Package: TCGAWorkflow

Version: 1.2.5

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAWorkflow

StartedAt: 2018-10-15 08:09:50 -0400 (Mon, 15 Oct 2018)

EndedAt: 2018-10-15 08:21:07 -0400 (Mon, 15 Oct 2018)

EllapsedTime: 676.5 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAWorkflow
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* checking for file ‘TCGAWorkflow/DESCRIPTION’ ... OK
* preparing ‘TCGAWorkflow’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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    aperm, apply

--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
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ooo Project: TCGA-GBM
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oo Filtering results
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ooo By file.type
ooo By barcode
----------------
oo Checking data
----------------
ooo Check if there are duplicated cases
ooo Check if there results for the query
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o Preparing output
-------------------
Downloading data for project TCGA-GBM
GDCdownload will download 2 files. A total of 60.483 KB
Downloading as: Mon_Oct_15_08_12_29_2018.tar.gz
To get the following information please change the clinical.info argument
=> new_tumor_events: new_tumor_event 
=> drugs: drug 
=> follow_ups: follow_up 
=> radiations: radiation
Parsing follow up version: follow_up_v1.0
gbm subtype information from:doi:10.1016/j.cell.2015.12.028
Starting GBM
trying URL 'ftp://ftp.broadinstitute.org/pub/GISTIC2.0/hg19_support/CNV.hg19.bypos.111213.txt'
Content type 'unknown' length 358469 bytes (350 KB)
==================================================
Parsed with column specification:
cols(
  ID = col_character(),
  Chromosome = col_integer(),
  Start = col_integer(),
  End = col_integer(),
  Flankingstart = col_integer(),
  Flankingend = col_integer()
)
Loading Marker Informations
........................
Done
Loading Copy Number Data
................................................
Done

Performing Data Preprocessing

Done

Computing Discontinuity Matrix
.
Done
Computing Probability Distribution
....
Done
Assessing the Significance of Observed Data
..
Done
Writing GAIA_GBM_flt.txt.igv.gistic File for Integrative Genomics Viewer (IGV) Tool
..
Done
Running Homogeneous peel-off Algorithm With Significance Threshold of 0.25 and Homogenous Threshold of 0.12
..
Done

Writing Output File 'GAIA_GBM_flt.txt' Containing the Significant Regions

File 'GAIA_GBM_flt.txt' Saved

silent variants: 38433
Summarizing..
Gene Summary..
NOTE: Possible FLAGS among top ten genes:
Checking clinical data..
Annotation missing for below samples in MAF
Done !
gbm subtype information from:doi:10.1016/j.cell.2015.12.028
lgg subtype information from:doi:10.1016/j.cell.2015.12.028
Looking for clinical data in annoatation slot of MAF..
Number of mutated samples for given genes: 
Median survival..
========================================
circlize version 0.4.4
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: http://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization 
  in R. Bioinformatics 2014.
========================================

Note: 2 points are out of plotting region in sector 'chr17', track '4'.

Note: 2 points are out of plotting region in sector 'chr17', track '4'.

Note: 2 points are out of plotting region in sector 'chr17', track '5'.

Note: 2 points are out of plotting region in sector 'chr17', track '5'.

Note: 1 point is out of plotting region in sector 'chr17', track '5'.

Note: 1 point is out of plotting region in sector 'chr17', track '5'.

I Need about  11 seconds for this Complete Normalization Upper Quantile  [Processing 80k elements /s]  
Step 1 of 4: newSeqExpressionSet ...
Step 2 of 4: withinLaneNormalization ...
Step 3 of 4: betweenLaneNormalization ...
Step 4 of 4: .quantileNormalization ...
Batch correction skipped since no factors provided
----------------------- DEA -------------------------------
there are Cond1 type LGG in  20 samples
there are Cond2 type GBM in  20 samples
there are  14477 features as miRNA or genes 
I Need about  19 seconds for this DEA. [Processing 30k elements /s]  
----------------------- END DEA -------------------------------
clusterProfiler v3.8.1  For help: https://guangchuangyu.github.io/software/clusterProfiler

If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.

Attaching package: 'clusterProfiler'

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Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi

'select()' returned 1:many mapping between keys and columns
Warning in bitr(dataDEGsFiltLevel$mRNA, fromType = "SYMBOL", toType = "ENTREZID",  :
  9.98% of input gene IDs are fail to map...
Info: Downloading xml files for hsa05214, 1/1 pathways..
Info: Downloading png files for hsa05214, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /tmp/RtmpQvEaBj/Rbuild55ca5b4999cd/TCGAWorkflow/vignettes
Info: Writing image file hsa05214.pathview.png
Info: some node width is different from others, and hence adjusted!
Loading required package: igraph

Attaching package: 'igraph'

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==================== DATA Summary ====================
==================== END DATA Summary ====================
==================== T test results ====================
==================== END T test results ====================
Group1:TCGA-GBM
Group2:TCGA-LGG
Calculating the diference between the mean methylation of the groups...
Calculating the p-values of each probe...
Loading required package: grid
========================================
ComplexHeatmap version 1.18.1
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://bioconductor.org/packages/ComplexHeatmap/

If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
  genomic data. Bioinformatics 2016.
========================================

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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Loading required package: BSgenome
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

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Loading required package: seqLogo
Loading required package: grImport
Loading required package: XML
Loading required package: MotIV

Attaching package: 'MotIV'

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Loading required package: ade4

Attaching package: 'ade4'

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Quitting from lines 1818-1832 (TCGAWorkflow.Rmd) 
Error: processing vignette 'TCGAWorkflow.Rmd' failed with diagnostics:
incorrect number of dimensions
Execution halted