Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:41:01 -0400 (Wed, 17 Oct 2018).
Package 781/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ldblock 1.10.0 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: ldblock |
Version: 1.10.0 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ldblock.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ldblock_1.10.0.tar.gz |
StartedAt: 2018-10-17 02:56:46 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 03:04:32 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 465.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ldblock.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ldblock.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ldblock_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ldblock.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 'ldblock/DESCRIPTION' ... OK * this is package 'ldblock' version '1.10.0' * 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 'ldblock' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpq806c5/R.INSTALL155836564b43/ldblock/man/hmld.Rd:19: file link 'read.delim' in package 'utils' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpq806c5/R.INSTALL155836564b43/ldblock/man/ldByGene.Rd:33: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpq806c5/R.INSTALL155836564b43/ldblock/man/s3_1kg.Rd:50: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ldblock.Rcheck/00install.out' for details. * checking installed package size ... NOTE installed size is 40.2Mb sub-directories of 1Mb or more: hapmap 39.9Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: 'BiocGenerics' A package should be listed in only one of these fields. * 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 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 stack1kg: no visible global function definition for 'Seqinfo' stack1kg: no visible global function definition for 'seqinfo<-' stack1kg: no visible global function definition for 'seqinfo' Undefined global functions or variables: Seqinfo seqinfo seqinfo<- * checking Rd files ... NOTE prepare_Rd: downloadPopByChr.Rd:49-51: Dropping empty section \seealso * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed expandSnpSet 26.43 0.96 29.04 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed expandSnpSet 27.52 1.22 28.74 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'ldblock_unit_tests.R' OK ** running tests for arch 'x64' ... Running 'ldblock_unit_tests.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, 5 NOTEs See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ldblock.Rcheck/00check.log' for details.
ldblock.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ldblock_1.10.0.tar.gz && rm -rf ldblock.buildbin-libdir && mkdir ldblock.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ldblock.buildbin-libdir ldblock_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ldblock_1.10.0.zip && rm ldblock_1.10.0.tar.gz ldblock_1.10.0.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 34 39.5M 34 13.5M 0 0 80.0M 0 --:--:-- --:--:-- --:--:-- 82.9M 100 39.5M 100 39.5M 0 0 98.8M 0 --:--:-- --:--:-- --:--:-- 100M install for i386 * installing *source* package 'ldblock' ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'ldblock' finding HTML links ... done downloadPopByChr html expandSnpSet html hmld html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpq806c5/R.INSTALL155836564b43/ldblock/man/hmld.Rd:19: file link 'read.delim' in package 'utils' does not exist and so has been treated as a topic ldByGene html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpq806c5/R.INSTALL155836564b43/ldblock/man/ldByGene.Rd:33: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic ldblock-package html ldstruct-class html s3_1kg html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpq806c5/R.INSTALL155836564b43/ldblock/man/s3_1kg.Rd:50: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'ldblock' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'ldblock' as ldblock_1.10.0.zip * DONE (ldblock) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'ldblock' successfully unpacked and MD5 sums checked In R CMD INSTALL
ldblock.Rcheck/tests_i386/ldblock_unit_tests.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('ldblock') 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows RUNIT TEST PROTOCOL -- Wed Oct 17 03:04:12 2018 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : ldblock 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 11.39 0.96 12.45 |
ldblock.Rcheck/tests_x64/ldblock_unit_tests.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('ldblock') 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows RUNIT TEST PROTOCOL -- Wed Oct 17 03:04:26 2018 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : ldblock 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 12.60 0.50 13.29 |
ldblock.Rcheck/examples_i386/ldblock-Ex.timings
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ldblock.Rcheck/examples_x64/ldblock-Ex.timings
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