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This page was generated on 2020-10-17 11:57:17 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE nuCpos PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1209/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
nuCpos 1.6.0 Hiroaki Kato
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK |
Package: nuCpos |
Version: 1.6.0 |
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nuCpos.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings nuCpos_1.6.0.tar.gz |
StartedAt: 2020-10-17 06:31:58 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 06:32:43 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 45.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: nuCpos.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nuCpos.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings nuCpos_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/nuCpos.Rcheck' * using R version 4.0.3 (2020-10-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'nuCpos/DESCRIPTION' ... OK * this is package 'nuCpos' version '1.6.0' * 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 'nuCpos' can be installed ... OK * 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 R/sysdata.rda ... NOTE Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress sysdata.rda 824Kb 495Kb bzip2 * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... WARNING File 'nuCpos/libs/i386/nuCpos.dll': Found '_gfortran_st_close', possibly from 'close' (Fortran) Objects: 'nuCpos_1.o', 'nuCpos_2.o' Found '_gfortran_st_open', possibly from 'open' (Fortran) Objects: 'nuCpos_1.o', 'nuCpos_2.o' 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. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'test_HBA.R' Running 'test_localHBA.R' Running 'test_mutNuCpos.R' Running 'test_predNuCposActLikePredNuPoP.R' OK ** running tests for arch 'x64' ... Running 'test_HBA.R' Running 'test_localHBA.R' Running 'test_mutNuCpos.R' Running 'test_predNuCposActLikePredNuPoP.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-3.11-bioc/meat/nuCpos.Rcheck/00check.log' for details.
nuCpos.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/nuCpos_1.6.0.tar.gz && rm -rf nuCpos.buildbin-libdir && mkdir nuCpos.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nuCpos.buildbin-libdir nuCpos_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL nuCpos_1.6.0.zip && rm nuCpos_1.6.0.tar.gz nuCpos_1.6.0.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 836k 100 836k 0 0 11.5M 0 --:--:-- --:--:-- --:--:-- 12.9M install for i386 * installing *source* package 'nuCpos' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gfortran -fno-optimize-sibling-calls -O2 -mfpmath=sse -msse2 -mstackrealign -c HBA_3.f90 -o HBA_3.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_nuCpos.c -o R_init_nuCpos.o "C:/rtools40/mingw32/bin/"gfortran -fno-optimize-sibling-calls -O2 -mfpmath=sse -msse2 -mstackrealign -c localHBA_3.f90 -o localHBA_3.o "C:/rtools40/mingw32/bin/"gfortran -fno-optimize-sibling-calls -O2 -mfpmath=sse -msse2 -mstackrealign -c nuCpos2_1.f90 -o nuCpos2_1.o "C:/rtools40/mingw32/bin/"gfortran -fno-optimize-sibling-calls -O2 -mfpmath=sse -msse2 -mstackrealign -c nuCpos2_2.f90 -o nuCpos2_2.o "C:/rtools40/mingw32/bin/"gfortran -fno-optimize-sibling-calls -O2 -mfpmath=sse -msse2 -mstackrealign -c nuCpos_1.f90 -o nuCpos_1.o "C:/rtools40/mingw32/bin/"gfortran -fno-optimize-sibling-calls -O2 -mfpmath=sse -msse2 -mstackrealign -c nuCpos_2.f90 -o nuCpos_2.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o nuCpos.dll tmp.def HBA_3.o R_init_nuCpos.o localHBA_3.o nuCpos2_1.o nuCpos2_2.o nuCpos_1.o nuCpos_2.