Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/EpiMix
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: EpiMix
Version: 0.99.9
RVersion: 4.2
BiocVersion: 3.15
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data EpiMix
BuildTime: 9 minutes 20.00 seconds
CheckCommand:
CheckTime:
BuildBinCommand:
BuildBinTime:
PackageFileSize: -1.00 KiB
BuildID:: EpiMix_20220526190603
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: EpiMix. 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 ‘EpiMix/DESCRIPTION’ ... OK
* preparing ‘EpiMix’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
duplicated vignette title:
  ‘vignette’

--- re-building ‘EpiMix_demo.Rmd’ using rmarkdown
Loading required package: EpiMix.data
Loading required package: ExperimentHub
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
snapshotDate(): 2022-04-26
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
require("GenomicRanges")
Warning: executing %dopar% sequentially: no parallel backend registered
snapshotDate(): 2022-04-26
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
trying URL 'https://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/core_K27ac/jointModel/final/E096_18_core_K27ac_hg38lift_mnemonics.bed.gz'
Content type 'application/x-gzip' length 3835377 bytes (3.7 MB)
==================================================
downloaded 3.7 MB

snapshotDate(): 2022-04-26
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
Returning distal probes: 160862
Searching for the 20 near genes
Identifying gene position for each probe
Warning in getRandomGenes(target.probe = target.probe, gene.expression.data = gene.expression.data,  :
  There is not enough genes to generate 1000 permutations. Using 805 random genes instead.
Warning in getRandomGenes(target.probe = target.probe, gene.expression.data = gene.expression.data,  :
  There is not enough genes to generate 1000 permutations. Using 793 random genes instead.
Warning in getRandomGenes(target.probe = target.probe, gene.expression.data = gene.expression.data,  :
  There is not enough genes to generate 1000 permutations. Using 798 random genes instead.
trying URL 'http://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 152968396 bytes (145.9 MB)
==================================================
downloaded 145.9 MB

trying URL 'http://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 51525820 bytes (49.1 MB)
==================================================
downloaded 49.1 MB

trying URL 'http://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 36996192 bytes (35.3 MB)
==================================================
downloaded 35.3 MB

trying URL 'http://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.miRseq_Preprocess.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 2663096 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

snapshotDate(): 2022-04-26
see ?EpiMix.data and browseVignettes('EpiMix.data') for documentation
loading from cache
`geom_smooth()` using formula 'y ~ x'
Loading required package: regioneR
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    cache

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

    cache


snapshotDate(): 2022-04-26
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
  403 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
'select()' returned 1:1 mapping between keys and columns
Warning in text.default(x = 0.281994261119082, y = c(chr12 = 95.7895435628561),  :
  "offest" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "offest" is not a graphical parameter
snapshotDate(): 2022-04-26
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
Searching for the 10 near genes
Identifying gene position for each probe

clusterProfiler v4.4.1  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/

If you use clusterProfiler in published research, please cite:
T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141

Attaching package: 'clusterProfiler'

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

    select

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

    slice

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

    rename

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

    filter

'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Reading KEGG annotation online:

Reading KEGG annotation online:

trying URL 'http://gdac.broadinstitute.org/runs/stddata__latest/data/LUAD/20160128/gdac.broadinstitute.org_LUAD.Merge_Clinical.Level_1.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 1777018 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

Loading required package: ggplot2
Loading required package: ggpubr

Attaching package: 'survminer'

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

    myeloma

trying URL 'http://gdac.broadinstitute.org/runs/stddata__latest/data/LUAD/20160128/gdac.broadinstitute.org_LUAD.Merge_Clinical.Level_1.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 1777018 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

--- finished re-building ‘EpiMix_demo.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
snapshotDate(): 2022-04-26
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
trying URL 'http://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 152968396 bytes (145.9 MB)
==================================================
downloaded 145.9 MB

trying URL 'http://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 51525820 bytes (49.1 MB)
==================================================
downloaded 49.1 MB

snapshotDate(): 2022-04-26
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
  403 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
'select()' returned 1:1 mapping between keys and columns
Warning in text.default(x = 0.281994261119082, y = c(chr12 = 95.7895435628561),  :
  "offest" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "offest" is not a graphical parameter
snapshotDate(): 2022-04-26
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
Searching for the 10 near genes
Identifying gene position for each probe
Quitting from lines 560-585 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
could not find function "function.enrich"
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Error: Duplicate vignette titles.
  Ensure that the %\VignetteIndexEntry lines in the vignette sources
  correspond to the vignette titles.
Execution halted

nebbiolo1 CHECK output

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nebbiolo1 BUILD BIN output
 
                    			
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merida1 Summary
 
                			
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Package: EpiMix
 
                					
Version: 0.99.9
 
                					
RVersion: 4.2
                
 
                					
BiocVersion: 3.15
                
 

