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BUILD report for cBioPortalData on malbec1

This page was generated on 2020-08-11 11:27:45 -0400 (Tue, 11 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE cBioPortalData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 232/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cBioPortalData 2.1.24
Marcel Ramos
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/cBioPortalData
Branch: master
Last Commit: 00f9795
Last Changed Date: 2020-08-07 14:15:01 -0400 (Fri, 07 Aug 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK [ ERROR ] skipped 
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
merida1 macOS 10.14.6 Mojave / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: cBioPortalData
Version: 2.1.24
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data cBioPortalData
StartedAt: 2020-08-10 22:27:35 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 22:29:08 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 93.4 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data cBioPortalData
###
##############################################################################
##############################################################################


* checking for file ‘cBioPortalData/DESCRIPTION’ ... OK
* preparing ‘cBioPortalData’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘cBioPortalData.Rmd’ using rmarkdown
Loading required package: AnVIL
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    combine, intersect, setdiff, union

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: S4Vectors

Attaching package: 'S4Vectors'

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

    first, rename

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    collapse, desc, slice

Loading required package: GenomeInfoDb
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")'.

Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

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

    expand

Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

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

    count


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

Study file in cache: laml_tcga
Working on: /tmp/RtmpfjyGpw/data_CNA.txt
Parsed with column specification:
cols(
  .default = col_double(),
  Hugo_Symbol = col_character()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  Hugo_Symbol = col_character()
)
Working on: /tmp/RtmpfjyGpw/data_RNA_Seq_expression_median.txt
Parsed with column specification:
cols(
  .default = col_double(),
  Hugo_Symbol = col_character()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  Hugo_Symbol = col_character()
)
Working on: /tmp/RtmpfjyGpw/data_RNA_Seq_mRNA_median_all_sample_Zscores.txt
Parsed with column specification:
cols(
  .default = col_double(),
  Hugo_Symbol = col_character()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  Hugo_Symbol = col_character()
)
Working on: /tmp/RtmpfjyGpw/data_RNA_Seq_v2_expression_median.txt
Parsed with column specification:
cols(
  .default = col_double(),
  Hugo_Symbol = col_character()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  Hugo_Symbol = col_character()
)
Working on: /tmp/RtmpfjyGpw/data_RNA_Seq_v2_mRNA_median_Zscores.txt
Parsed with column specification:
cols(
  .default = col_double(),
  Hugo_Symbol = col_character()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  Hugo_Symbol = col_character()
)
Working on: /tmp/RtmpfjyGpw/data_RNA_Seq_v2_mRNA_median_all_sample_Zscores.txt
Parsed with column specification:
cols(
  .default = col_double(),
  Hugo_Symbol = col_character()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  Hugo_Symbol = col_character()
)
Working on: /tmp/RtmpfjyGpw/data_cna_hg19.seg
Parsed with column specification:
cols(
  ID = col_character(),
  chrom = col_double(),
  loc.start = col_double(),
  loc.end = col_double(),
  num.mark = col_double(),
  seg.mean = col_double()
)
Working on: /tmp/RtmpfjyGpw/data_linear_CNA.txt
Parsed with column specification:
cols(
  .default = col_double(),
  Hugo_Symbol = col_character()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  Hugo_Symbol = col_character()
)
Working on: /tmp/RtmpfjyGpw/data_methylation_hm27.txt
Parsed with column specification:
cols(
  .default = col_double(),
  Hugo_Symbol = col_character()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  Hugo_Symbol = col_character()
)
Working on: /tmp/RtmpfjyGpw/data_methylation_hm450.txt
Parsed with column specification:
cols(
  .default = col_double(),
  Hugo_Symbol = col_character()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  Hugo_Symbol = col_character()
)
Working on: /tmp/RtmpfjyGpw/data_mutations_extended.txt
Parsed with column specification:
cols(
  .default = col_character(),
  Entrez_Gene_Id = col_double(),
  Start_Position = col_double(),
