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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nuCpos.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nuCpos_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/nuCpos.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nuCpos/DESCRIPTION’ ... OK
* this is package ‘nuCpos’ version ‘1.14.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... NOTE
File ‘nuCpos/libs/nuCpos.so’:
  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’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘nuCpos_1.o’, ‘nuCpos_2.o’
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/nuCpos.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL nuCpos
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘nuCpos’ ...
** using staged installation
** libs
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c  HBA_3.f90 -o HBA_3.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_nuCpos.c -o R_init_nuCpos.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c  localHBA_3.f90 -o localHBA_3.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c  nuCpos2_1.f90 -o nuCpos2_1.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c  nuCpos2_2.f90 -o nuCpos2_2.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c  nuCpos_1.f90 -o nuCpos_1.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c  nuCpos_2.f90 -o nuCpos_2.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o nuCpos.so HBA_3.o R_init_nuCpos.o localHBA_3.o nuCpos2_1.o nuCpos2_2.o nuCpos_1.o nuCpos_2.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-nuCpos/00new/nuCpos/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (nuCpos)

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  0.326   0.073   0.375 

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  0.343   0.078   0.396 

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  0.344   0.080   0.398 

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  0.335   0.076   0.386