Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-14 10:53:23 -0400 (Sun, 14 Oct 2018).
Package 248/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
CINdex 1.8.0 Yuriy Gusev
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | ![]() | ||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | ![]() |
Package: CINdex |
Version: 1.8.0 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CINdex.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CINdex_1.8.0.tar.gz |
StartedAt: 2018-10-14 01:07:40 -0400 (Sun, 14 Oct 2018) |
EndedAt: 2018-10-14 01:10:38 -0400 (Sun, 14 Oct 2018) |
EllapsedTime: 178.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: CINdex.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CINdex.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CINdex_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CINdex.Rcheck' * using R version 3.5.1 Patched (2018-07-24 r75005) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'CINdex/DESCRIPTION' ... OK * this is package 'CINdex' version '1.8.0' * 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 'CINdex' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'CINdex' See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CINdex.Rcheck/00install.out' for details. * checking installed package size ... NOTE installed size is 17.9Mb sub-directories of 1Mb or more: data 17.7Mb * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE comp.heatmap: no visible binding for global variable 'dataMatrix' process.probe.anno: no visible binding for global variable 'ID' process.probe.anno: no visible binding for global variable 'midpoint' process.reference.genome: no visible binding for global variable 'chrom' process.reference.genome: no visible binding for global variable 'name' process.reference.genome: no visible binding for global variable 'stain' run.cin.chr: no visible global function definition for 'is' run.cin.cyto: no visible global function definition for 'is' Undefined global functions or variables: ID chrom dataMatrix is midpoint name stain Consider adding importFrom("methods", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 run.cin.cyto 11.24 0.53 11.77 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed run.cin.cyto 12.92 0.72 13.69 * 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: 1 WARNING, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CINdex.Rcheck/00check.log' for details.
CINdex.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/CINdex_1.8.0.tar.gz && rm -rf CINdex.buildbin-libdir && mkdir CINdex.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CINdex.buildbin-libdir CINdex_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CINdex_1.8.0.zip && rm CINdex_1.8.0.tar.gz CINdex_1.8.0.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 80 11.8M 80 9728k 0 0 42.5M 0 --:--:-- --:--:-- --:--:-- 43.5M 100 11.8M 100 11.8M 0 0 42.8M 0 --:--:-- --:--:-- --:--:-- 43.8M install for i386 * installing *source* package 'CINdex' ... ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'CINdex' ** help *** installing help indices converting help for package 'CINdex' finding HTML links ... done clin.crc html cnvgr.18.auto html comp.heatmap html cyto.cin4heatmap html cytobands.cin html extract.genes.in.cyto.regions html geneAnno html grl.data html hg18.ucsctrack html run.cin.chr html run.cin.cyto html snpgr.18.auto html ttest.cyto.cin.heatmap html ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'CINdex' In R CMD INSTALL install for x64 * installing *source* package 'CINdex' ... ** testing if installed package can be loaded Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'CINdex' * MD5 sums packaged installation of 'CINdex' as CINdex_1.8.0.zip * DONE (CINdex) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'CINdex' successfully unpacked and MD5 sums checked In R CMD INSTALL
CINdex.Rcheck/tests_i386/RunTests.Rout R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray" 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. > BiocGenerics:::testPackage("CINdex") 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 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows RUNIT TEST PROTOCOL -- Sun Oct 14 01:10:29 2018 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : CINdex RUnit Tests - 0 test functions, 0 errors, 0 failures Number of test functions: 0 Number of errors: 0 Number of failures: 0 Warning message: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'CINdex' > > proc.time() user system elapsed 3.14 0.25 3.37 |
CINdex.Rcheck/tests_x64/RunTests.Rout R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray" 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. > BiocGenerics:::testPackage("CINdex") 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 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows RUNIT TEST PROTOCOL -- Sun Oct 14 01:10:33 2018 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : CINdex RUnit Tests - 0 test functions, 0 errors, 0 failures Number of test functions: 0 Number of errors: 0 Number of failures: 0 Warning message: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'CINdex' > > proc.time() user system elapsed 3.14 0.20 3.32 |
CINdex.Rcheck/examples_i386/CINdex-Ex.timings
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CINdex.Rcheck/examples_x64/CINdex-Ex.timings
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