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/nuCpos.buildbin-libdir/00LOCK-nuCpos/00new/nuCpos/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'nuCpos' finding HTML links ... done HBA html localHBA html mutNuCpos html nuCpos-package html predNuCpos 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 'nuCpos' ... ** libs "C:/rtools40/mingw64/bin/"gfortran -fno-optimize-sibling-calls -O2 -mfpmath=sse -msse2 -mstackrealign -c HBA_3.f90 -o HBA_3.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_nuCpos.c -o R_init_nuCpos.o "C:/rtools40/mingw64/bin/"gfortran -fno-optimize-sibling-calls -O2 -mfpmath=sse -msse2 -mstackrealign -c localHBA_3.f90 -o localHBA_3.o "C:/rtools40/mingw64/bin/"gfortran -fno-optimize-sibling-calls -O2 -mfpmath=sse -msse2 -mstackrealign -c nuCpos2_1.f90 -o nuCpos2_1.o "C:/rtools40/mingw64/bin/"gfortran -fno-optimize-sibling-calls -O2 -mfpmath=sse -msse2 -mstackrealign -c nuCpos2_2.f90 -o nuCpos2_2.o "C:/rtools40/mingw64/bin/"gfortran -fno-optimize-sibling-calls -O2 -mfpmath=sse -msse2 -mstackrealign -c nuCpos_1.f90 -o nuCpos_1.o "C:/rtools40/mingw64/bin/"gfortran -fno-optimize-sibling-calls -O2 -mfpmath=sse -msse2 -mstackrealign -c nuCpos_2.f90 -o nuCpos_2.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o nuCpos.dll tmp.def HBA_3.o R_init_nuCpos.o localHBA_3.o nuCpos2_1.o nuCpos2_2.o nuCpos_1.o nuCpos_2.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/nuCpos.buildbin-libdir/nuCpos/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'nuCpos' as nuCpos_1.6.0.zip * DONE (nuCpos) * installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library' package 'nuCpos' successfully unpacked and MD5 sums checked
nuCpos.Rcheck/tests_i386/test_HBA.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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_HBA <- function(){ + load(system.file("extdata","inseq.RData",package="nuCpos")) + load(system.file("extdata","INSEQ_DNAString.RData",package="nuCpos")) + inseq.N <- gsub(pattern = "A", replacement = "N", inseq) + mm.HBA <- -5.108546 + sc.HBA <- -2.460025 + sp.HBA <- -2.627370 + expect_equal(unname(HBA(inseq, species = "mm", silent = TRUE)), + mm.HBA, tolerance = 1.0e-6) + expect_equal(unname(HBA(inseq, species = "sc", silent = TRUE)), + sc.HBA, tolerance = 1.0e-6) + expect_equal(unname(HBA(inseq, species = "sp", silent = TRUE)), + sp.HBA, tolerance = 1.0e-6) + expect_equal(unname(HBA(INSEQ, species = "mm", silent = TRUE)), + mm.HBA, tolerance = 1.0e-6) + expect_equal(unname(HBA(INSEQ, species = "sc", silent = TRUE)), + sc.HBA, tolerance = 1.0e-6) + expect_equal(unname(HBA(INSEQ, species = "sp", silent = TRUE)), + sp.HBA, tolerance = 1.0e-6) + expect_true(is.na(HBA("AAA", species = "mm", silent = TRUE))) + expect_true(is.na(HBA(123, species = "mm", silent = TRUE))) + expect_true(is.na(HBA(inseq.N, species = "mm", silent = TRUE))) + } > > proc.time() user system elapsed 0.31 0.04 0.32 |
nuCpos.Rcheck/tests_x64/test_HBA.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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_HBA <- function(){ + load(system.file("extdata","inseq.RData",package="nuCpos")) + load(system.file("extdata","INSEQ_DNAString.RData",package="nuCpos")) + inseq.N <- gsub(pattern = "A", replacement = "N", inseq) + mm.HBA <- -5.108546 + sc.HBA <- -2.460025 + sp.HBA <- -2.627370 + expect_equal(unname(HBA(inseq, species = "mm", silent = TRUE)), + mm.HBA, tolerance = 1.0e-6) + expect_equal(unname(HBA(inseq, species = "sc", silent = TRUE)), + sc.HBA, tolerance = 1.0e-6) + expect_equal(unname(HBA(inseq, species = "sp", silent = TRUE)), + sp.HBA, tolerance = 1.0e-6) + expect_equal(unname(HBA(INSEQ, species = "mm", silent = TRUE)), + mm.HBA, tolerance = 1.0e-6) + expect_equal(unname(HBA(INSEQ, species = "sc", silent = TRUE)), + sc.HBA, tolerance = 1.0e-6) + expect_equal(unname(HBA(INSEQ, species = "sp", silent = TRUE)), + sp.HBA, tolerance = 1.0e-6) + expect_true(is.na(HBA("AAA", species = "mm", silent = TRUE))) + expect_true(is.na(HBA(123, species = "mm", silent = TRUE))) + expect_true(is.na(HBA(inseq.N, species = "mm", silent = TRUE))) + } > > proc.time() user system elapsed 0.21 0.04 0.25 |
