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This page was generated on 2018-04-12 13:24:12 -0400 (Thu, 12 Apr 2018).
Package 565/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GenomicFiles 1.14.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: GenomicFiles |
Version: 1.14.0 |
Command: rm -rf GenomicFiles.buildbin-libdir GenomicFiles.Rcheck && mkdir GenomicFiles.buildbin-libdir GenomicFiles.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFiles.buildbin-libdir GenomicFiles_1.14.0.tar.gz >GenomicFiles.Rcheck\00install.out 2>&1 && cp GenomicFiles.Rcheck\00install.out GenomicFiles-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicFiles.buildbin-libdir --install="check:GenomicFiles-install.out" --force-multiarch --no-vignettes --timings GenomicFiles_1.14.0.tar.gz |
StartedAt: 2018-04-12 00:17:46 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 00:36:18 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 1112.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GenomicFiles.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf GenomicFiles.buildbin-libdir GenomicFiles.Rcheck && mkdir GenomicFiles.buildbin-libdir GenomicFiles.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFiles.buildbin-libdir GenomicFiles_1.14.0.tar.gz >GenomicFiles.Rcheck\00install.out 2>&1 && cp GenomicFiles.Rcheck\00install.out GenomicFiles-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicFiles.buildbin-libdir --install="check:GenomicFiles-install.out" --force-multiarch --no-vignettes --timings GenomicFiles_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicFiles.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'GenomicFiles/DESCRIPTION' ... OK * this is package 'GenomicFiles' version '1.14.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics' 'GenomicRanges' 'SummarizedExperiment' 'BiocParallel' 'Rsamtools' 'rtracklayer' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 'GenomicFiles' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/GenomicFiles-class.Rd:111: missing file link 'SummarizedExperiment' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:77: missing file link 'DataFrame' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:97: missing file link 'GRanges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:128: missing file link 'VcfFileList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:129: missing file link 'VcfFileList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:132: missing file link 'seqinfo<-' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:138: missing file link 'seqlevelsStyle<-' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:142: missing file link 'DataFrame' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:147: missing file link 'GRanges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:154: missing file link 'GRanges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:162: missing file link 'genotypeToSnpMatrix' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:172: missing file link 'ScanVcfParam' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:219: missing file link 'VcfFile' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:219: missing file link 'VcfFileList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/reduceByYield.Rd:12: missing file link 'BamFile' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/reduceByYield.Rd:29: missing file link 'BamFile' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/reduceByYield.Rd:121: missing file link 'BamFile' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/reduceByYield.Rd:122: missing file link 'TabixFile' See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicFiles.Rcheck/00install.out' for details. * checking installed package size ... OK * 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 ... OK * 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed VcfStack-class 4.44 0.02 31.92 reduceByYield 1.24 0.07 36.03 GenomicFiles-class 0.83 0.06 33.27 reduceByRange-methods 0.22 0.01 44.89 reduceByFile-methods 0.21 0.00 64.36 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed VcfStack-class 4.78 0.04 32.29 reduceByYield 1.84 0.08 25.09 GenomicFiles-class 1.61 0.03 32.94 reduceByRange-methods 0.28 0.02 55.82 reduceByFile-methods 0.30 0.00 65.09 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'GenomicFiles_unit_tests.R' OK ** running tests for arch 'x64' ... Running 'GenomicFiles_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, 1 NOTE See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicFiles.Rcheck/00check.log' for details.
