j. Saez-Rodriguez
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/DrugVsDisease |
| Branch: RELEASE_3_9 |
| Last Commit: 9538392 |
| Last Changed Date: 2019-05-02 11:53:40 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:27:26 -0400 (Wed, 16 Oct 2019).
| Package 466/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DrugVsDisease 2.26.0 j. Saez-Rodriguez
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DrugVsDisease |
| Version: 2.26.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DrugVsDisease.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DrugVsDisease_2.26.0.tar.gz |
| StartedAt: 2019-10-16 03:23:17 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:28:28 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 310.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DrugVsDisease.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DrugVsDisease.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DrugVsDisease_2.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DrugVsDisease.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'DrugVsDisease/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'DrugVsDisease' version '2.26.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'affy', 'limma', 'biomaRt', 'ArrayExpress', 'GEOquery', 'DrugVsDiseasedata', 'cMap2data', 'qvalue' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 'DrugVsDisease' 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 'library' or 'require' calls to packages already attached by Depends: 'ArrayExpress' 'DrugVsDiseasedata' 'GEOquery' 'affy' 'biomaRt' 'limma' 'qvalue' Please remove these calls from your code. Namespaces in Imports field not imported from: 'BiocGenerics' 'RUnit' 'annotate' 'hgu133a.db' 'hgu133a2.db' 'hgu133plus2.db' 'xtable' All declared Imports should be used. Packages in Depends field not imported from: 'ArrayExpress' 'DrugVsDiseasedata' 'GEOquery' 'affy' 'biomaRt' 'cMap2data' 'limma' 'qvalue' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .averagecluster: no visible binding for global variable 'drugClusters' .averagecluster: no visible binding for global variable 'diseaseClusters' .calculateES: no visible binding for global variable 'drugRL' .calculateES: no visible binding for global variable 'diseaseRL' .calculateES :: no visible global function definition for 'qvalue' .convertEnsembl: no visible binding for global variable 'annotationlist' .convertEnsembl: no visible global function definition for 'useMart' .convertEnsembl: no visible global function definition for 'getBM' .datafromAE: no visible global function definition for 'ArrayExpress' .datafromAE: no visible global function definition for 'annotation' .datafromAE: no visible global function definition for 'pData' .datafromGEO: no visible global function definition for 'getGEO' .datafromGEO: no visible global function definition for 'GDS2eSet' .datafromGEO: no visible global function definition for 'pData' .datafromGEO: no visible global function definition for 'annotation' .datafromGEO: no visible binding for global variable 'GEOfactorvalues' .datafromGEO: no visible global function definition for 'exprs' .findCluster: no visible binding for global variable 'drugClusters' .findCluster: no visible binding for global variable 'diseaseClusters' .findSignifCompounds: no visible global function definition for 'qvalue' .fitlms: no visible global function definition for 'lmFit' .multcontrast: no visible global function definition for 'contrasts.fit' .multcontrast: no visible global function definition for 'eBayes' .normalisedata: no visible global function definition for 'rma' .normalisedata: no visible global function definition for 'mas5' .readlocalAE: no visible global function definition for 'ReadAffy' .readlocalCEL: no visible global function definition for 'ReadAffy' .singlecontrast: no visible global function definition for 'lmFit' .singlecontrast: no visible global function definition for 'contrasts.fit' .singlecontrast: no visible global function definition for 'eBayes' .treatmentonlyfit: no visible global function definition for 'lmFit' .writecytoscape: no visible binding for global variable 'drugClusters' .writecytoscape: no visible binding for global variable 'cytodrug' .writecytoscape: no visible binding for global variable 'druglabels' .writecytoscape: no visible binding for global variable 'diseaseClusters' .writecytoscape: no visible binding for global variable 'cytodisease' .writecytoscape: no visible binding for global variable 'diseaselabels' generateprofiles: no visible binding for global variable 'genelist' generateprofiles: no visible global function definition for 'exprs' Undefined global functions or variables: ArrayExpress GDS2eSet GEOfactorvalues ReadAffy annotation annotationlist contrasts.fit cytodisease cytodrug diseaseClusters diseaseRL diseaselabels drugClusters drugRL druglabels eBayes exprs genelist getBM getGEO lmFit mas5 pData qvalue rma useMart * 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 classifyprofile 17.36 3.22 26.71 selectrankedlists 15.47 3.25 18.72 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed classifyprofile 24.23 2.28 26.55 selectrankedlists 15.22 2.11 17.33 * 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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DrugVsDisease.Rcheck/00check.log' for details.
DrugVsDisease.Rcheck/00install.out
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### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DrugVsDisease_2.26.0.tar.gz && rm -rf DrugVsDisease.buildbin-libdir && mkdir DrugVsDisease.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DrugVsDisease.buildbin-libdir DrugVsDisease_2.26.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DrugVsDisease_2.26.0.zip && rm DrugVsDisease_2.26.0.tar.gz DrugVsDisease_2.26.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'DrugVsDisease' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DrugVsDisease'
finding HTML links ... done
DrugVsDisease-package html
classifyprofile html
combineProfiles html
customClust html
customdb html
customedge html
customsif html
generateprofiles html
profiles html
selectrankedlists html
selprofile 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 'DrugVsDisease' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DrugVsDisease' as DrugVsDisease_2.26.0.zip
* DONE (DrugVsDisease)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'DrugVsDisease' successfully unpacked and MD5 sums checked
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DrugVsDisease.Rcheck/tests_i386/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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("DrugVsDisease")||stop("unable to load DrugVsDisease")
Loading required package: DrugVsDisease
Loading required package: affy
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
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")'.
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: biomaRt
Loading required package: ArrayExpress
Loading required package: GEOquery
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: DrugVsDiseasedata
Loading required package: cMap2data
Attaching package: 'cMap2data'
The following object is masked from 'package:DrugVsDiseasedata':
genelist
Loading required package: qvalue
[1] TRUE
> library(BiocGenerics)
> library(RUnit)
> BiocGenerics:::testPackage("DrugVsDisease")
RUNIT TEST PROTOCOL -- Wed Oct 16 03:28:11 2019
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
DrugVsDisease RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
8.56 0.68 9.23
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DrugVsDisease.Rcheck/tests_x64/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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("DrugVsDisease")||stop("unable to load DrugVsDisease")
Loading required package: DrugVsDisease
Loading required package: affy
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
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")'.
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: biomaRt
Loading required package: ArrayExpress
Loading required package: GEOquery
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: DrugVsDiseasedata
Loading required package: cMap2data
Attaching package: 'cMap2data'
The following object is masked from 'package:DrugVsDiseasedata':
genelist
Loading required package: qvalue
[1] TRUE
> library(BiocGenerics)
> library(RUnit)
> BiocGenerics:::testPackage("DrugVsDisease")
RUNIT TEST PROTOCOL -- Wed Oct 16 03:28:22 2019
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
DrugVsDisease RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
9.53 0.43 9.95
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DrugVsDisease.Rcheck/examples_i386/DrugVsDisease-Ex.timings
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DrugVsDisease.Rcheck/examples_x64/DrugVsDisease-Ex.timings
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