  End_Position = col_double(),
  dbSNP_Val_Status = col_logical(),
  Score = col_double(),
  t_ref_count = col_double(),
  t_alt_count = col_double(),
  n_ref_count = col_double(),
  n_alt_count = col_double(),
  Protein_position = col_double(),
  Hotspot = col_double(),
  RNAVAF_WU = col_double(),
  RNAVarReads_WU = col_double(),
  stop = col_double(),
  NormalVAF_WU = col_double(),
  start = col_double(),
  TumorVAF_WU = col_double(),
  RNARefReads_WU = col_double()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  .default = col_character()
)
See spec(...) for full column specifications.
Warning in .find_seqnames_col(df_colnames0, seqnames.field0, xfix) :
  cannnot determine seqnames column unambiguously
Warning in .find_seqnames_col(df_colnames0, seqnames.field0, xfix) :
  cannnot determine seqnames column unambiguously
Warning in .find_seqnames_col(df_colnames0, seqnames.field0, xfix) :
  cannnot determine seqnames column unambiguously
Working on: /tmp/RtmpfjyGpw/data_mutations_mskcc.txt
Parsed with column specification:
cols(
  .default = col_character(),
  Entrez_Gene_Id = col_double(),
  Start_Position = col_double(),
  End_Position = col_double(),
  dbSNP_Val_Status = col_logical(),
  Score = col_double(),
  t_ref_count = col_double(),
  t_alt_count = col_double(),
  n_ref_count = col_double(),
  n_alt_count = col_double(),
  Protein_position = col_double(),
  Hotspot = col_double(),
  RNAVAF_WU = col_double(),
  RNAVarReads_WU = col_double(),
  stop = col_double(),
  NormalVAF_WU = col_double(),
  start = col_double(),
  TumorVAF_WU = col_double(),
  RNARefReads_WU = col_double()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  .default = col_character()
)
See spec(...) for full column specifications.
Warning in .find_seqnames_col(df_colnames0, seqnames.field0, xfix) :
  cannnot determine seqnames column unambiguously
Warning in .find_seqnames_col(df_colnames0, seqnames.field0, xfix) :
  cannnot determine seqnames column unambiguously
Warning in .find_seqnames_col(df_colnames0, seqnames.field0, xfix) :
  cannnot determine seqnames column unambiguously
Parsed with column specification:
cols(
  .default = col_character(),
  INITIAL_PATHOLOGIC_DX_YEAR = col_double(),
  AGE = col_double(),
  PLATELET_COUNT_PRERESECTION = col_double(),
  BLAST_COUNT = col_double(),
  BASOPHILS_COUNT = col_double(),
  ABNORMAL_LYMPHOCYTE_PERCENT = col_double(),
  OS_MONTHS = col_double()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  .default = col_character(),
  SAMPLE_TYPE_ID = col_double()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  .default = col_character(),
  SAMPLE_TYPE_ID = col_double()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  .default = col_character()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  index = col_double(),
  chromosome = col_double(),
  region_start = col_double(),
  region_end = col_double(),
  peak_start = col_double(),
  peak_end = col_double(),
  enlarged_peak_start = col_double(),
  enlarged_peak_end = col_double(),
  n_genes_in_region = col_double(),
  genes_in_region = col_character(),
  n_genes_in_peak = col_double(),
  genes_in_peak = col_character(),
  n_genes_on_chip = col_character(),
  genes_on_chip = col_character(),
  `top 3` = col_character(),
  amp = col_double(),
  cytoband = col_character(),
  q_value = col_double()
)
Warning in .find_with_xfix(df_colnames, prefixes1, prefixes2, start.field,  :
   Multiple prefixes found, using keyword 'region' or taking first one
Parsed with column specification:
cols(
  index = col_double(),
  chromosome = col_double(),
  region_start = col_double(),
  region_end = col_double(),
  peak_start = col_double(),
  peak_end = col_double(),
  enlarged_peak_start = col_double(),
  enlarged_peak_end = col_double(),
  n_genes_in_region = col_double(),
  genes_in_region = col_character(),
  n_genes_in_peak = col_double(),
  genes_in_peak = col_character(),
  n_genes_on_chip = col_character(),
  genes_on_chip = col_character(),
  `top 3` = col_character(),
  amp = col_double(),
  cytoband = col_character(),
  q_value = col_double()
)
Warning in .find_with_xfix(df_colnames, prefixes1, prefixes2, start.field,  :
   Multiple prefixes found, using keyword 'region' or taking first one
Quitting from lines 54-60 (cBioPortalData.Rmd) 
Error: processing vignette 'cBioPortalData.Rmd' failed with diagnostics:
object 'full' not found
--- failed re-building ‘cBioPortalData.Rmd’

--- re-building ‘cBioPortalRClient.Rmd’ using rmarkdown
Quitting from lines 73-74 (cBioPortalRClient.Rmd) 
Error: processing vignette 'cBioPortalRClient.Rmd' failed with diagnostics:
object 'full' not found
--- failed re-building ‘cBioPortalRClient.Rmd’

SUMMARY: processing the following files failed:
  ‘cBioPortalData.Rmd’ ‘cBioPortalRClient.Rmd’

Error: Vignette re-building failed.
Execution halted