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This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1400/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nuCpos 1.18.0  (landing page)
Hiroaki Kato
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/nuCpos
git_branch: RELEASE_3_17
git_last_commit: 3aa150e
git_last_commit_date: 2023-04-25 11:03:43 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for nuCpos on kjohnson2


To the developers/maintainers of the nuCpos package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: nuCpos
Version: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2023-10-18 11:55:57 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 11:57:04 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 66.7 seconds
RetCode: 0
Status:   OK  
CheckDir: nuCpos.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/nuCpos.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nuCpos/DESCRIPTION’ ... OK
* this is package ‘nuCpos’ version ‘1.18.0’
* 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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    2.2Mb    998Kb       xz
* 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’
 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-3.17-bioc-mac-arm64/meat/nuCpos.Rcheck/00check.log’
for details.

Installation output

nuCpos.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL nuCpos
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘nuCpos’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (nuCpos)

Tests output

nuCpos.Rcheck/tests/test_HBA.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
  0.215   0.067   0.443

nuCpos.Rcheck/tests/test_localHBA.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
  0.212   0.065   0.447

Example timings

nuCpos.Rcheck/nuCpos-Ex.timings

nameusersystemelapsed
HBA3.0680.1334.905
localHBA0.0200.0020.032
nuCpos-package0.0080.0010.013