Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-13 11:22:37 -0400 (Sat, 13 Apr 2019).
Package 437/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
DrugVsDisease 2.24.2 j. Saez-Rodriguez
| malbec1 | Linux (Ubuntu 16.04.6 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: DrugVsDisease |
Version: 2.24.2 |
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DrugVsDisease.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DrugVsDisease_2.24.2.tar.gz |
StartedAt: 2019-04-13 01:55:04 -0400 (Sat, 13 Apr 2019) |
EndedAt: 2019-04-13 02:00:49 -0400 (Sat, 13 Apr 2019) |
EllapsedTime: 345.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DrugVsDisease.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DrugVsDisease.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DrugVsDisease_2.24.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DrugVsDisease.Rcheck' * using R version 3.5.3 (2019-03-11) * 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 '2.24.2' * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 global function definition for 'data' .averagecluster: no visible binding for global variable 'drugClusters' .averagecluster: no visible binding for global variable 'diseaseClusters' .averagecluster: no visible global function definition for 'median' .calculateES: no visible binding for global variable 'drugRL' .calculateES: no visible binding for global variable 'diseaseRL' .calculateES: no visible binding for global variable 'p.adjust' .calculateES : <anonymous>: no visible global function definition for 'qvalue' .combinemed: no visible global function definition for 'medpolish' .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 global function definition for 'data' .findCluster: no visible binding for global variable 'drugClusters' .findCluster: no visible binding for global variable 'diseaseClusters' .findSignifCompounds: no visible global function definition for 'ecdf' .findSignifCompounds: no visible global function definition for 'p.adjust' .findSignifCompounds: no visible global function definition for 'qvalue' .fitlms: no visible global function definition for 'read.table' .fitlms: no visible global function definition for 'model.matrix' .fitlms: no visible global function definition for 'lmFit' .multcontrast: no visible global function definition for 'combn' .multcontrast: no visible global function definition for 'contrasts.fit' .multcontrast: no visible global function definition for 'eBayes' .norm_mrs : <anonymous>: no visible global function definition for 'median' .normalisedata: no visible global function definition for 'rma' .normalisedata: no visible global function definition for 'mas5' .ptog: no visible global function definition for 'setNames' .readlocalAE: no visible global function definition for 'ReadAffy' .readlocalAE: no visible global function definition for 'read.delim' .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 global function definition for 'data' .writecytoscape: no visible binding for global variable 'cytodrug' .writecytoscape: no visible binding for global variable 'drugClusters' .writecytoscape: no visible binding for global variable 'druglabels' .writecytoscape: no visible binding for global variable 'cytodisease' .writecytoscape: no visible binding for global variable 'diseaseClusters' .writecytoscape: no visible binding for global variable 'diseaselabels' .writecytoscape: no visible global function definition for 'write.table' classifyprofile: no visible global function definition for 'read.table' generateprofiles: no visible global function definition for 'data' generateprofiles: no visible binding for global variable 'genelist' generateprofiles: no visible binding for global variable 'annotationlist' generateprofiles: no visible global function definition for 'read.table' generateprofiles: no visible global function definition for 'exprs' Undefined global functions or variables: ArrayExpress GDS2eSet GEOfactorvalues ReadAffy annotation annotationlist combn contrasts.fit cytodisease cytodrug data diseaseClusters diseaseRL diseaselabels drugClusters drugRL druglabels eBayes ecdf exprs genelist getBM getGEO lmFit mas5 median medpolish model.matrix p.adjust pData qvalue read.delim read.table rma setNames useMart write.table Consider adding importFrom("stats", "ecdf", "median", "medpolish", "model.matrix", "p.adjust", "setNames") importFrom("utils", "combn", "data", "read.delim", "read.table", "write.table") 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 classifyprofile 19.02 5.36 24.37 selectrankedlists 16.78 1.50 18.29 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed classifyprofile 19.22 1.91 21.13 selectrankedlists 14.60 1.63 16.22 * 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-3.8-bioc/meat/DrugVsDisease.Rcheck/00check.log' for details.
DrugVsDisease.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DrugVsDisease_2.24.2.tar.gz && rm -rf DrugVsDisease.buildbin-libdir && mkdir DrugVsDisease.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DrugVsDisease.buildbin-libdir DrugVsDisease_2.24.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DrugVsDisease_2.24.2.zip && rm DrugVsDisease_2.24.2.tar.gz DrugVsDisease_2.24.2.zip ### ############################################################################## ############################################################################## % 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 1691k 100 1691k 0 0 12.2M 0 --:--:-- --:--:-- --:--:-- 12.5M install for i386 * installing *source* package 'DrugVsDisease' ... ** 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 In R CMD INSTALL install for x64 * installing *source* package 'DrugVsDisease' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'DrugVsDisease' as DrugVsDisease_2.24.2.zip * DONE (DrugVsDisease) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library' package 'DrugVsDisease' successfully unpacked and MD5 sums checked In R CMD INSTALL
DrugVsDisease.Rcheck/tests_i386/runTests.Rout R version 3.5.3 (2019-03-11) -- "Great Truth" 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, colMeans, colSums, colnames, dirname, 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 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 -- Sat Apr 13 02:00:34 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 10.96 0.84 11.79 |
DrugVsDisease.Rcheck/tests_x64/runTests.Rout R version 3.5.3 (2019-03-11) -- "Great Truth" 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, colMeans, colSums, colnames, dirname, 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 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 -- Sat Apr 13 02:00:44 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 0.51 10.03 |
DrugVsDisease.Rcheck/examples_i386/DrugVsDisease-Ex.timings
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DrugVsDisease.Rcheck/examples_x64/DrugVsDisease-Ex.timings
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