Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:35:20 -0400 (Wed, 17 Oct 2018).
Package 1159/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
qrqc 1.34.0 Vince Buffalo
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: qrqc |
Version: 1.34.0 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qrqc.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings qrqc_1.34.0.tar.gz |
StartedAt: 2018-10-17 04:10:22 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 04:17:34 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 432.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: qrqc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qrqc.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings qrqc_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/qrqc.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 'qrqc/DESCRIPTION' ... OK * this is package 'qrqc' version '1.34.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'reshape' 'ggplot2' 'Biostrings' 'biovizBase' 'brew' 'xtable' 'Rsamtools' 'testthat' 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 'qrqc' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'reshape' 'ggplot2' 'Biostrings' 'biovizBase' 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 Packages in Depends field not imported from: 'Rsamtools' 'brew' 'testthat' 'xtable' 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 binned2boxplot: no visible global function definition for 'quantile' calcKL : kmerDist: no visible global function definition for 'aggregate' generateReads: no visible global function definition for 'DNAStringSet' generateReads: no visible global function definition for 'write.XStringSet' makeReportDir: no visible global function definition for 'na.exclude' basePlot,SequenceSummary: no visible binding for global variable 'base' basePlot,list: no visible binding for global variable 'base' gcPlot,SequenceSummary: no visible binding for global variable 'position' gcPlot,list: no visible binding for global variable 'position' getBase,SequenceSummary: no visible global function definition for 'aggregate' getBase,SequenceSummary: no visible binding for global variable 'base' getBaseProp,SequenceSummary: no visible global function definition for 'aggregate' getBaseProp,SequenceSummary: no visible binding for global variable 'base' getGC,SequenceSummary : <local>: no visible global function definition for 'aggregate' kmerEntropyPlot,SequenceSummary: no visible binding for global variable 'position' kmerEntropyPlot,SequenceSummary: no visible binding for global variable 'entropy' kmerEntropyPlot,list: no visible binding for global variable 'position' kmerEntropyPlot,list: no visible binding for global variable 'entropy' kmerKLPlot,SequenceSummary: no visible binding for global variable 'kmer' kmerKLPlot,SequenceSummary: no visible binding for global variable 'position' kmerKLPlot,SequenceSummary: no visible binding for global variable 'kl' kmerKLPlot,list : <anonymous>: no visible binding for global variable 'kmer' kmerKLPlot,list: no visible binding for global variable 'position' kmerKLPlot,list: no visible binding for global variable 'kl' kmerKLPlot,list: no visible binding for global variable 'kmer' plotGC,SequenceSummary : <local>: no visible global function definition for 'aggregate' qualPlot,FASTQSummary: no visible binding for global variable 'position' qualPlot,list: no visible binding for global variable 'position' Undefined global functions or variables: DNAStringSet aggregate base entropy kl kmer na.exclude position quantile write.XStringSet Consider adding importFrom("stats", "aggregate", "na.exclude", "quantile") to your NAMESPACE file. * 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/qrqc/libs/i386/qrqc.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed kmerKLPlot 9.12 0.13 9.25 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed kmerKLPlot 10.26 0.11 10.66 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'test-functions.R' OK ** running tests for arch 'x64' ... Running 'test-functions.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: 5 NOTEs See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/qrqc.Rcheck/00check.log' for details.
