Bioconductor Single Package Builder - Build History

Snapshot Date:

URL: https://git.bioconductor.org/packages/HiBED

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo1	Linux (Ubuntu 22.04.1 LTS)/x86_64	OK	ERROR	skipped	OK

nebbiolo1 Summary

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Package: HiBED

Version: 0.99.5

RVersion: 4.3

BiocVersion: 3.17

BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data HiBED

BuildTime: 1 minutes 13.55 seconds

CheckCommand: BiocCheckGitClone('HiBED') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2965/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2965/b984d854f3f4a87b043982e76fd6733b25d333e9/HiBED.install-out.txt HiBED_0.99.5.tar.gz && BiocCheck('HiBED_0.99.5.tar.gz', `new-package`=TRUE)

CheckTime: 5 minutes 4.66 seconds

BuildBinCommand:

BuildBinTime:

PackageFileSize: 41.96 KiB

BuildID:: HiBED_20230413193452

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: HiBED. Starting Build package. Starting Check package.

PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1.

nebbiolo1 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘HiBED/DESCRIPTION’ ... OK
* preparing ‘HiBED’:
* 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
  NB: this package now depends on R (>= 3.5.0)
  WARNING: Added dependency on R >= 3.5.0 because serialized objects in
  serialize/load version 3 cannot be read in older versions of R.
  File(s) containing such objects:
    ‘HiBED/data/HiBED_Libraries.rda’
* building ‘HiBED_0.99.5.tar.gz’

nebbiolo1 CHECK output

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

 BiocCheckGitClone('HiBED')

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

─ BiocCheckVersion: 1.35.18
─ BiocVersion: 3.17
─ Package: HiBED
─ PackageVersion: 0.99.5
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2965/b984d854f3f4a87b043982e76fd6733b25d333e9/HiBED
─ 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')




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

 R CMD CHECK

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

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2965/b984d854f3f4a87b043982e76fd6733b25d333e9/HiBED.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiBED/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiBED’ version ‘0.99.5’
* 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 ‘HiBED’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [15s/15s] OK
* checking whether the package can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the package can be unloaded cleanly ... [14s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [14s/14s] OK
* checking loading without being on the library search path ... [15s/15s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error: there is no package called ‘minfi’
Call sequence:
8: doWithOneRestart(return(expr), restart)
7: withOneRestart(expr, restarts[[1L]])
6: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
1: loadNamespace(package, lib.loc)
Execution halted
* checking S3 generic/method consistency ... WARNING
Error: there is no package called ‘minfi’
Call sequence:
8: doWithOneRestart(return(expr), restart)
7: withOneRestart(expr, restarts[[1L]])
6: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
1: loadNamespace(package, lib.loc)
Execution halted
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Error: there is no package called ‘minfi’
Call sequence:
8: doWithOneRestart(return(expr), restart)
7: withOneRestart(expr, restarts[[1L]])
6: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
1: loadNamespace(package, lib.loc)
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Error: there is no package called ‘minfi’
Call sequence:
8: doWithOneRestart(return(expr), restart)
7: withOneRestart(expr, restarts[[1L]])
6: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
1: loadNamespace(package, lib.loc)
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [33s/33s] NOTE
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘minfi’
Calls: <Anonymous>
Execution halted
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [35s/35s] OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
HiBED_deconvolution 15.025  2.092  17.117
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [30s/30s]
 [31s/31s] 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 ... [2s/2s] OK
* DONE

Status: 2 WARNINGs, 4 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2965/b984d854f3f4a87b043982e76fd6733b25d333e9/HiBED.Rcheck/00check.log’
for details.






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

 BiocCheck('HiBED_0.99.5.tar.gz')

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

─ BiocCheckVersion: 1.35.18
─ BiocVersion: 3.17
─ Package: HiBED
─ PackageVersion: 0.99.5
─ sourceDir: /tmp/RtmpD9JZzD/file364a4f2e167bce/HiBED
─ installDir: /tmp/RtmpD9JZzD/file364a4f6c9889b5
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2965/b984d854f3f4a87b043982e76fd6733b25d333e9/HiBED.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 3.5.0 to 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    ExperimentData
* 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...
    * NOTE: The Description field in the DESCRIPTION is made up by less
      than 3 sentences. Please consider expanding this field, and
      structure it as a full paragraph
* 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 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 HiBED...
* 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
      is 1 function greater than 50 lines.
* Checking man page documentation...
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘AnnotationHub’
Calls: BiocCheck ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted

nebbiolo1 BUILD BIN output

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