Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/DegCre
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
merida1 macOS 12.7.1 Monterey/x86_64   OK     ERROR     ERROR     OK  
nebbiolo1 /   OK     TIMEOUT     skipped     OK  

merida1 Summary

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Package: DegCre
Version: 0.99.4
RVersion: 4.4
BiocVersion: 3.19
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DegCre
BuildTime: 6 minutes 11.49 seconds
CheckCommand: BiocCheckGitClone('DegCre') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3265/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3265/0d6714503fb988fa57381c12893c09fdbf6da75b/DegCre.install-out.txt DegCre_0.99.4.tar.gz && BiocCheck('DegCre_0.99.4.tar.gz', `new-package`=TRUE)
CheckTime: 14 minutes 59.95 seconds
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh DegCre_0.99.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir
BuildBinTime: 0 minutes 9.26 seconds
PackageFileSize: 2248.91 KiB
BuildID:: DegCre_20240213194932
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: DegCre. Starting Build package. Starting Check package. Starting Build package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1. Build Package status: 1.

merida1 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* 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

merida1 CHECK output

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===============================

 BiocCheckGitClone('DegCre')

===============================

 BiocCheckVersion: 1.39.23
 BiocVersion: 3.19
 Package: DegCre
 PackageVersion: 0.99.4
 sourceDir: /Users/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')




===============================

 R CMD CHECK

===============================

* using log directory /Users/pkgbuild/packagebuilder/workers/jobs/3265/0d6714503fb988fa57381c12893c09fdbf6da75b/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 0.99.4
* 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 ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] 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 ... [35s/35s] 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 ... WARNING: R CMD check exceeded 10 min requirement






===============================

 BiocCheck('DegCre_0.99.4.tar.gz')

===============================

    * ERROR:
      /Users/pkgbuild/packagebuilder/workers/jobs/3265/0d6714503fb988fa57381c12893c09fdbf6da75b/DegCre_0.99.4.tar.gz
      must be installable.
    * ERROR:
      /Users/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: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//RtmpWP4Lht/file4458e2004ab/DegCre
 installDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//RtmpWP4Lht/file44582600c799
 BiocCheckDir: /Users/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...
Warning in packageDescription(pkgname, lib.loc = lib.loc) :
  no package 'DegCre' was found
Error in pkg_desc$Imports : $ operator is invalid for atomic vectors
Calls: BiocCheck ... checkDescriptionNamespaceConsistency -> cleanupDependency
Execution halted

merida1 BUILD BIN output

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===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir DegCre_0.99.4.tar.gz'
>>>>>>> 

* installing *source* package DegCre ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called DelayedArray
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package DegCre
* removing /Users/pkgbuild/packagebuilder/workers/jobs/3265/0d6714503fb988fa57381c12893c09fdbf6da75b/libdir/DegCre

nebbiolo1 Summary

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Package: DegCre
Version: 0.0.0
RVersion:
BiocVersion: 3.19
BuildCommand: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data DegCre
BuildTime: 5 minutes 18.09 seconds
CheckCommand: BiocCheckGitClone('DegCre') && /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3265/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3265/0d6714503fb988fa57381c12893c09fdbf6da75b/DegCre.install-out.txt DegCre_0.99.4.tar.gz && BiocCheck('DegCre_0.99.4.tar.gz', `new-package`=TRUE)
CheckTime: 15 minutes 0.00 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 2101.36 KiB
BuildID:: DegCre_20240213194932
PreProcessing: Installing dependencies. Checking Git Clone. Installing package: DegCre. Starting Build package. Starting Check package.
PostProcessing: Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: -9.

nebbiolo1 BUILD SRC output

[top]

===============================

 R CMD BUILD

===============================

* 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

nebbiolo1 CHECK output

[top]

===============================

 BiocCheckGitClone('DegCre')

===============================

 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')




===============================

 R CMD CHECK

===============================

* 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






===============================

 BiocCheck('DegCre_0.99.4.tar.gz')

===============================

    * 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

nebbiolo1 BUILD BIN output

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