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This page was generated on 2021-05-06 12:31:28 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the GenomicFiles package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 717/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicFiles 1.26.0 (landing page) Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: GenomicFiles |
Version: 1.26.0 |
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFiles.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GenomicFiles_1.26.0.tar.gz |
StartedAt: 2021-05-06 03:06:03 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 03:35:22 -0400 (Thu, 06 May 2021) |
EllapsedTime: 1758.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GenomicFiles.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFiles.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GenomicFiles_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GenomicFiles.Rcheck' * using R version 4.0.5 (2021-03-31) * 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 '1.26.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'MatrixGenerics', '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-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/GenomicFiles-class.Rd:111: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:78: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:98: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:129: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:130: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:133: file link 'seqinfo<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:139: file link 'seqlevelsStyle<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:143: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:148: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:155: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:162: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:170: file link 'genotypeToSnpMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:180: file link 'ScanVcfParam' in package 'VariantAnnotation' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:227: file link 'VcfFile' in package 'VariantAnnotation' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:227: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/reduceByYield.Rd:12: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/reduceByYield.Rd:29: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/reduceByYield.Rd:121: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/reduceByYield.Rd:122: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.12-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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed VcfStack-class 6.23 0.50 70.11 reduceByRange-methods 3.98 0.03 86.58 reduceByFile-methods 3.14 0.00 88.63 GenomicFiles-class 2.94 0.09 41.56 reduceByYield 1.61 0.10 28.36 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed VcfStack-class 7.64 0.08 81.84 reduceByRange-methods 4.75 0.03 90.17 reduceByFile-methods 4.73 0.03 93.58 GenomicFiles-class 3.50 0.00 51.45 reduceByYield 1.86 0.05 30.22 * 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-3.12-bioc/meat/GenomicFiles.Rcheck/00check.log' for details.
GenomicFiles.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/GenomicFiles_1.26.0.tar.gz && rm -rf GenomicFiles.buildbin-libdir && mkdir GenomicFiles.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFiles.buildbin-libdir GenomicFiles_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GenomicFiles_1.26.0.zip && rm GenomicFiles_1.26.0.tar.gz GenomicFiles_1.26.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 289k 100 289k 0 0 20.0M 0 --:--:-- --:--:-- --:--:-- 21.7M install for i386 * installing *source* package 'GenomicFiles' ... ** using staged installation ** R ** inst ** byte-compile and prepare 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-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/GenomicFiles-class.Rd:111: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic GenomicFiles-deprecated html VcfStack-class html Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:78: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:98: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:129: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:130: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:133: file link 'seqinfo<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:139: file link 'seqlevelsStyle<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:143: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:148: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:155: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:162: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:170: file link 'genotypeToSnpMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:180: file link 'ScanVcfParam' in package 'VariantAnnotation' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:227: file link 'VcfFile' in package 'VariantAnnotation' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/VcfStack-class.Rd:227: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic pack-methods html reduceByFile-methods html reduceByRange-methods html reduceByYield html Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/reduceByYield.Rd:12: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/reduceByYield.Rd:29: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/reduceByYield.Rd:121: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp4CJqom/R.INSTALL1eac23421eb0/GenomicFiles/man/reduceByYield.Rd:122: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic registry-utils html unpack-methods html ** 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 install for x64 * installing *source* package 'GenomicFiles' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'GenomicFiles' as GenomicFiles_1.26.0.zip * DONE (GenomicFiles) * installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library' package 'GenomicFiles' successfully unpacked and MD5 sums checked
GenomicFiles.Rcheck/tests_i386/GenomicFiles_unit_tests.Rout R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 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, 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.max, which.min Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit RUNIT TEST PROTOCOL -- Thu May 06 03:28:46 2021 *********************************************** Number of test functions: 20 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomicFiles RUnit Tests - 20 test functions, 0 errors, 0 failures Number of test functions: 20 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 ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not 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 56.43 1.78 279.81 |
GenomicFiles.Rcheck/tests_x64/GenomicFiles_unit_tests.Rout R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 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, 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.max, which.min Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit RUNIT TEST PROTOCOL -- Thu May 06 03:35:13 2021 *********************************************** Number of test functions: 20 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomicFiles RUnit Tests - 20 test functions, 0 errors, 0 failures Number of test functions: 20 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 ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not 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 72.62 0.60 385.67 |
GenomicFiles.Rcheck/examples_i386/GenomicFiles-Ex.timings
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GenomicFiles.Rcheck/examples_x64/GenomicFiles-Ex.timings
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