nuCpos.Rcheck/tests_i386/test_localHBA.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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_localHBA <- function(){ + load(system.file("extdata","inseq.RData",package="nuCpos")) + load(system.file("extdata","INSEQ_DNAString.RData",package="nuCpos")) + inseq.N <- gsub(pattern = "A", replacement = "N", inseq) + mm.lHBA <- c(-1.26144039, -1.60878614, 0.04168163, + 0.67028283, 0.64609413, -2.04965343, -2.87359702, + -0.23010702, -0.45807823, -0.46043330, -0.45175477, + 0.02487367, -0.30991794) + sc.lHBA <- c(-1.56140949, -1.62502354, 0.48885990, + 2.37615568, 2.90458625, -1.35195919, -3.13228907, + -0.32208031, 0.27650871, 0.01922002, 0.49787625, + -0.17151500, -1.27186158) + sp.lHBA <- c(-1.566757163, -2.249651890, 1.188983606, + 1.808008192, 2.304915648, -0.290338951, -1.741081053, + -0.093952092, 0.119058916, -1.335654721, -0.001721381, + 0.244317796, -0.968842314) + expect_equal(unname(localHBA(inseq, species = "mm", silent = TRUE)), + mm.lHBA, tolerance = 1.0e-6) + expect_equal(unname(localHBA(inseq, species = "sc", silent = TRUE)), + sc.lHBA, tolerance = 1.0e-6) + expect_equal(unname(localHBA(inseq, species = "sp", silent = TRUE)), + sp.lHBA, tolerance = 1.0e-6) + expect_equal(unname(localHBA(INSEQ, species = "mm", silent = TRUE)), + mm.lHBA, tolerance = 1.0e-6) + expect_equal(unname(localHBA(INSEQ, species = "sc", silent = TRUE)), + sc.lHBA, tolerance = 1.0e-6) + expect_equal(unname(localHBA(INSEQ, species = "sp", silent = TRUE)), + sp.lHBA, tolerance = 1.0e-6) + expect_true(is.na(localHBA("AAA", species = "mm", silent = TRUE))) + expect_true(is.na(localHBA(123, species = "mm", silent = TRUE))) + expect_true(is.na(localHBA(inseq.N, species = "mm", silent = TRUE))) + } > > proc.time() user system elapsed 0.25 0.06 0.29 |
nuCpos.Rcheck/tests_x64/test_localHBA.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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_localHBA <- function(){ + load(system.file("extdata","inseq.RData",package="nuCpos")) + load(system.file("extdata","INSEQ_DNAString.RData",package="nuCpos")) + inseq.N <- gsub(pattern = "A", replacement = "N", inseq) + mm.lHBA <- c(-1.26144039, -1.60878614, 0.04168163, + 0.67028283, 0.64609413, -2.04965343, -2.87359702, + -0.23010702, -0.45807823, -0.46043330, -0.45175477, + 0.02487367, -0.30991794) + sc.lHBA <- c(-1.56140949, -1.62502354, 0.48885990, + 2.37615568, 2.90458625, -1.35195919, -3.13228907, + -0.32208031, 0.27650871, 0.01922002, 0.49787625, + -0.17151500, -1.27186158) + sp.lHBA <- c(-1.566757163, -2.249651890, 1.188983606, + 1.808008192, 2.304915648, -0.290338951, -1.741081053, + -0.093952092, 0.119058916, -1.335654721, -0.001721381, + 0.244317796, -0.968842314) + expect_equal(unname(localHBA(inseq, species = "mm", silent = TRUE)), + mm.lHBA, tolerance = 1.0e-6) + expect_equal(unname(localHBA(inseq, species = "sc", silent = TRUE)), + sc.lHBA, tolerance = 1.0e-6) + expect_equal(unname(localHBA(inseq, species = "sp", silent = TRUE)), + sp.lHBA, tolerance = 1.0e-6) + expect_equal(unname(localHBA(INSEQ, species = "mm", silent = TRUE)), + mm.lHBA, tolerance = 1.0e-6) + expect_equal(unname(localHBA(INSEQ, species = "sc", silent = TRUE)), + sc.lHBA, tolerance = 1.0e-6) + expect_equal(unname(localHBA(INSEQ, species = "sp", silent = TRUE)), + sp.lHBA, tolerance = 1.0e-6) + expect_true(is.na(localHBA("AAA", species = "mm", silent = TRUE))) + expect_true(is.na(localHBA(123, species = "mm", silent = TRUE))) + expect_true(is.na(localHBA(inseq.N, species = "mm", silent = TRUE))) + } > > proc.time() user system elapsed 0.26 0.01 0.28 |