qrqc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/qrqc_1.34.0.tar.gz && rm -rf qrqc.buildbin-libdir && mkdir qrqc.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qrqc.buildbin-libdir qrqc_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL qrqc_1.34.0.zip && rm qrqc_1.34.0.tar.gz qrqc_1.34.0.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 350k 100 350k 0 0 4908k 0 --:--:-- --:--:-- --:--:-- 5478k install for i386 * installing *source* package 'qrqc' ... ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_init_io.c -o R_init_io.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c io.c -o io.o In file included from io.c:11:0: C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include/samtools/kseq.h:158:13: warning: 'kseq_destroy' defined but not used [-Wunused-function] SCOPE void kseq_destroy(kseq_t *ks) \ ^ C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include/samtools/kseq.h:223:2: note: in expansion of macro '__KSEQ_BASIC' __KSEQ_BASIC(SCOPE, type_t) \ ^ C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include/samtools/kseq.h:226:35: note: in expansion of macro 'KSEQ_INIT2' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ io.c:28:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(FILE_TYPE*, gzreadclone) ^ C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o qrqc.dll tmp.def R_init_io.o io.o C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/qrqc.buildbin-libdir/qrqc/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'qrqc' finding HTML links ... done FASTASummary-class html FASTQSummary-class html SequenceSummary-class html basePlot-methods html calcKL html gcPlot-methods html geom_qlinerange html getBase-methods html getBaseProp-methods html getGC-methods html getKmer-methods html getMCQual-methods html getQual-methods html getSeqlen-methods html kmerEntropyPlot html kmerKLPlot html list2df html makeReport html plotBases html plotGC html plotQuals html plotSeqLengths html qualPlot-methods html readSeqFile html scale_color_dna html scale_color_iupac html seqlenPlot-methods html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'qrqc' ... ** libs C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_init_io.c -o R_init_io.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c io.c -o io.o In file included from io.c:11:0: C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include/samtools/kseq.h:158:13: warning: 'kseq_destroy' defined but not used [-Wunused-function] SCOPE void kseq_destroy(kseq_t *ks) \ ^ C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include/samtools/kseq.h:223:2: note: in expansion of macro '__KSEQ_BASIC' __KSEQ_BASIC(SCOPE, type_t) \ ^ C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include/samtools/kseq.h:226:35: note: in expansion of macro 'KSEQ_INIT2' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ io.c:28:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(FILE_TYPE*, gzreadclone) ^ C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o qrqc.dll tmp.def R_init_io.o io.o C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/qrqc.buildbin-libdir/qrqc/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'qrqc' as qrqc_1.34.0.zip * DONE (qrqc) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'qrqc' successfully unpacked and MD5 sums checked In R CMD INSTALL
qrqc.Rcheck/tests_i386/test-functions.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. > ## test-functions.R - unit test some functions > require(testthat) Loading required package: testthat > EPSILON <- 0.001 > > test_that(".trimRightCols", { + t1 <- matrix(c(2, 3, 4, 5, 0, 4, 0, 0), 2, 4) + expect_that(qrqc:::.trimRightCols(t1), is_equivalent_to(t1[, -4])) + }) > > test_that(".trimArray", { + t1 <- c(2, 3, 4, 5, 0, 4, 0, 0) + expect_that(qrqc:::.trimArray(t1), is_equivalent_to(t1[1:6])) + }) > > > test_that("length2weights", { + l <- c(0, 0, 0, 0, 10, 20, 30, 40) + expect_that(qrqc:::lengths2weights(l), + is_equivalent_to(c(100, 100, 100, 100, 100, 90, 70, 40))) + }) > > test_that("meanFromBins", { + m1 <- structure(list(`26` = c(2L, 0L, 0L, 2L, 3L, 0L, 0L, 0L, 1L, 0L), + `27` = c(1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L), + `28` = c(3L, 7L, 5L, 4L, 4L, 1L, 0L, 3L, 2L, 2L), + `29` = c(1L, 0L, 1L, 1L, 1L, 3L, 0L, 4L, 1L, 1L), + `30` = c(4L, 2L, 5L, 3L, 4L, 3L, 3L, 4L, 3L, 5L), + `31` = c(0L, 0L, 2L, 0L, 1L, 1L, 1L, 1L, 1L, 3L), + `32` = c(3L, 8L, 3L, 2L, 7L, 5L, 0L, 4L, 8L, 4L), + `33` = c(4L, 1L, 3L, 3L, 4L, 2L, 1L, 5L, 1L, 5L), + `34` = c(2L, 6L, 3L, 1L, 3L, 2L, 12L, 4L, 4L, 1L), + `35` = c(10L, 6L, 11L, 14L, 8L, 13L, 8L, 