Carlos Ruiz-Arenas
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/MultiDataSet |
| Branch: RELEASE_3_10 |
| Last Commit: 157af5f |
| Last Changed Date: 2019-10-29 13:09:38 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:26:38 -0400 (Wed, 15 Apr 2020).
| Package 1113/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MultiDataSet 1.14.0 Carlos Ruiz-Arenas
| 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: MultiDataSet |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MultiDataSet.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MultiDataSet_1.14.0.tar.gz |
| StartedAt: 2020-04-15 05:00:33 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:05:42 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 309.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MultiDataSet.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MultiDataSet.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MultiDataSet_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/MultiDataSet.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.14.0'
* 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 ... 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 or elapsed time > 5s
user system elapsed
add_methy 13.39 1.89 29.69
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
add_methy 14.26 0.71 15.55
* 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-3.10-bioc/meat/MultiDataSet.Rcheck/00check.log'
for details.
MultiDataSet.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/MultiDataSet_1.14.0.tar.gz && rm -rf MultiDataSet.buildbin-libdir && mkdir MultiDataSet.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MultiDataSet.buildbin-libdir MultiDataSet_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL MultiDataSet_1.14.0.zip && rm MultiDataSet_1.14.0.tar.gz MultiDataSet_1.14.0.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 69415 100 69415 0 0 1177k 0 --:--:-- --:--:-- --:--:-- 1279k
install for i386
* installing *source* package 'MultiDataSet' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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 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 'MultiDataSet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MultiDataSet' as MultiDataSet_1.14.0.zip
* DONE (MultiDataSet)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'MultiDataSet' successfully unpacked and MD5 sums checked
|
MultiDataSet.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> test_check("MultiDataSet")
Object of class 'MultiDataSet'
. assayData: 1 elements
. rnaseq: 3 features, 2 samples
. featureData:
. rnaseq: 3 rows, 5 cols (chromosome, ..., status)
. rowRanges:
. rnaseq: NO
. phenoData:
. rnaseq: 2 samples, 1 cols (id)
Object of class 'MultiDataSet'
. assayData: 1 elements
. rnaseq: 3 features, 2 samples
. featureData:
. rnaseq: 3 rows, 5 cols (chromosome, ..., status)
. rowRanges:
. rnaseq: YES
. phenoData:
. rnaseq: 2 samples, 1 cols (id)
Object of class 'MultiDataSet'
. assayData: 1 elements
. rnaseq: 3 features, 2 samples
. featureData:
. rnaseq: 3 rows, 5 cols (chromosome, ..., status)
. rowRanges:
. rnaseq: NO
. phenoData:
. rnaseq: 2 samples, 2 cols (id, sex)
Object of class 'ResultSet'
. created with: test
. sva:
. #results: 1 ( error: 1 )
. featureData: 0
Object of class 'ResultSet'
. created with: association
. via: a and b
. sva:
. #results: 1 ( error: 1 )
. featureData: 10 probes x 2 variables
Object of class 'ResultSet'
. created with: crossomics
. sva:
. method: met ( metpac )
. #results: 2 ( error: 1 )
. featureData: 2
. pac: 10x2
. cot: 10x2
== testthat results ===========================================================
[ OK: 178 | SKIPPED: 0 | WARNINGS: 27 | FAILED: 0 ]
>
> proc.time()
user system elapsed
27.87 2.75 36.00
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MultiDataSet.Rcheck/tests_x64/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-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, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> test_check("MultiDataSet")
Object of class 'MultiDataSet'
. assayData: 1 elements
. rnaseq: 3 features, 2 samples
. featureData:
. rnaseq: 3 rows, 5 cols (chromosome, ..., status)
. rowRanges:
. rnaseq: NO
. phenoData:
. rnaseq: 2 samples, 1 cols (id)
Object of class 'MultiDataSet'
. assayData: 1 elements
. rnaseq: 3 features, 2 samples
. featureData:
. rnaseq: 3 rows, 5 cols (chromosome, ..., status)
. rowRanges:
. rnaseq: YES
. phenoData:
. rnaseq: 2 samples, 1 cols (id)
Object of class 'MultiDataSet'
. assayData: 1 elements
. rnaseq: 3 features, 2 samples
. featureData:
. rnaseq: 3 rows, 5 cols (chromosome, ..., status)
. rowRanges:
. rnaseq: NO
. phenoData:
. rnaseq: 2 samples, 2 cols (id, sex)
Object of class 'ResultSet'
. created with: test
. sva:
. #results: 1 ( error: 1 )
. featureData: 0
Object of class 'ResultSet'
. created with: association
. via: a and b
. sva:
. #results: 1 ( error: 1 )
. featureData: 10 probes x 2 variables
Object of class 'ResultSet'
. created with: crossomics
. sva:
. method: met ( metpac )
. #results: 2 ( error: 1 )
. featureData: 2
. pac: 10x2
. cot: 10x2
== testthat results ===========================================================
[ OK: 178 | SKIPPED: 0 | WARNINGS: 27 | FAILED: 0 ]
>
> proc.time()
user system elapsed
28.53 1.26 30.71
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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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