                					
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data EpiMix
 
                					
BuildTime: 13 minutes 58.25 seconds
 
                					
CheckCommand: 

   							
CheckTime: 

                 					
BuildBinCommand: 

 							
BuildBinTime: 

                					
PackageFileSize: -1.00 KiB
 
                					
BuildID:: EpiMix_20220526190603
 
                					
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: EpiMix. 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 ‘EpiMix/DESCRIPTION’ ... OK
* preparing ‘EpiMix’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
duplicated vignette title:
  ‘vignette’

--- re-building ‘EpiMix_demo.Rmd’ using rmarkdown
Loading required package: EpiMix.data
Loading required package: ExperimentHub
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
snapshotDate(): 2022-04-26
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
require("GenomicRanges")
Warning: executing %dopar% sequentially: no parallel backend registered
snapshotDate(): 2022-04-26
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
trying URL 'https://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/core_K27ac/jointModel/final/E096_18_core_K27ac_hg38lift_mnemonics.bed.gz'
Content type 'application/x-gzip' length 3835377 bytes (3.7 MB)
==================================================
downloaded 3.7 MB

snapshotDate(): 2022-04-26
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
Returning distal probes: 160862
Searching for the 20 near genes
Identifying gene position for each probe
Warning in getRandomGenes(target.probe = target.probe, gene.expression.data = gene.expression.data,  :
  There is not enough genes to generate 1000 permutations. Using 805 random genes instead.
Warning in getRandomGenes(target.probe = target.probe, gene.expression.data = gene.expression.data,  :
  There is not enough genes to generate 1000 permutations. Using 793 random genes instead.
Warning in getRandomGenes(target.probe = target.probe, gene.expression.data = gene.expression.data,  :
  There is not enough genes to generate 1000 permutations. Using 798 random genes instead.
trying URL 'http://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 152968396 bytes (145.9 MB)
==================================================
downloaded 145.9 MB

trying URL 'http://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 51525820 bytes (49.1 MB)
==================================================
downloaded 49.1 MB

trying URL 'http://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 36996192 bytes (35.3 MB)
==================================================
downloaded 35.3 MB

trying URL 'http://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.miRseq_Preprocess.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 2663096 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

snapshotDate(): 2022-04-26
see ?EpiMix.data and browseVignettes('EpiMix.data') for documentation
loading from cache
Fontconfig warning: ignoring UTF-8: not a valid region tag
`geom_smooth()` using formula 'y ~ x'
Loading required package: regioneR
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    cache

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

    cache


snapshotDate(): 2022-04-26
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
  403 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
'select()' returned 1:1 mapping between keys and columns
Warning in text.default(x = 0.281994261119082, y = c(chr12 = 95.7895435628561),  :
  "offest" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "offest" is not a graphical parameter
snapshotDate(): 2022-04-26
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
Searching for the 10 near genes
Identifying gene position for each probe

clusterProfiler v4.4.1  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/

If you use clusterProfiler in published research, please cite:
T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141

Attaching package: 'clusterProfiler'

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

    select

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

    slice

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

    rename

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

    filter

'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Reading KEGG annotation online:

Reading KEGG annotation online:

trying URL 'http://gdac.broadinstitute.org/runs/stddata__latest/data/LUAD/20160128/gdac.broadinstitute.org_LUAD.Merge_Clinical.Level_1.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 1777018 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

Loading required package: ggplot2
Loading required package: ggpubr

Attaching package: 'survminer'

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

    myeloma

trying URL 'http://gdac.broadinstitute.org/runs/stddata__latest/data/LUAD/20160128/gdac.broadinstitute.org_LUAD.Merge_Clinical.Level_1.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 1777018 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

Quitting from lines 558-559 (EpiMix_demo.Rmd) 
Error: processing vignette 'EpiMix_demo.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘EpiMix_demo.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
snapshotDate(): 2022-04-26
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
trying URL 'http://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 152968396 bytes (145.9 MB)
==================================================
downloaded 145.9 MB

trying URL 'http://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 51525820 bytes (49.1 MB)
==================================================
downloaded 49.1 MB

snapshotDate(): 2022-04-26
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
  403 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
'select()' returned 1:1 mapping between keys and columns
Warning in text.default(x = 0.281994261119082, y = c(chr12 = 95.7895435628561),  :
  "offest" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "offest" is not a graphical parameter
snapshotDate(): 2022-04-26
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
Searching for the 10 near genes
Identifying gene position for each probe
Quitting from lines 560-585 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
could not find function "function.enrich"
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following files failed:
  ‘EpiMix_demo.Rmd’ ‘overview.Rmd’

Error: Vignette re-building failed.
Error: Duplicate vignette titles.
  Ensure that the %\VignetteIndexEntry lines in the vignette sources
  correspond to the vignette titles.
Execution halted


                				
 

                			
 
                			    
                				
merida1 CHECK output
 
                    			
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merida1 BUILD BIN output
 
                    			
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