Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:11:13 -0400 (Wed, 15 Apr 2020).
Package 292/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
CINdex 1.14.0 Yuriy Gusev
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: CINdex |
Version: 1.14.0 |
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CINdex.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CINdex_1.14.0.tar.gz |
StartedAt: 2020-04-15 03:43:29 -0400 (Wed, 15 Apr 2020) |
EndedAt: 2020-04-15 03:46:04 -0400 (Wed, 15 Apr 2020) |
EllapsedTime: 154.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CINdex.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CINdex.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CINdex_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/CINdex.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CINdex/DESCRIPTION’ ... OK * this is package ‘CINdex’ 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 for sufficient/correct file permissions ... OK * checking whether package ‘CINdex’ can be installed ... OK * 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 * 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 ... OK Examples with CPU or elapsed time > 5s user system elapsed run.cin.cyto 16.608 0.236 16.905 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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 ‘/home/biocbuild/bbs-3.10-bioc/meat/CINdex.Rcheck/00check.log’ for details.
CINdex.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL CINdex ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘CINdex’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (CINdex)
CINdex.Rcheck/tests/RunTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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, 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 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid RUNIT TEST PROTOCOL -- Wed Apr 15 03:46:01 2020 *********************************************** 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 > > proc.time() user system elapsed 4.612 0.216 5.124
CINdex.Rcheck/CINdex-Ex.timings
name | user | system | elapsed | |
comp.heatmap | 0.360 | 0.008 | 0.416 | |
extract.genes.in.cyto.regions | 1.880 | 0.032 | 1.912 | |
run.cin.chr | 0.076 | 0.000 | 0.076 | |
run.cin.cyto | 16.608 | 0.236 | 16.905 | |
ttest.cyto.cin.heatmap | 0.836 | 0.008 | 0.847 | |