===============================
BiocCheckGitClone('DegCre')
===============================
─ BiocCheckVersion: 1.39.25
─ BiocVersion: 3.19
─ Package: DegCre
─ PackageVersion: 0.99.9
─ sourceDir: /home/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')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3265/b89e13f52ba4572523e65bbd06a3f30373089255/DegCre.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* 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 ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] 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 ... [37s/37s] 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 ... [78s/78s] 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’ [58s/58s]
[59s/59s] 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 ... [3s/3s] OK
* DONE
Status: 1 ERROR, 2 WARNINGs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3265/b89e13f52ba4572523e65bbd06a3f30373089255/DegCre.Rcheck/00check.log’
for details.
===============================
BiocCheck('DegCre_0.99.9.tar.gz')
===============================
─ BiocCheckVersion: 1.39.25
─ BiocVersion: 3.19
─ Package: DegCre
─ PackageVersion: 0.99.9
─ sourceDir: /tmp/Rtmphp0Uck/file2e098125c03cbf/DegCre
─ installDir: /tmp/Rtmphp0Uck/file2e098141f27b6b
─ BiocCheckDir: /home/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.