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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_0.99.4.tar.gz’
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BiocCheckGitClone('DegCre')
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─ BiocCheckVersion: 1.39.23
─ BiocVersion: 3.19
─ Package: DegCre
─ PackageVersion: 0.99.4
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3265/0d6714503fb988fa57381c12893c09fdbf6da75b/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 ‘/home/pkgbuild/packagebuilder/workers/jobs/3265/0d6714503fb988fa57381c12893c09fdbf6da75b/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 ‘0.99.4’
* 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 ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] 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 ... [33s/33s] 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 ... [573s/573s] ERROR
Running examples in ‘DegCre-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotBrowserDegCre
> ### Title: Make Browser Plots from DegCre Results
> ### Aliases: plotBrowserDegCre
>
> ### ** Examples
>
> #Load example data.
> data(DexNR3C1)
>
> #Generate DegCre results.
> degCreResListDexNR3C1 <- runDegCre(DegGR=DexNR3C1$DegGR,
+ DegP=DexNR3C1$DegGR$pVal,
+ DegLfc=DexNR3C1$DegGR$logFC,
+ CreGR=DexNR3C1$CreGR,
+ CreP=DexNR3C1$CreGR$pVal,
+ CreLfc=DexNR3C1$CreGR$logFC)
Analyzing 779231 DegGR to CreGR hits for optimal distance bin size.
Hit distance bin n = 3896
Small last bin resolved.
Running over 201 hit distance thresholds
Adjusting association probability for distance.
Calculation of assoc probabilities over hit bins complete.
Assoc FDR calculation complete.
DegCre calculations complete.
>
> #Make browser plot from specified gene name.
> browserOuts <- plotBrowserDegCre(degCreResList=degCreResListDexNR3C1,
+ geneName="ERRFI1",
+ geneNameColName="GeneSymb",
+ CreSignalName="NR3C1")
Using GeneSymb as gene name column.
Minimum display region size = 20291 bp.
All smaller regions will be expanded.
ERRFI1 promoters have been merged for plotting.
SLC2A5 promoters have been merged for plotting.
SPSB1 promoters have been merged for plotting.
arches[arches1]
heatmapLegend[heatmapLegend1]
signal[signal1_h]
yaxis[yaxis1]
Warning: Start label is rounded.
Warning: End label is rounded.
genomeLabel[genomeLabel1]
genes[genes1]
genes[genes1]
text[text2]
text[text2]
text[text2]
> dev.off()
null device
1
>
> #Make plot of specified region.
> zoomGR <- GRanges(seqnames="chr1",ranges=IRanges(start=7900e3,end=8400e3))
Error in GRanges(seqnames = "chr1", ranges = IRanges(start = 7900000, :
could not find function "GRanges"
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ ERROR
TIMEOUT: R CMD check exceeded 15 mins
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BiocCheck('DegCre_0.99.4.tar.gz')
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* ERROR:
/home/pkgbuild/packagebuilder/workers/jobs/3265/0d6714503fb988fa57381c12893c09fdbf6da75b/DegCre_0.99.4.tar.gz
must be loadable.
─ BiocCheckVersion: 1.39.23
─ BiocVersion: 3.19
─ Package: DegCre
─ PackageVersion: 0.99.4
─ sourceDir: /tmp/RtmpHSosq9/file1a504837bfa4d1/DegCre
─ installDir: /tmp/RtmpHSosq9/file1a504872f2f97a
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3265/0d6714503fb988fa57381c12893c09fdbf6da75b/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...
* NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* 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...
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘Rsamtools’
Calls: BiocCheck ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted