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CHECK report for nuCpos on riesling1

This page was generated on 2021-01-25 12:40:15 -0500 (Mon, 25 Jan 2021).

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 1214/1938HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nuCpos 1.9.0
Hiroaki Kato
Snapshot Date: 2021-01-24 14:40:26 -0500 (Sun, 24 Jan 2021)
URL: https://git.bioconductor.org/packages/nuCpos
Branch: master
Last Commit: 3d552b8
Last Changed Date: 2020-10-27 11:37:59 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: nuCpos
Version: 1.9.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nuCpos.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings nuCpos_1.9.0.tar.gz
StartedAt: 2021-01-24 21:17:31 -0500 (Sun, 24 Jan 2021)
EndedAt: 2021-01-24 21:18:08 -0500 (Sun, 24 Jan 2021)
EllapsedTime: 37.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: nuCpos.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nuCpos.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings nuCpos_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-bioc/meat/nuCpos.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* 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 '1.9.0'
* 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
  'D:/biocbuild/bbs-3.13-bioc/meat/nuCpos.Rcheck/00check.log'
for details.



Installation output

nuCpos.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/bioc/src/contrib/nuCpos_1.9.0.tar.gz && rm -rf nuCpos.buildbin-libdir && mkdir nuCpos.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nuCpos.buildbin-libdir nuCpos_1.9.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL nuCpos_1.9.0.zip && rm nuCpos_1.9.0.tar.gz nuCpos_1.9.0.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  81.6M      0 --:--:-- --:--:-- --:--:-- 90.7M

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"D:/biocbuild/bbs-3.13-bioc/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 -LD:/biocbuild/bbs-3.13-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.13-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  
REDIRECT:topic	 HBA -> HBA.html [ SUCCESS ]
    localHBA                                html  
REDIRECT:topic	 localHBA -> localHBA.html [ SUCCESS ]
    mutNuCpos                               html  
REDIRECT:topic	 mutNuCpos -> mutNuCpos.html [ SUCCESS ]
    nuCpos-package                          html  
REDIRECT:topic	 nuCpos-package -> nuCpos-package.html [ SUCCESS ]
REDIRECT:topic	 nuCpos -> nuCpos-package.html [ SUCCESS ]
    predNuCpos                              html  
REDIRECT:topic	 predNuCpos -> predNuCpos.html [ SUCCESS ]
** 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"D:/biocbuild/bbs-3.13-bioc/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 -LD:/biocbuild/bbs-3.13-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.13-bioc/meat/nuCpos.buildbin-libdir/nuCpos/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nuCpos' as nuCpos_1.9.0.zip
* DONE (nuCpos)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'nuCpos' successfully unpacked and MD5 sums checked

Tests output

nuCpos.Rcheck/tests_i386/test_HBA.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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 
   0.10    0.03    0.12 

nuCpos.Rcheck/tests_x64/test_HBA.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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 
   0.09    0.04    0.12 

nuCpos.Rcheck/tests_i386/test_localHBA.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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 
   0.14    0.01    0.14 

nuCpos.Rcheck/tests_x64/test_localHBA.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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 
   0.12    0.01    0.12 

nuCpos.Rcheck/tests_i386/test_mutNuCpos.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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 
   0.09    0.07    0.14 

nuCpos.Rcheck/tests_x64/test_mutNuCpos.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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 
   0.12    0.07    0.21 

nuCpos.Rcheck/tests_i386/test_predNuCposActLikePredNuPoP.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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 
   0.10    0.03    0.12 

nuCpos.Rcheck/tests_x64/test_predNuCposActLikePredNuPoP.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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    0.01    0.20 

Example timings

nuCpos.Rcheck/examples_i386/nuCpos-Ex.timings

nameusersystemelapsed
HBA0.010.000.01
localHBA0.020.000.02
mutNuCpos0.760.000.76
nuCpos-package0.020.000.04
predNuCpos0.120.000.15

nuCpos.Rcheck/examples_x64/nuCpos-Ex.timings

nameusersystemelapsed
HBA0.020.000.01
localHBA000
mutNuCpos1.050.031.10
nuCpos-package0.050.010.08
predNuCpos0.130.020.16