Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:01 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the cpvSNP package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cpvSNP.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 406/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cpvSNP 1.24.0 (landing page) Caitlin McHugh
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: cpvSNP |
Version: 1.24.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cpvSNP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings cpvSNP_1.24.0.tar.gz |
StartedAt: 2021-10-14 21:40:36 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:50:33 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 596.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cpvSNP.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cpvSNP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings cpvSNP_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/cpvSNP.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'cpvSNP/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'cpvSNP' version '1.24.0' * 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 'cpvSNP' 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' call to 'GSEABase' which was already attached by Depends. Please remove these calls from your code. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE assocPvalBySetPlot: no visible global function definition for 'rgb' assocPvalBySetPlot: no visible global function definition for 'col2rgb' assocPvalBySetPlot : <anonymous>: no visible global function definition for 'density' assocPvalBySetPlot: no visible global function definition for 'legend' assocPvalBySetPlot: no visible global function definition for 'polygon' assocPvalBySetPlot: no visible global function definition for 'lines' assocPvalBySetPlot: no visible global function definition for 'points' createArrayData: no visible global function definition for 'GRanges' createArrayData: no visible global function definition for 'Rle' createArrayData: no visible global function definition for 'IRanges' createArrayData: no visible global function definition for 'elementMetadata<-' geneToSNPList: no visible global function definition for 'findOverlaps' glossiMarginal: no visible global function definition for 'pgamma' plotPvals: no visible binding for global variable 'df' plotPvals: no visible binding for global variable 'pval' simulate_chisq: no visible global function definition for 'rnorm' vegasMarginal: no visible global function definition for 'rbinom' vegasMarginal: no visible global function definition for 'qchisq' vegasPrep: no visible global function definition for 'elementMetadata' show,VEGASResult: no visible global function definition for 'var' Undefined global functions or variables: GRanges IRanges Rle col2rgb density df elementMetadata elementMetadata<- findOverlaps legend lines pgamma points polygon pval qchisq rbinom rgb rnorm var Consider adding importFrom("grDevices", "col2rgb", "rgb") importFrom("graphics", "legend", "lines", "points", "polygon") importFrom("stats", "density", "df", "pgamma", "qchisq", "rbinom", "rnorm", "var") 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 (user + system) or elapsed time > 5s user system elapsed geneToSNPList 4.95 0.25 73.77 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed geneToSNPList 5.27 0.09 81.08 * 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-3.13-bioc/meat/cpvSNP.Rcheck/00check.log' for details.
cpvSNP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/cpvSNP_1.24.0.tar.gz && rm -rf cpvSNP.buildbin-libdir && mkdir cpvSNP.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cpvSNP.buildbin-libdir cpvSNP_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL cpvSNP_1.24.0.zip && rm cpvSNP_1.24.0.tar.gz cpvSNP_1.24.0.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 0 1759k 0 2485 0 0 30303 0 0:00:59 --:--:-- 0:00:59 30304 96 1759k 96 1703k 0 0 1577k 0 0:00:01 0:00:01 --:--:-- 1577k 100 1759k 100 1759k 0 0 1626k 0 0:00:01 0:00:01 --:--:-- 1626k install for i386 * installing *source* package 'cpvSNP' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'cpvSNP' finding HTML links ... done GLOSSIResult-class html GLOSSIResultCollection-class html GeneSetResult-class html GeneSetResultCollection-class html VEGASResult-class html VEGASResultCollection-class html assocPvalBySetPlot html createArrayData html degreesOfFreedom-method html exampleArrayData html geneSetAnalysis html geneSetName-methods html geneSets html geneToSNPList html glossi html glossiMarginal html pValue-method html plotPvals html show-methods html simulate_chisq html simulatedStats-method html statistic-methods html vegas html vegasMarginal 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 'cpvSNP' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'cpvSNP' as cpvSNP_1.24.0.zip * DONE (cpvSNP) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'cpvSNP' successfully unpacked and MD5 sums checked
cpvSNP.Rcheck/tests_i386/runTests.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" 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. > BiocGenerics:::testPackage("cpvSNP") 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 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'graph' The following object is masked from 'package:XML': addNode making GRanges object 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: 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: annotate Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: XML Loading required package: graph Attaching package: 'graph' The following object is masked from 'package:XML': addNode 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: 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: annotate Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: XML Loading required package: graph Attaching package: 'graph' The following object is masked from 'package:XML': addNode Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. RUNIT TEST PROTOCOL -- Thu Oct 14 21:49:28 2021 *********************************************** Number of test functions: 4 Number of errors: 0 Number of failures: 0 1 Test Suite : cpvSNP RUnit Tests - 4 test functions, 0 errors, 0 failures Number of test functions: 4 Number of errors: 0 Number of failures: 0 Warning message: In mode(current) : NAs introduced by coercion > > proc.time() user system elapsed 15.75 1.45 55.75 |
cpvSNP.Rcheck/tests_x64/runTests.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" 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. > BiocGenerics:::testPackage("cpvSNP") 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 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'graph' The following object is masked from 'package:XML': addNode making GRanges object 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: 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: annotate Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: XML Loading required package: graph Attaching package: 'graph' The following object is masked from 'package:XML': addNode 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: 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: annotate Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: XML Loading required package: graph Attaching package: 'graph' The following object is masked from 'package:XML': addNode Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. Warning: coercing ldMatrix from data.frame to matrix. RUNIT TEST PROTOCOL -- Thu Oct 14 21:50:22 2021 *********************************************** Number of test functions: 4 Number of errors: 0 Number of failures: 0 1 Test Suite : cpvSNP RUnit Tests - 4 test functions, 0 errors, 0 failures Number of test functions: 4 Number of errors: 0 Number of failures: 0 Warning message: In mode(current) : NAs introduced by coercion > > proc.time() user system elapsed 16.75 0.73 52.78 |
cpvSNP.Rcheck/examples_i386/cpvSNP-Ex.timings
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cpvSNP.Rcheck/examples_x64/cpvSNP-Ex.timings
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