021-05-06 02:03:56 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 02:15:58 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 721.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DEGreport.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEGreport.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DEGreport_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/DEGreport.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DEGreport/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DEGreport' version '1.26.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
.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'
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 fdrtool gene genes itemConsensus k keys lm
log2FoldChange log2fc logFC max_sd min_median 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
significants 10.18 0.11 13.08
degResults 10.17 0.07 10.32
degPlot 9.50 0.03 9.53
degComps 8.82 0.12 8.94
degMean 8.87 0.04 8.92
degVB 8.67 0.06 9.52
degQC 7.88 0.03 7.90
degVar 7.45 0.02 7.50
degSummary 6.86 0.03 6.89
DEGSet 6.10 0.75 6.86
degColors 6.65 0.07 6.71
degMB 6.65 0.03 6.69
degPlotWide 6.58 0.05 6.63
degMV 6.30 0.06 6.36
degDefault 5.23 0.04 5.27
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
degResults 13.49 0.04 13.53
degComps 11.91 0.02 11.92
degQC 10.48 0.04 10.51
degMV 9.77 0.07 13.38
degMB 9.06 0.04 9.11
degColors 8.81 0.06 8.88
degSummary 8.75 0.03 8.78
significants 8.70 0.03 8.73
degPlot 8.67 0.01 8.69
degVB 8.59 0.03 8.64
DEGSet 7.96 0.16 8.12
degMean 7.76 0.03 7.80
degVar 7.53 0.02 7.55
degPlotWide 7.32 0.03 7.36
degMA 6.41 0.02 7.33
degDefault 4.92 0.21 6.06
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.12-bioc/meat/DEGreport.Rcheck/00check.log'
for details.
DEGreport.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/DEGreport_1.26.0.tar.gz && rm -rf DEGreport.buildbin-libdir && mkdir DEGreport.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEGreport.buildbin-libdir DEGreport_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL DEGreport_1.26.0.zip && rm DEGreport_1.26.0.tar.gz DEGreport_1.26.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
42 18.1M 42 7898k 0 0 59.9M 0 --:--:-- --:--:-- --:--:-- 59.7M
100 18.1M 100 18.1M 0 0 58.3M 0 --:--:-- --:--:-- --:--:-- 58.4M
install for i386
* installing *source* package 'DEGreport' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DEGreport'
finding HTML links ... done
DEGSet html
DEGreport-deprecated html
createReport html
deg html
degCheckFactors html
degColors html
degComps html
degCorCov html
degCovariates html
degDefault html
degFilter html
degMA html
finding level-2 HTML links ... done
degMB html
degMDS html
degMV html
degMean html
degMerge html
degObj html
degPCA html
degPatterns html
degPlot html
degPlotCluster html
degPlotWide html
degQC html
degResults html
degSignature html
degSummary html
degVB html
degVar html
degVolcano html
geneInfo html
geom_cor html
humanGender html
significants html
** 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
install for x64
* installing *source* package 'DEGreport' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEGreport' as DEGreport_1.26.0.zip
* DONE (DEGreport)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'DEGreport' successfully unpacked and MD5 sums checked
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DEGreport.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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 2 | SKIP 0 | PASS 64 ]
>
> proc.time()
user system elapsed
54.23 1.85 56.11
|
DEGreport.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
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.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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 2 | SKIP 0 | PASS 64 ]
>
> proc.time()
user system elapsed
55.12 0.76 55.87
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DEGreport.Rcheck/examples_i386/DEGreport-Ex.timings
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DEGreport.Rcheck/examples_x64/DEGreport-Ex.timings
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