Jean-Philippe Fortin
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/shinyMethyl |
| Branch: RELEASE_3_12 |
| Last Commit: 1dab127 |
| Last Changed Date: 2020-10-27 10:57:34 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:33:36 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the shinyMethyl package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1695/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| shinyMethyl 1.26.0 (landing page) Jean-Philippe Fortin
| 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: shinyMethyl |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:shinyMethyl.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings shinyMethyl_1.26.0.tar.gz |
| StartedAt: 2021-05-06 06:54:25 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 07:06:57 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 751.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: shinyMethyl.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:shinyMethyl.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings shinyMethyl_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/shinyMethyl.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 'shinyMethyl/DESCRIPTION' ... OK
* this is package 'shinyMethyl' version '1.26.0'
* 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 'shinyMethyl' 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
addHoverDensity: no visible global function definition for 'lines'
addHoverPoints: no visible global function definition for 'points'
addHoverQC: no visible global function definition for 'points'
densitiesPlot: no visible global function definition for 'lines'
plotDesign450k: no visible global function definition for 'par'
plotDiscrepancyGenders: no visible global function definition for
'legend'
plotInternalControls: no visible global function definition for 'grid'
plotInternalControls: no visible global function definition for
'abline'
plotLegendDesign450k: no visible global function definition for
'legend'
plotPCA: no visible global function definition for 'legend'
plotPCA: no visible global function definition for 'grid'
plotPlate: no visible global function definition for 'rect'
plotPredictedGender: no visible global function definition for 'abline'
plotQC: no visible global function definition for 'grid'
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
assignment to 'mouse.click.indices'
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
assignment to 'colorSet'
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
assignment to 'genderCutoff'
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
assignment to 'current.control.type'
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
assignment to 'current.probe.type'
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
assignment to 'current.density.type'
server.shinyMethyl : <anonymous> : set.palette: no visible global
function definition for 'palette'
server.shinyMethyl : <anonymous>: no visible binding for global
variable 'current.control.type'
server.shinyMethyl : <anonymous>: no visible binding for global
variable 'mouse.click.indices'
server.shinyMethyl : <anonymous>: no visible binding for global
variable 'current.probe.type'
server.shinyMethyl : <anonymous>: no visible binding for global
variable 'current.density.type'
server.shinyMethyl : <anonymous> : content: no visible global function
definition for 'write.csv'
server.shinyMethyl : <anonymous>: no visible global function definition
for 'abline'
server.shinyMethyl : <anonymous>: no visible binding for global
variable 'genderCutoff'
server.shinyMethyl : <anonymous>: no visible global function definition
for 'complete.cases'
server.shinyMethyl : <anonymous>: no visible global function definition
for 'lm'
server.shinyMethyl : <anonymous>: no visible global function definition
for 'lines'
server.shinyMethyl : <anonymous>: no visible global function definition
for 'legend'
ui.shinyMethyl: no visible binding for '<<-' assignment to
'sampleColors'
shinySummarize,GenomicRatioSet: no visible global function definition
for 'prcomp'
shinySummarize,RGChannelSet: no visible global function definition for
'prcomp'
Undefined global functions or variables:
abline complete.cases current.control.type current.density.type
current.probe.type genderCutoff grid legend lines lm
mouse.click.indices palette par points prcomp rect write.csv
Consider adding
importFrom("grDevices", "palette")
importFrom("graphics", "abline", "grid", "legend", "lines", "par",
"points", "rect")
importFrom("stats", "complete.cases", "lm", "prcomp")
importFrom("utils", "write.csv")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
shinySummarize-methods 42.56 3.89 46.47
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
shinySummarize-methods 46.81 2.28 49.18
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/shinyMethyl.Rcheck/00check.log'
for details.
shinyMethyl.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/shinyMethyl_1.26.0.tar.gz && rm -rf shinyMethyl.buildbin-libdir && mkdir shinyMethyl.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=shinyMethyl.buildbin-libdir shinyMethyl_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL shinyMethyl_1.26.0.zip && rm shinyMethyl_1.26.0.tar.gz shinyMethyl_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
100 9041k 100 9041k 0 0 57.2M 0 --:--:-- --:--:-- --:--:-- 57.7M
install for i386
* installing *source* package 'shinyMethyl' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'shinyMethyl'
finding HTML links ... done
runShinyMethyl html
shinyMethyl-package html
shinyMethylSet-class html
finding level-2 HTML links ... done
shinySummarize-methods 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 'shinyMethyl' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'shinyMethyl' as shinyMethyl_1.26.0.zip
* DONE (shinyMethyl)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'shinyMethyl' successfully unpacked and MD5 sums checked
|
shinyMethyl.Rcheck/tests_i386/runTests.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.
> require("shinyMethyl") || stop("unable to load shinyMethyl")
Loading required package: shinyMethyl
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 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
Loading required package: shiny
Loading required package: minfi
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
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: 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
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.4 2020-03-24
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: IlluminaHumanMethylation450kmanifest
[1] TRUE
> BiocGenerics:::testPackage("shinyMethyl")
Loading required package: minfiData
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Loading required package: digest
[shinySummarize] Extracting Red and Green channels
[shinySummarize] Raw preprocessing
[shinySummarize] Mapping to genome
[shinySummarize] Computing quantiles
[shinySummarize] Computing principal components
RUNIT TEST PROTOCOL -- Thu May 06 07:05:44 2021
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
shinyMethyl RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
55.60 4.82 62.01
|
shinyMethyl.Rcheck/tests_x64/runTests.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.
> require("shinyMethyl") || stop("unable to load shinyMethyl")
Loading required package: shinyMethyl
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 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
Loading required package: shiny
Loading required package: minfi
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
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: 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
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.4 2020-03-24
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: IlluminaHumanMethylation450kmanifest
[1] TRUE
> BiocGenerics:::testPackage("shinyMethyl")
Loading required package: minfiData
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Loading required package: digest
[shinySummarize] Extracting Red and Green channels
[shinySummarize] Raw preprocessing
[shinySummarize] Mapping to genome
[shinySummarize] Computing quantiles
[shinySummarize] Computing principal components
RUNIT TEST PROTOCOL -- Thu May 06 07:06:53 2021
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
shinyMethyl RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
63.34 3.00 68.03
|
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shinyMethyl.Rcheck/examples_i386/shinyMethyl-Ex.timings
|
shinyMethyl.Rcheck/examples_x64/shinyMethyl-Ex.timings
|