Carlos Ruiz-Arenas
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/MultiDataSet |
| Branch: RELEASE_3_6 |
| Last Commit: 3a35038 |
| Last Changed Date: 2017-10-30 12:41:16 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:28:03 -0400 (Thu, 12 Apr 2018).
| Package 911/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MultiDataSet 1.6.0 Carlos Ruiz-Arenas
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: MultiDataSet |
| Version: 1.6.0 |
| Command: rm -rf MultiDataSet.buildbin-libdir MultiDataSet.Rcheck && mkdir MultiDataSet.buildbin-libdir MultiDataSet.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MultiDataSet.buildbin-libdir MultiDataSet_1.6.0.tar.gz >MultiDataSet.Rcheck\00install.out 2>&1 && cp MultiDataSet.Rcheck\00install.out MultiDataSet-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MultiDataSet.buildbin-libdir --install="check:MultiDataSet-install.out" --force-multiarch --no-vignettes --timings MultiDataSet_1.6.0.tar.gz |
| StartedAt: 2018-04-12 01:41:32 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:45:45 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 252.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MultiDataSet.Rcheck |
| Warnings: 3 |
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### Running command:
###
### rm -rf MultiDataSet.buildbin-libdir MultiDataSet.Rcheck && mkdir MultiDataSet.buildbin-libdir MultiDataSet.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MultiDataSet.buildbin-libdir MultiDataSet_1.6.0.tar.gz >MultiDataSet.Rcheck\00install.out 2>&1 && cp MultiDataSet.Rcheck\00install.out MultiDataSet-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MultiDataSet.buildbin-libdir --install="check:MultiDataSet-install.out" --force-multiarch --no-vignettes --timings MultiDataSet_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/MultiDataSet.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MultiDataSet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MultiDataSet' version '1.6.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'MultiDataSet' 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 ... NOTE
Unexported objects imported by ':::' calls:
'Biobase:::assayDataEnvLock' 'Biobase:::assayDataStorageMode'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
downloadGEO : <anonymous>: no visible global function definition for
'methylationSet'
lambdaClayton: no visible global function definition for 'qnorm'
lambdaClayton: no visible global function definition for 'qchisq'
qq_plot: no visible global function definition for 'qbeta'
Undefined global functions or variables:
methylationSet qbeta qchisq qnorm
Consider adding
importFrom("stats", "qbeta", "qchisq", "qnorm")
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 ... WARNING
Codoc mismatches from documentation object 'ResultSet':
\S4method{plot}{ResultSet,ANY}
Code: function(x, y, rid = 1, coef = 2, contrast = NULL, type, tFC =
2, tPV = -log10(0.001), show.labels = TRUE,
show.effect = FALSE, show.lambda = TRUE, fNames =
c("chromosome", "start"), subset, highlight, ...)
Docs: function(x, y, rid = 1, coef = 2, contrast = NULL, type, tFC =
2, tPV = -log10(0.001), show.effect = FALSE,
show.lambda = TRUE, fNames = c("chromosome", "start"),
subset, highlight, ...)
Argument names in code not in docs:
show.labels
Mismatches in argument names (first 3):
Position: 9 Code: show.labels Docs: show.effect
Position: 10 Code: show.effect Docs: show.lambda
Position: 11 Code: show.lambda Docs: fNames
Codoc mismatches from documentation object 'getAssociation':
getAssociation
Code: function(object, rid, coef = 2, contrast = NULL, fNames = NULL,
...)
Docs: function(object, rid, coef = 2, contrast = NULL, fNames =
c("chromosome", "start", "end", "genesymbol"), ...)
Mismatches in argument default values:
Name: 'fNames' Code: NULL Docs: c("chromosome", "start", "end", "genesymbol")
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'MultiDataSet-class'
'...' 'methySet'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' call not declared from: 'BRGEdata'
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 3 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/MultiDataSet.Rcheck/00check.log'
for details.
MultiDataSet.Rcheck/00install.out
install for i386
* installing *source* package 'MultiDataSet' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
in method for 'add_methy' with signature '"MultiDataSet","GenomicRatioSet"': no definition for class "GenomicRatioSet"
** help
*** installing help indices
converting help for package 'MultiDataSet'
finding HTML links ... done
MultiDataSet-class html
MultiDataSet html
ResultSet-class html
add_eset html
add_genexp html
add_methy html
add_rnaseq-methods html
add_rse html
add_se html
add_snps html
add_table html
chrNumToChar html
commonIds html
commonSamples html
getAssociation-methods html
lambdaClayton html
mae2mds html
mds2mae html
opt-methods html
qq_plot html
rowRangesElements html
rset html
volcano_plot html
w_iclusterplus html
w_mcia html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'MultiDataSet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MultiDataSet' as MultiDataSet_1.6.0.zip
* DONE (MultiDataSet)
In R CMD INSTALL
In R CMD INSTALL
|
MultiDataSet.Rcheck/tests_i386/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(MultiDataSet)
Loading required package: Biobase
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, cbind, colMeans, colSums, colnames, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> test_check("MultiDataSet")
== testthat results ===========================================================
OK: 146 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
20.18 0.92 21.20
|
MultiDataSet.Rcheck/tests_x64/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(MultiDataSet)
Loading required package: Biobase
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, cbind, colMeans, colSums, colnames, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> test_check("MultiDataSet")
== testthat results ===========================================================
OK: 146 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
25.73 0.93 26.87
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MultiDataSet.Rcheck/examples_i386/MultiDataSet-Ex.timings
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MultiDataSet.Rcheck/examples_x64/MultiDataSet-Ex.timings
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