Bioconductor Single Package Builder - Build History

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

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo1 Linux (Ubuntu 20.04.4 LTS)/x86_64   ERROR     skipped     skipped     skipped  
merida1 macOS 10.14.6 Mojave/x86_64   ERROR     skipped     skipped     skipped  

nebbiolo1 Summary

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Package: SPOTlight
Version: 0.99.7
RVersion: 4.2
BiocVersion: 3.15
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SPOTlight
BuildTime: 1 minutes 29.11 seconds
CheckCommand:
CheckTime:
BuildBinCommand:
BuildBinTime:
PackageFileSize: -1.00 KiB
BuildID:: SPOTlight_20220315180722
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SPOTlight. 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: 1.

nebbiolo1 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘SPOTlight/DESCRIPTION’ ... OK
* preparing ‘SPOTlight’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘SPOTlight_kidney.Rmd’ using rmarkdown
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

The following object is masked from 'package:Biobase':

    rowMedians

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: scuttle
Loading required package: ExperimentHub
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

The following object is masked from 'package:Biobase':

    cache

snapshotDate(): 2022-03-01
see ?TENxVisiumData and browseVignettes('TENxVisiumData') for documentation
loading from cache
snapshotDate(): 2022-03-01
see ?TabulaMurisSenisData and browseVignettes('TabulaMurisSenisData') for documentation
loading from cache
require("rhdf5")
see ?TabulaMurisSenisData and browseVignettes('TabulaMurisSenisData') for documentation
loading from cache
see ?TabulaMurisSenisData and browseVignettes('TabulaMurisSenisData') for documentation
loading from cache
see ?TabulaMurisSenisData and browseVignettes('TabulaMurisSenisData') for documentation
loading from cache
see ?TabulaMurisSenisData and browseVignettes('TabulaMurisSenisData') for documentation
loading from cache
see ?TabulaMurisSenisData and browseVignettes('TabulaMurisSenisData') for documentation
loading from cache
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:S4Vectors':

    new2

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 71/72
  To enable shared memory capabilities, try: install.extras('
NMF
')

Attaching package: 'NMF'

The following object is masked from 'package:S4Vectors':

    nrun

Quitting from lines 392-395 (SPOTlight_kidney.Rmd) 
Error: processing vignette 'SPOTlight_kidney.Rmd' failed with diagnostics:
object 'y' not found
--- failed re-building ‘SPOTlight_kidney.Rmd’

SUMMARY: processing the following file failed:
  ‘SPOTlight_kidney.Rmd’

Error: Vignette re-building failed.
Execution halted

nebbiolo1 CHECK output

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nebbiolo1 BUILD BIN output
 
                    			
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merida1 Summary
 
                			
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Package: SPOTlight
 
                					
Version: 0.99.7
 
                					
RVersion: 4.2
                
 
                					
BiocVersion: 3.15
                
 

                					
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SPOTlight
 
                					
BuildTime: 2 minutes 0.25 seconds
 
                					
CheckCommand: 

   							
CheckTime: 

                 					
BuildBinCommand: 

 							
BuildBinTime: 

                					
PackageFileSize: -1.00 KiB
 
                					
BuildID:: SPOTlight_20220315180722
 
                					
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SPOTlight. 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: 1. 
        				
                				
 
                			
 
                			
 
                			    
                				
merida1 BUILD SRC output
 
                    			
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===============================

 R CMD BUILD

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

* checking for file ‘SPOTlight/DESCRIPTION’ ... OK
* preparing ‘SPOTlight’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘SPOTlight_kidney.Rmd’ using rmarkdown
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

The following object is masked from 'package:Biobase':

    rowMedians

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: scuttle
Loading required package: ExperimentHub
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

The following object is masked from 'package:Biobase':

    cache

snapshotDate(): 2022-03-01
see ?TENxVisiumData and browseVignettes('TENxVisiumData') for documentation
loading from cache
snapshotDate(): 2022-03-01
see ?TabulaMurisSenisData and browseVignettes('TabulaMurisSenisData') for documentation
loading from cache
require("rhdf5")
see ?TabulaMurisSenisData and browseVignettes('TabulaMurisSenisData') for documentation
loading from cache
see ?TabulaMurisSenisData and browseVignettes('TabulaMurisSenisData') for documentation
loading from cache
see ?TabulaMurisSenisData and browseVignettes('TabulaMurisSenisData') for documentation
loading from cache
see ?TabulaMurisSenisData and browseVignettes('TabulaMurisSenisData') for documentation
loading from cache
see ?TabulaMurisSenisData and browseVignettes('TabulaMurisSenisData') for documentation
loading from cache
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:S4Vectors':

    new2

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 23/24
  To enable shared memory capabilities, try: install.extras('
NMF
')

Attaching package: 'NMF'

The following object is masked from 'package:S4Vectors':

    nrun

Quitting from lines 392-395 (SPOTlight_kidney.Rmd) 
Error: processing vignette 'SPOTlight_kidney.Rmd' failed with diagnostics:
object 'y' not found
--- failed re-building ‘SPOTlight_kidney.Rmd’

SUMMARY: processing the following file failed:
  ‘SPOTlight_kidney.Rmd’

Error: Vignette re-building failed.
Execution halted


                				
 

                			
 
                			    
                				
merida1 CHECK output
 
                    			
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merida1 BUILD BIN output
 
                    			
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