Bioconductor Single Package Builder - Build History

Snapshot Date:

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

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo1	Linux (Ubuntu 22.04.2 LTS)/x86_64	OK	ERROR	skipped	OK

nebbiolo1 Summary

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Package: CRISPRball

Version: 0.99.9

RVersion: 4.4

BiocVersion: 3.19

BuildCommand: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data CRISPRball

BuildTime: 1 minutes 14.81 seconds

CheckCommand: BiocCheckGitClone('CRISPRball') && /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3163/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3163/8316cd0fc65c3f7d067421d23a1b2d826277d69b/CRISPRball.install-out.txt CRISPRball_0.99.9.tar.gz && BiocCheck('CRISPRball_0.99.9.tar.gz', `new-package`=TRUE)

CheckTime: 5 minutes 23.81 seconds

BuildBinCommand:

BuildBinTime:

PackageFileSize: 2677.04 KiB

BuildID:: CRISPRball_20231128210935

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

nebbiolo1 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘CRISPRball/DESCRIPTION’ ... OK
* preparing ‘CRISPRball’:
* 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 ‘CRISPRball_0.99.9.tar.gz’

nebbiolo1 CHECK output

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

 BiocCheckGitClone('CRISPRball')

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

─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.19
─ Package: CRISPRball
─ PackageVersion: 0.99.9
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3163/8316cd0fc65c3f7d067421d23a1b2d826277d69b/CRISPRball
─ 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/3163/8316cd0fc65c3f7d067421d23a1b2d826277d69b/CRISPRball.Rcheck’
* using R Under development (unstable) (2023-11-11 r85510)
* 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 ‘CRISPRball/DESCRIPTION’ ... OK
* this is package ‘CRISPRball’ 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CRISPRball’ 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 ... 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 ... [21s/22s] OK
* checking whether the package can be loaded with stated dependencies ... [21s/22s] OK
* checking whether the package can be unloaded cleanly ... [13s/14s] WARNING
Error: package or namespace load failed for ‘CRISPRball’ in namespaceExport(ns, exports):
 undefined exports: EXTID2NAME, clusterSim, doSim, doseSim, enrichDGN, enrichDGNv, enrichDO, enrichHPO, enrichMPO, enrichNCG, gene2DO, geneID, geneInCategory, geneSim, gseDGN, gseDO, gseHPO, gseMPO, gseNCG, gsfilter, hpoSim, mclusterSim, mpoSim, parse_ratio, setReadable, simplot, theme_dose
In addition: Warning message:
S3 methods ‘$.enrichResult’, ‘$.gseaResult’, ‘[.enrichResult’, ‘[.gseaResult’, ‘[[.enrichResult’, ‘[[.gseaResult’, ‘as.data.frame.enrichResult’, ‘as.data.frame.gseaResult’, ‘dim.enrichResult’, ‘dim.gseaResult’, ‘geneID.compareClusterResult’, ‘geneID.enrichResult’, ‘geneID.gseaResult’, ‘geneInCategory.compareClusterResult’, ‘geneInCategory.enrichResult’, ‘geneInCategory.gseaResult’, ‘head.enrichResult’, ‘head.gseaResult’, ‘tail.enrichResult’, ‘tail.gseaResult’ were declared in NAMESPACE but not found 
Execution halted
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] WARNING
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘DOSE’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... [3s/3s] WARNING
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘DOSE’
Calls: suppressMessages ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking loading without being on the library search path ... [3s/3s] WARNING
Loading required package: shinyBS
Error: package or namespace load failed for ‘CRISPRball’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘DOSE’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error: there is no package called ‘DOSE’
Call sequence:
9: doWithOneRestart(return(expr), restart)
8: withOneRestart(expr, restarts[[1L]])
7: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
* checking S3 generic/method consistency ... WARNING
Error: there is no package called ‘DOSE’
Call sequence:
9: doWithOneRestart(return(expr), restart)
8: withOneRestart(expr, restarts[[1L]])
7: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], 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 ‘DOSE’
Call sequence:
9: doWithOneRestart(return(expr), restart)
8: withOneRestart(expr, restarts[[1L]])
7: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], 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 ‘DOSE’
Call sequence:
9: doWithOneRestart(return(expr), restart)
8: withOneRestart(expr, restarts[[1L]])
7: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], 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 ... [49s/52s] NOTE
Error: there is no package called ‘enrichplot’
Call sequence:
13: doWithOneRestart(return(expr), restart)
12: withOneRestart(expr, restarts[[1L]])
11: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
10: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
9: asNamespace(ns)
8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
6: asNamespace(ns)
5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
Error in namespaceExport(ns, exports) : 
  undefined exports: autofacet, cnetplot, color_palette, dotplot, drag_network, emapplot, emapplot_cluster, geom_gsea_gene, ggtable, goplot, gseadist, gseaplot, gseaplot2, gsearank, heatplot, pmcplot, ridgeplot, set_enrichplot_color, ssplot, treeplot, upsetplot
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 ... WARNING
Error: package or namespace load failed for ‘CRISPRball’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘clusterProfiler’
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = 
Execution halted
Error: package or namespace load failed for ‘CRISPRball’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘clusterProfiler’
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = 
Execution halted
* 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [51s/52s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [17s/18s]
 [17s/18s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(CRISPRball)
  Loading required package: shinyBS
  