13L, 12L, 13L), + `36` = c(14L, 13L, 16L, 15L, 14L, 18L, 21L, 15L, 20L, 16L)), + .Names = c("26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36"), + row.names = c(NA, 10L), class = "data.frame") + m1 <- cbind(position=1:nrow(m1), m1) + expect_that(qrqc:::meanFromBins(m1) - 33.60487 < EPSILON, is_true()) + }) > > test_that("binned2quantilefunc", { + b <- c(0, 1, 2, 3, 4, 5, 6, 7, 6, 5, 4, 3, 2, 1, 0) + names(b) <- 1:length(b) + f <- qrqc:::binned2quantilefunc(b) + expect_that(f(0.25), is_equivalent_to(5.45)) + expect_that(f(0.5), is_equivalent_to(7.5)) + expect_that(f(0.75), is_equivalent_to(9.55)) + }) > > test_that("binned2boxplot", { + b <- c(0, 1, 2, 3, 4, 5, 6, 7, 6, 5, 4, 3, 2, 1, 0) + names(b) <- 1:length(b) + f <- qrqc:::binned2quantilefunc(b) + ans <- structure(c(2, 3.63333333333333, 5.45, 7.5, 9.55, 11.3666666666667, 14), + .Names = c("ymin", "alt.lower", "lower", "middle", "upper", "alt.upper", "ymax")) + + expect_that(qrqc:::binned2boxplot(b), is_equivalent_to(ans)) + }) > > > test_that("calcKL", { + ## Check that our sample spaces sum to 1 + s.fastq <- qrqc:::readSeqFile(system.file('extdata', 'test.fastq', + package='qrqc'), hash.prop=1) + + eps <- 1e-4 + kld <- qrqc:::calcKL(s.fastq) + expect_that(all(with(kld, aggregate(p, list(position), sum))[, 2] - 1 < EPSILON), is_true()) + expect_that(all(with(kld, aggregate(q, list(position), sum))[, 2] - 1 < EPSILON), is_true()) + }) > > proc.time() user system elapsed 13.73 0.79 14.51 |
qrqc.Rcheck/tests_x64/test-functions.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. > ## test-functions.R - unit test some functions > require(testthat) Loading required package: testthat > EPSILON <- 0.001 > > test_that(".trimRightCols", { + t1 <- matrix(c(2, 3, 4, 5, 0, 4, 0, 0), 2, 4) + expect_that(qrqc:::.trimRightCols(t1), is_equivalent_to(t1[, -4])) + }) > > test_that(".trimArray", { + t1 <- c(2, 3, 4, 5, 0, 4, 0, 0) + expect_that(qrqc:::.trimArray(t1), is_equivalent_to(t1[1:6])) + }) > > > test_that("length2weights", { + l <- c(0, 0, 0, 0, 10, 20, 30, 40) + expect_that(qrqc:::lengths2weights(l), + is_equivalent_to(c(100, 100, 100, 100, 100, 90, 70, 40))) + }) > > test_that("meanFromBins", { + m1 <- structure(list(`26` = c(2L, 0L, 0L, 2L, 3L, 0L, 0L, 0L, 1L, 0L), + `27` = c(1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L), + `28` = c(3L, 7L, 5L, 4L, 4L, 1L, 0L, 3L, 2L, 2L), + `29` = c(1L, 0L, 1L, 1L, 1L, 3L, 0L, 4L, 1L, 1L), + `30` = c(4L, 2L, 5L, 3L, 4L, 3L, 3L, 4L, 3L, 5L), + `31` = c(0L, 0L, 2L, 0L, 1L, 1L, 1L, 1L, 1L, 3L), + `32` = c(3L, 8L, 3L, 2L, 7L, 5L, 0L, 4L, 8L, 4L), + `33` = c(4L, 1L, 3L, 3L, 4L, 2L, 1L, 5L, 1L, 5L), + `34` = c(2L, 6L, 3L, 1L, 3L, 2L, 12L, 4L, 4L, 1L), + `35` = c(10L, 6L, 11L, 14L, 8L, 13L, 8L, 13L, 12L, 13L), + `36` = c(14L, 13L, 16L, 15L, 14L, 18L, 21L, 15L, 20L, 16L)), + .Names = c("26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36"), + row.names = c(NA, 10L), class = "data.frame") + m1 <- cbind(position=1:nrow(m1), m1) + expect_that(qrqc:::meanFromBins(m1) - 33.60487 < EPSILON, is_true()) + }) > > test_that("binned2quantilefunc", { + b <- c(0, 1, 2, 3, 4, 5, 6, 7, 6, 5, 4, 3, 2, 1, 0) + names(b) <- 1:length(b) + f <- qrqc:::binned2quantilefunc(b) + expect_that(f(0.25), is_equivalent_to(5.45)) + expect_that(f(0.5), is_equivalent_to(7.5)) + expect_that(f(0.75), is_equivalent_to(9.55)) + }) > > test_that("binned2boxplot", { + b <- c(0, 1, 2, 3, 4, 5, 6, 7, 6, 5, 4, 3, 2, 1, 0) + names(b) <- 1:length(b) + f <- qrqc:::binned2quantilefunc(b) + ans <- structure(c(2, 3.63333333333333, 5.45, 7.5, 9.55, 11.3666666666667, 14), + .Names = c("ymin", "alt.lower", "lower", "middle", "upper", "alt.upper", "ymax")) + + expect_that(qrqc:::binned2boxplot(b), is_equivalent_to(ans)) + }) > > > test_that("calcKL", { + ## Check that our sample spaces sum to 1 + s.fastq <- qrqc:::readSeqFile(system.file('extdata', 'test.fastq', + package='qrqc'), hash.prop=1) + + eps <- 1e-4 + kld <- qrqc:::calcKL(s.fastq) + expect_that(all(with(kld, aggregate(p, list(position), sum))[, 2] - 1 < EPSILON), is_true()) + expect_that(all(with(kld, aggregate(q, list(position), sum))[, 2] - 1 < EPSILON), is_true()) + }) > > proc.time() user system elapsed 15.79 0.57 16.36 |
qrqc.Rcheck/examples_i386/qrqc-Ex.timings
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qrqc.Rcheck/examples_x64/qrqc-Ex.timings
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