Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:31:55 -0400 (Tue, 09 Apr 2019).
Package 725/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
gwascat 2.15.1 VJ Carey
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: gwascat |
Version: 2.15.1 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:gwascat.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings gwascat_2.15.1.tar.gz |
StartedAt: 2019-04-09 01:07:31 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 01:14:17 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 406.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gwascat.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:gwascat.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings gwascat_2.15.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/gwascat.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gwascat/DESCRIPTION’ ... OK * this is package ‘gwascat’ version ‘2.15.1’ * 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 36.6Mb sub-directories of 1Mb or more: data 28.7Mb obo 3.1Mb 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 ... NOTE Package in Depends field not imported from: 'Homo.sapiens' 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 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 global function definition for ‘autoplot’ traitsManh: no visible global function definition for ‘aes’ traitsManh: no visible binding for global variable ‘PVALUE_MLOG’ variantProps: no visible binding for global variable ‘gwrngs’ Undefined global functions or variables: PVALUE_MLOG aes autoplot 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed riskyAlleleCount 11.513 0.076 11.655 gwcex2gviz 11.148 0.260 11.487 ldtagr 3.045 0.043 6.582 * 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.9-bioc/meat/gwascat.Rcheck/00check.log’ for details.
gwascat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL gwascat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘gwascat’ ... ** using staged installation ** 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 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 (gwascat)
gwascat.Rcheck/tests/test-all.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" Copyright (C) 2019 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("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, 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 Apr 9 01:14:13 2019 *********************************************** 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 12.142 0.405 12.549
gwascat.Rcheck/gwascat-Ex.timings
name | user | system | elapsed | |
bindcadd_snv | 0 | 0 | 0 | |
gwascat-package | 0.929 | 0.025 | 3.151 | |
gwastagger | 2.688 | 0.019 | 2.846 | |
gwaswloc-class | 0.002 | 0.000 | 0.002 | |
gwcex2gviz | 11.148 | 0.260 | 11.487 | |
gwdf_2012_02_02 | 0 | 0 | 0 | |
ldtagr | 3.045 | 0.043 | 6.582 | |
locon6 | 0.04 | 0.00 | 0.04 | |
makeCurrentGwascat | 0 | 0 | 0 | |
obo2graphNEL | 0.278 | 0.000 | 0.307 | |
riskyAlleleCount | 11.513 | 0.076 | 11.655 | |
topTraits | 0.471 | 0.012 | 0.484 | |
traitsManh | 0 | 0 | 0 | |