GenomicFiles.Rcheck/00install.out
install for i386 * installing *source* package 'GenomicFiles' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'GenomicFiles' finding HTML links ... done GenomicFiles-class html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/GenomicFiles-class.Rd:111: missing file link 'SummarizedExperiment' GenomicFiles-deprecated html VcfStack-class html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:77: missing file link 'DataFrame' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:97: missing file link 'GRanges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:128: missing file link 'VcfFileList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:129: missing file link 'VcfFileList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:132: missing file link 'seqinfo<-' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:138: missing file link 'seqlevelsStyle<-' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:142: missing file link 'DataFrame' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:147: missing file link 'GRanges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:154: missing file link 'GRanges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:162: missing file link 'genotypeToSnpMatrix' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:172: missing file link 'ScanVcfParam' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:219: missing file link 'VcfFile' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/VcfStack-class.Rd:219: missing file link 'VcfFileList' pack-methods html reduceByFile-methods html reduceByRange-methods html reduceByYield html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/reduceByYield.Rd:12: missing file link 'BamFile' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/reduceByYield.Rd:29: missing file link 'BamFile' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/reduceByYield.Rd:121: missing file link 'BamFile' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCObmLN/R.INSTALL192049bd456f/GenomicFiles/man/reduceByYield.Rd:122: missing file link 'TabixFile' registry-utils html unpack-methods html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'GenomicFiles' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'GenomicFiles' as GenomicFiles_1.14.0.zip * DONE (GenomicFiles) In R CMD INSTALL In R CMD INSTALL
GenomicFiles.Rcheck/tests_i386/GenomicFiles_unit_tests.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" 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("GenomicFiles") 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, cbind, colMeans, colSums, colnames, 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following object is masked from 'package:base': apply Attaching package: 'Biostrings' The following object is masked from 'package:DelayedArray': type The following object is masked from 'package:base': strsplit Warning messages: Warning messages: 1: 1: In Ops.factor(left, right) : '+' not meaningful for factors In Ops.factor(left, right) :2: '+' not meaningful for factors 2: In Ops.factor(left, right) : '+' not meaningful for factors 3: In Ops.factor(left, right) : '+' not meaningful for factors In Ops.factor(left, right) :3: '+' not meaningful for factors 4: In Ops.factor(left, right) : '+' not meaningful for factors In Ops.factor(left, right) :4: '+' not meaningful for factors In Ops.factor(left, right) : '+' not meaningful for factors Warning messages: 1: In Ops.factor(left, right) : '+' not meaningful for factors 2: In Ops.factor(left, right) : '+' not meaningful for factors Warning messages: Warning messages: 1: 1: In Ops.factor(left, right) : '+' not meaningful for factors 2: In Ops.factor(left, right) : '+' not meaningful for factors 2: In Ops.factor(left, right) : '+' not meaningful for factors In Ops.factor(left, right) : '+' not meaningful for factors RUNIT TEST PROTOCOL -- Thu Apr 12 00:32:49 2018 *********************************************** Number of test functions: 19 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomicFiles RUnit Tests - 19 test functions, 0 errors, 0 failures Number of test functions: 19 Number of errors: 0 Number of failures: 0 Warning message: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence 19. Note that only ranges located on a non-circular sequence whose length is not NA can be considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. > > proc.time() user system elapsed 39.20 0.84 179.46 |
GenomicFiles.Rcheck/tests_x64/GenomicFiles_unit_tests.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" 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("GenomicFiles") 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, cbind, colMeans, colSums, colnames, 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following object is masked from 'package:base': apply Attaching package: 'Biostrings' The following object is masked from 'package:DelayedArray': type The following object is masked from 'package:base': strsplit Warning messages: 1: In Ops.factor(left, right) : '+' not meaningful for factors 2: In Ops.factor(left, right) : '+' not meaningful for factors Warning messages: 3: 1: In Ops.factor(left, right) : '+' not meaningful for factors 4: In Ops.factor(left, right) :In Ops.factor(left, right) : '+' not meaningful for factors '+' not meaningful for factors 2: In Ops.factor(left, right) : '+' not meaningful for factors 3: In Ops.factor(left, right) : '+' not meaningful for factors 4: In Ops.factor(left, right) : '+' not meaningful for factors Warning messages: Warning messages: 1: In Ops.factor(left, right) : '+' not meaningful for factors 2: 1: In Ops.factor(left, right) : '+' not meaningful for factors In Ops.factor(left, right) : '+' not meaningful for factors 2: In Ops.factor(left, right) : '+' not meaningful for factors Warning messages: 1: In Ops.factor(left, right) : '+' not meaningful for factors 2: In Ops.factor(left, right) : '+' not meaningful for factors RUNIT TEST PROTOCOL -- Thu Apr 12 00:36:14 2018 *********************************************** Number of test functions: 19 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomicFiles RUnit Tests - 19 test functions, 0 errors, 0 failures Number of test functions: 19 Number of errors: 0 Number of failures: 0 Warning message: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence 19. Note that only ranges located on a non-circular sequence whose length is not NA can be considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. > > proc.time() user system elapsed 42.07 0.62 204.07 |
GenomicFiles.Rcheck/examples_i386/GenomicFiles-Ex.timings
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GenomicFiles.Rcheck/examples_x64/GenomicFiles-Ex.timings
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