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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:InPAS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings InPAS_2.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/InPAS.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘InPAS/DESCRIPTION’ ... OK
* this is package ‘InPAS’ version ‘2.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘InPAS’ 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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘adjust_distalCPs’ ‘adjust_proximalCPs’ ‘adjust_proximalCPsByNBC’
  ‘adjust_proximalCPsByPWM’ ‘calculate_mse’ ‘find_valleyBySpline’
  ‘get_PAscore’ ‘get_PAscore2’ ‘remove_convergentUTR3s’
  ‘search_distalCPs’ ‘search_proximalCPs’
* 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 ... WARNING
Missing link(s) in Rd file 'get_ssRleCov.Rd':
  ‘[BSgenome:BSgenomeForge]{BSgenome::forgeBSgenomeDataPkg()}’

Missing link(s) in Rd file 'set_globals.Rd':
  ‘[BSgenome:BSgenomeForge]{BSgenome::forgeBSgenomeDataPkg()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  UTR3eSet-class.Rd: GRanges-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'get_UTR3TotalCov.Rd':
  ‘gcCompensationensation’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
get_usage4plot   17.804  1.099  19.372
get_chromosomes   6.272  0.222   6.491
extract_UTR3Anno  5.831  0.318   6.205
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/InPAS.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL InPAS
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘InPAS’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (InPAS)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> pkgs_required <- c(
+   "BSgenome.Mmusculus.UCSC.mm10",
+   "TxDb.Mmusculus.UCSC.mm10.knownGene",
+   "EnsDb.Mmusculus.v79",
+   "rtracklayer",
+   "GenomicRanges",
+   "RUnit",
+   "limma", "future.apply"
+ )
> for (pkg in pkgs_required)
+ {
+   require(pkg, character.only = TRUE) || stop(pkg, " can't be loaded!")
+ }
Loading required package: BSgenome.Mmusculus.UCSC.mm10
Loading required package: BSgenome
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

The following object is masked from 'package:BiocIO':

    FileForFormat

Loading required package: TxDb.Mmusculus.UCSC.mm10.knownGene
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: EnsDb.Mmusculus.v79
Loading required package: ensembldb
Loading required package: AnnotationFilter

Attaching package: 'ensembldb'

The following object is masked from 'package:stats':

    filter

Loading required package: RUnit
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: future.apply
Loading required package: future

Attaching package: 'future'

The following object is masked from 'package:AnnotationFilter':

    value

> 
> BiocGenerics:::testPackage("InPAS")
InPAS : Version 2.15.0
For more information see our website : https://bioconductor.org/packages/release/bioc/vignettes/InPAS/inst/doc/InPAS.html
If you encounter a bug, please report : https://github.com/jianhong/InPAS/InPAS/issues
coverage per sample per chromosome start at Wed Nov 27 23:10:30 2024.

coverage per sample per chromosome done at Wed Nov 27 23:10:30 2024.

total coverage start at Wed Nov 27 23:10:30 2024.

total coverage done at Wed Nov 27 23:10:30 2024.

backgroud around 3utr done at Wed Nov 27 23:10:30 2024.

utr3 TotalCov done at Wed Nov 27 23:10:30 2024.

chromsome chr1 coverage merged.

Preparation for CPsite search done at Wed Nov 27 23:10:30 2024.

No readable configuration file found
Created registry in '/private/tmp/RtmpvEdYXe/006.CPsites.out_chr1' using cluster functions 'Interactive'
Adding 1 jobs ...
Submitting 1 jobs in 1 chunks using cluster functions 'Interactive' ...
coverage per sample per chromosome start at Wed Nov 27 23:10:37 2024.

coverage per sample per chromosome done at Wed Nov 27 23:10:37 2024.

total coverage start at Wed Nov 27 23:10:37 2024.

total coverage done at Wed Nov 27 23:10:37 2024.

backgroud around 3utr done at Wed Nov 27 23:10:37 2024.

utr3 TotalCov done at Wed Nov 27 23:10:37 2024.

chromsome chr1 coverage merged.

Preparation for CPsite search done at Wed Nov 27 23:10:37 2024.

No readable configuration file found
Created registry in '/private/tmp/RtmpvEdYXe/006.CPsites.out_chr1' using cluster functions 'Interactive'
Adding 1 jobs ...
Submitting 1 jobs in 1 chunks using cluster functions 'Interactive' ...
Error in get_ssRleCov(bedgraph = filenames[i], tag = tags[i], genome = genome,  : 
  seqlevelsStyle of genome is different from bedgraph file.


RUNIT TEST PROTOCOL -- Wed Nov 27 23:10:38 2024 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
InPAS RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 27.115   1.299  28.644