Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:50:17 -0400 (Wed, 17 Oct 2018).
Package 668/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
gwascat 2.12.0 VJ Carey
| 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: gwascat |
Version: 2.12.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gwascat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gwascat_2.12.0.tar.gz |
StartedAt: 2018-10-16 21:56:09 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 22:04:15 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 485.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gwascat.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gwascat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gwascat_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/gwascat.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gwascat/DESCRIPTION’ ... OK * this is package ‘gwascat’ version ‘2.12.0’ * 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 ‘gwascat’ can be installed ... OK * checking installed package size ... NOTE installed size is 36.7Mb sub-directories of 1Mb or more: data 28.7Mb obo 3.0Mb olddata 2.2Mb tab 1.1Mb * 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 chklocs: no visible binding for global variable 'gwrngs19' chklocs: no visible global function definition for 'snpsBySeqname' lo38to19: no visible binding for global variable 'si.hs.37' makeCurrentGwascat: no visible binding for global variable 'si.hs.38' makeCurrentGwascat.legacy: no visible binding for global variable 'si.hs.38' snpGenos: no visible global function definition for 'getSNPlocs' tfilt: no visible binding for global variable 'phr' tpad: no visible binding for global variable 'phr' traitsManh: no visible binding for global variable 'PVALUE_MLOG' variantProps: no visible binding for global variable 'gwrngs' Undefined global functions or variables: PVALUE_MLOG getSNPlocs gwrngs gwrngs19 phr si.hs.37 si.hs.38 snpsBySeqname * 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 ... NOTE Note: found 6 marked Latin-1 strings Note: found 1 marked UTF-8 string * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed riskyAlleleCount 15.016 0.117 15.258 gwcex2gviz 10.536 0.281 10.938 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-all.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 ‘/Users/biocbuild/bbs-3.7-bioc/meat/gwascat.Rcheck/00check.log’ for details.
gwascat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gwascat ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘gwascat’ ... ** R ** data ** 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 * DONE (gwascat)
gwascat.Rcheck/tests/test-all.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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("gwascat") 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid gwascat loaded. Use data(ebicat38) for hg38 coordinates; data(ebicat37) for hg19 coordinates. RUNIT TEST PROTOCOL -- Tue Oct 16 22:04:09 2018 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : gwascat 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 19.746 0.934 21.486
gwascat.Rcheck/gwascat-Ex.timings
name | user | system | elapsed | |
bindcadd_snv | 0.002 | 0.000 | 0.002 | |
gwascat-package | 0.001 | 0.000 | 0.001 | |
gwastagger | 1.536 | 0.048 | 1.598 | |
gwaswloc-class | 0.002 | 0.000 | 0.003 | |
gwcex2gviz | 10.536 | 0.281 | 10.938 | |
gwdf_2012_02_02 | 0.001 | 0.000 | 0.002 | |
ldtagr | 0.810 | 0.024 | 0.848 | |
locon6 | 0.035 | 0.005 | 0.040 | |
makeCurrentGwascat | 0.001 | 0.000 | 0.001 | |
obo2graphNEL | 0.280 | 0.005 | 0.287 | |
riskyAlleleCount | 15.016 | 0.117 | 15.258 | |
topTraits | 0.548 | 0.028 | 0.576 | |
traitsManh | 1.095 | 0.032 | 1.131 | |