nuCpos.Rcheck/tests_i386/test_mutNuCpos.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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_mutNuCpos <- function(){ + TALS <- paste(scan(file = system.file("extdata", "TALS.fasta", + package="nuCpos"), what = character(), skip = 1), sep = "", + collapse = "") + TTAGGGx12 <- paste(scan(file = system.file("extdata", + "TTAGGGx12.fasta", package="nuCpos"), what = character(), + skip = 1), sep = "", collapse = "") + results <- mutNuCpos(TALS, site = 1464, ins= TTAGGGx12, species="sc", + prob.dyad = TRUE, smoothHBA=TRUE, plot.window = 601, + ylim.HBA = c(-11, 0), + annotation = data.frame(name = "alpha2", + color = "purple", left = 1534, right = 1559), full = TRUE) + expect_equal(results$results$pstart[101], 0.0005697254, tolerance = 1.0e-8) + expect_equal(results$results$nucoccup[101], 0.9874718, tolerance = 1.0e-6) + expect_equal(results$results$viterbi[101], 1) + expect_equal(results$results$affinity[101], -0.89849, tolerance = 1.0e-5) + expect_equal(results$results$pos[101], -3673) + } > > proc.time() user system elapsed 0.25 0.04 0.28 |
nuCpos.Rcheck/tests_x64/test_mutNuCpos.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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_mutNuCpos <- function(){ + TALS <- paste(scan(file = system.file("extdata", "TALS.fasta", + package="nuCpos"), what = character(), skip = 1), sep = "", + collapse = "") + TTAGGGx12 <- paste(scan(file = system.file("extdata", + "TTAGGGx12.fasta", package="nuCpos"), what = character(), + skip = 1), sep = "", collapse = "") + results <- mutNuCpos(TALS, site = 1464, ins= TTAGGGx12, species="sc", + prob.dyad = TRUE, smoothHBA=TRUE, plot.window = 601, + ylim.HBA = c(-11, 0), + annotation = data.frame(name = "alpha2", + color = "purple", left = 1534, right = 1559), full = TRUE) + expect_equal(results$results$pstart[101], 0.0005697254, tolerance = 1.0e-8) + expect_equal(results$results$nucoccup[101], 0.9874718, tolerance = 1.0e-6) + expect_equal(results$results$viterbi[101], 1) + expect_equal(results$results$affinity[101], -0.89849, tolerance = 1.0e-5) + expect_equal(results$results$pos[101], -3673) + } > > proc.time() user system elapsed 0.25 0.03 0.28 |
nuCpos.Rcheck/tests_i386/test_predNuCposActLikePredNuPoP.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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_predNuCposActLikePredNuPoP <- function(){ + predNuCposActLikePredNuPoP(system.file("extdata", "test.seq", + package="nuCpos"), species="mm", smoothHBA=FALSE, + std=FALSE) + results <- read.table(file = "test.seq_Prediction4.txt", skip = 1) + expect_equal(results$V1[101], 101) + expect_equal(results$V2[101], 0.001) + expect_equal(results$V3[101], 0.742) + expect_equal(results$V4[101], 0) + expect_equal(results$V5[101], -2.303) + } > > proc.time() user system elapsed 0.20 0.06 0.25 |
nuCpos.Rcheck/tests_x64/test_predNuCposActLikePredNuPoP.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > test_predNuCposActLikePredNuPoP <- function(){ + predNuCposActLikePredNuPoP(system.file("extdata", "test.seq", + package="nuCpos"), species="mm", smoothHBA=FALSE, + std=FALSE) + results <- read.table(file = "test.seq_Prediction4.txt", skip = 1) + expect_equal(results$V1[101], 101) + expect_equal(results$V2[101], 0.001) + expect_equal(results$V3[101], 0.742) + expect_equal(results$V4[101], 0) + expect_equal(results$V5[101], -2.303) + } > > proc.time() user system elapsed 0.20 0.06 0.25 |
nuCpos.Rcheck/examples_i386/nuCpos-Ex.timings
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nuCpos.Rcheck/examples_x64/nuCpos-Ex.timings
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