Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file DegCre/DESCRIPTION ... OK
* preparing DegCre:
* 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
* looking to see if a data/datalist file should be added
* building DegCre_0.99.9.tar.gz

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 BiocCheckGitClone('DegCre')

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 BiocCheckVersion: 1.39.25
 BiocVersion: 3.19
 Package: DegCre
 PackageVersion: 0.99.9
 sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3265/b89e13f52ba4572523e65bbd06a3f30373089255/DegCre
 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...
* Checking that provided CITATION file is correctly formatted...

 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/3265/b89e13f52ba4572523e65bbd06a3f30373089255/DegCre.Rcheck
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option --no-vignettes
* checking for file DegCre/DESCRIPTION ... OK
* checking extension type ... Package
* this is package DegCre version 0.99.9
* 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 DegCre 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 ... WARNING
Dependence on R version 4.2.1 not with patchlevel 0
* 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [12s/12s] OK
* checking use of S3 registration ... 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 ... [41s/41s] OK
* checking Rd files ... [0s/0s] WARNING
checkRd: (7) DexNR3C1.Rd:30: Invalid URL: \url{https://bioconductor.org/packages/release/bioc/html/csaw.html}
checkRd: (7) DexNR3C1.Rd:32: Invalid URL: \url{https://bioconductor.org/packages/release/bioc/html/csaw.html}
checkRd: (7) DexNR3C1.Rd:34: Invalid URL: \url{https://bioconductor.org/packages/release/bioc/html/csaw.html}
checkRd: (7) plotBrowserDegCre.Rd:88: Invalid URL: \url{https://bioconductor.org/packages/release/bioc/html/plotgardener.html}
checkRd: (7) plotBrowserDegCre.Rd:132: Invalid URL: \url{https://bioconductor.org/packages/release/bioc/html/plotgardener.html}
checkRd: (7) runDegCre.Rd:127: Invalid URL: \url{https://bioconductor.org/packages/release/bioc/html/csaw.html}
* 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 contents of data directory ... OK
* checking data for non-ASCII characters ... [3s/3s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [80s/80s] ERROR
Running examples in DegCre-Ex.R failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: runDegCre
> ### Title: Generate DegCre associations
> ### Aliases: runDegCre
> 
> ### ** Examples
> 
> #Load required packages.
> library(GenomicRanges)
Loading required package: stats4
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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

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
> 
> #Load sample data.
> data(DexNR3C1)
> 
> subDegGR <-
+  DexNR3C1$DegGR[which(GenomicRanges::seqnames(DexNR3C1$DegGR)=="chr1")]
> subCreGR <-
+  DexNR3C1$CreGR[which(GenomicRanges::seqnames(DexNR3C1$CreGR)=="chr1")]
> 
> #With defaults.
> degCreResListDexNR3C1 <- runDegCre(DegGR=subDegGR,
+                                    DegP=subDegGR$pVal,
+                                    DegLfc=subDegGR$logFC,
+                                    CreGR=subCreGR,
+                                    CreP=subCreGR$pVal,
+                                    CreLfc=subCreGR$logFC)
Analyzing 34169 DegGR to CreGR hits for optimal distance bin size.
Hit distance bin n = 2277
Small last bin resolved.
Running over 16 hit distance thresholds
Adjusting association probability for distance.
Calculation of assoc probabilities over hit bins complete.
Assoc FDR calculation complete.
DegCre calculations complete.
> 
> #With custom settings.
> modDegCreResList <- runDegCre(DegGR=subDegGR,
+                            DegP=subDegGR$DegGR$pVal,
+                            CreGR=subCreGR,
+                            CreP=subCreGR$pVal,
+                            reqEffectDirConcord=FALSE,
+                            maxDist=1e5,
+                            alphaVal=0.001)
Error in `[[<-`(`*tmp*`, name, value = numeric(0)) : 
  0 elements in value to replace 2791 elements
Calls: runDegCre -> $<- -> $<- -> [[<- -> [[<-
Execution halted
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running testthat.R [63s/63s]
 [63s/63s] 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 ... [7s/7s] OK
* DONE

Status: 1 ERROR, 2 WARNINGs
See
  /Users/pkgbuild/packagebuilder/workers/jobs/3265/b89e13f52ba4572523e65bbd06a3f30373089255/DegCre.Rcheck/00check.log
for details.





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 BiocCheck('DegCre_0.99.9.tar.gz')

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 BiocCheckVersion: 1.39.25
 BiocVersion: 3.19
 Package: DegCre
 PackageVersion: 0.99.9
 sourceDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//RtmpIEbKcj/file16dd148080f43/DegCre
 installDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//RtmpIEbKcj/file16dd11e871ca0
 BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3265/b89e13f52ba4572523e65bbd06a3f30373089255/DegCre.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...
    * NOTE: Update R version dependency from 4.2.1 to 4.4.0.
* 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...
* 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (57%).
* Checking for pinned package versions in DESCRIPTION...
* 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 DegCre...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 12 functions greater than 50 lines.
* 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; 26 lines (1%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 572 lines
      (15%) 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 is in the Support Site Watched Tags.

 BiocCheck results 
0 ERRORS | 0 WARNINGS | 4 NOTES

See the DegCre.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 DegCre_0.99.9.tar.gz'
>>>>>>> 

* installing *source* package DegCre ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (DegCre)