  
  ##############################################################################
  Pathview is an open source software package distributed under GNU General
  Public License version 3 (GPLv3). Details of GPLv3 is available at
  http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
  formally cite the original Pathview paper (not just mention it) in publications
  or products. For details, do citation("pathview") within R.
  
  The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
  license agreement (details at http://www.kegg.jp/kegg/legal.html).
  ##############################################################################
  Error: package or namespace load failed for 'CRISPRball' in namespaceExport(ns, exports):
   undefined exports: BarView, BatchRemove, ConsistencyView, CutoffCalling, DensityDiffView, DensityView, EnrichAnalyzer, EnrichedFilter, EnrichedGeneView, EnrichedView, FluteMLE, FluteRRA, HeatmapView, IdentBarView, IncorporateDepmap, LoadDepmap, MAView, MapRatesView, NormalizeBeta, OmitCommonEssential, RankView, ReadBeta, ReadGMT, ReadRRA, ReadsgRRA, ResembleDepmap, ScatterView, Selector, SquareView, TransGeneID, ViolinView, VolcanoView, arrangePathview, enrich.GSE, enrich.HGT, enrich.ORT, getCols, getGeneAnn, getOrg, getOrtAnn, gsGetter, hclustView, normalize.loess, retrieve_gs, sgRankView, writeGMT
  Execution halted
* 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 ... [4s/4s] OK
* DONE

Status: 1 ERROR, 7 WARNINGs, 4 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3163/8316cd0fc65c3f7d067421d23a1b2d826277d69b/CRISPRball.Rcheck/00check.log’
for details.





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

 BiocCheck('CRISPRball_0.99.9.tar.gz')

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

    * ERROR:
      /home/pkgbuild/packagebuilder/workers/jobs/3163/8316cd0fc65c3f7d067421d23a1b2d826277d69b/CRISPRball_0.99.9.tar.gz
      must be installable.
    * ERROR:
      /home/pkgbuild/packagebuilder/workers/jobs/3163/8316cd0fc65c3f7d067421d23a1b2d826277d69b/CRISPRball_0.99.9.tar.gz
      must be loadable.
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.19
─ Package: CRISPRball
─ PackageVersion: 0.99.9
─ sourceDir: /tmp/RtmpUJ7oEz/filee8e7518933766/CRISPRball
─ installDir: /tmp/RtmpUJ7oEz/filee8e7569e17204
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3163/8316cd0fc65c3f7d067421d23a1b2d826277d69b/CRISPRball.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...
* 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 recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
Warning in packageDescription(pkgname, lib.loc = lib.loc) :
  no package 'CRISPRball' was found
Error in pkg_desc$Imports : $ operator is invalid for atomic vectors
Calls: BiocCheck ... checkDescriptionNamespaceConsistency -> cleanupDependency
Execution halted

nebbiolo1 BUILD BIN output

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