Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘gDNAx/DESCRIPTION’ ... OK
* preparing ‘gDNAx’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘gDNAx_0.99.8.tar.gz’

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 BiocCheckGitClone('gDNAx')

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─ BiocCheckVersion: 1.37.10
─ BiocVersion: 3.18
─ Package: gDNAx
─ PackageVersion: 0.99.8
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3082/11bdc19185a103e4c5580f666713d6e7053c4947/gDNAx
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3082/11bdc19185a103e4c5580f666713d6e7053c4947/gDNAx.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDNAx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDNAx’ version ‘0.99.8’
* package encoding: UTF-8
* 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 ‘gDNAx’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘GenomicAlignments:::.make_GAlignmentPairs_from_GAlignments’
  ‘GenomicAlignments:::.normargParam’ ‘S4Vectors:::makePowersOfTwo’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [29s/30s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 files in ‘vignettes’ ... OK
* checking examples ... [138s/166s] ERROR
Running examples in ‘gDNAx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gDNAdx
> ### Title: Calculate gDNA diagnostics
> ### Aliases: gDNAdx plot,gDNAx,ANY-method plotAlnOrigins plotFrgLength
> 
> ### ** Examples
> 
> library(gDNAinRNAseqData)
> 
> library(TxDb.Hsapiens.UCSC.hg38.knownGene)
Loading required package: GenomicFeatures
Loading required package: BiocGenerics

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, 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: 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")'.

> txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
> 
> # Retrieving BAM files
> bamfiles <- LiYu22subsetBAMfiles()
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
require(“Rsamtools”)
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
> 
> # Getting information about the gDNA concentrations of each BAM file
> pdat <- LiYu22phenoData(bamfiles)
> 
> gdnax <- gDNAdx(bamfiles, txdb, singleEnd=FALSE, strandMode=NA)
Fetching annotations for hg38
Start processing BAM file(s)
Reading first 100000 alignments from s32gDNA0.bam
Processing alignments from s32gDNA0.bam
Reading first 100000 alignments from s33gDNA0.bam
Processing alignments from s33gDNA0.bam
Reading first 100000 alignments from s34gDNA0.bam
Processing alignments from s34gDNA0.bam
Reading first 100000 alignments from s26gDNA1.bam
Processing alignments from s26gDNA1.bam
Reading first 100000 alignments from s27gDNA1.bam
Processing alignments from s27gDNA1.bam
Reading first 100000 alignments from s28gDNA1.bam
Processing alignments from s28gDNA1.bam
Reading first 100000 alignments from s23gDNA10.bam
Processing alignments from s23gDNA10.bam
Reading first 100000 alignments from s24gDNA10.bam
Processing alignments from s24gDNA10.bam
Reading first 100000 alignments from s25gDNA10.bam
Processing alignments from s25gDNA10.bam
Collecting diagnostics
> gdnax
gDNAx object
# BAM files (9): s32gDNA0.bam, ..., s25gDNA10.bam
# Library layout: paired-end (2x50nt)
# Strand mode: NA
# Sequences: only standard chromosomes
# Annotation pkg: TxDb.Hsapiens.UCSC.hg38.knownGene
# Alignments employed: first 100000
> 
> library(gDNAinRNAseqData)
> 
> library(TxDb.Hsapiens.UCSC.hg38.knownGene)
> txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
> 
> # Retrieving BAM files
> bamfiles <- LiYu22subsetBAMfiles()
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
> 
> # Getting information about the gDNA concentrations of each BAM file
> pdat <- LiYu22phenoData(bamfiles)
> 
> # Getting the 'gDNAx' object. Can be done using the commented code
> # gdnax <- gDNAdx(bamfiles, txdb, singleEnd=FALSE, strandMode=NA)
> 
> # Here to reduce example running time, the 'gDNAx' object is loaded
> gdnax <- file.path(system.file("extdata", package="gDNAx"), "gdnax.rds")
> 
> # plot gDNA diagnostic measures
> plot(gdnax, group=pdat$gDNA, pch=19)
Warning in xy.coords(x, y, xlabel, ylabel, log) :
  NAs introduced by coercion
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Warning in plot.window(...) : "group" is not a graphical parameter
Error in plot.window(...) : need finite 'ylim' values
Calls: plot -> plot -> plot.default -> localWindow -> plot.window
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [163s/213s]
 [163s/213s] 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 ... [5s/5s] OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3082/11bdc19185a103e4c5580f666713d6e7053c4947/gDNAx.Rcheck/00check.log’
for details.





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 BiocCheck('gDNAx_0.99.8.tar.gz')

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─ BiocCheckVersion: 1.37.10
─ BiocVersion: 3.18
─ Package: gDNAx
─ PackageVersion: 0.99.8
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXdqiYR/file131d26590c743/gDNAx
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXdqiYR/file131d239ced9cd
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3082/11bdc19185a103e4c5580f666713d6e7053c4947/gDNAx.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
    * NOTE: Consider adding these automatically suggested biocViews:
      LongRead
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of gDNAx...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6
      times)
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 21 lines (1%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 72 lines
      (2%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 6 NOTES

See the gDNAx.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir gDNAx_0.99.8.tar.gz'
>>>>>>> 

* installing *source* package ‘gDNAx’ ...
** 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 (gDNAx)