TCGAWorkflow 1.2.5
Tiago Chedraoui Silva
| Snapshot Date: 2018-10-15 07:35:11 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/TCGAWorkflow |
| Branch: RELEASE_3_7 |
| Last Commit: 8c13579 |
| Last Changed Date: 2018-10-12 10:05:39 -0400 (Fri, 12 Oct 2018) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | ERROR | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | [ ERROR ] | |
##############################################################################
##############################################################################
###
### Running command:
###
### chmod a+r TCGAWorkflow -R && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data TCGAWorkflow
###
##############################################################################
##############################################################################
* 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'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
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
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-GBM
--------------------
oo Filtering results
--------------------
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
-------------------
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_06_39_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'
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
downloaded 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
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "TCGAWorkflow_files/figure-html/unnamed-chunk-28-1.png" -trim "TCGAWorkflow_files/figure-html/unnamed-chunk-28-1.png"' execution failed with error code 4
silent variants: 38433
Summarizing..
Gene Summary..
NOTE: Possible FLAGS among top ten genes:
Checking clinical data..
Annotation missing for below samples in MAF
Done !
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "TCGAWorkflow_files/figure-html/unnamed-chunk-35-1.png" -trim "TCGAWorkflow_files/figure-html/unnamed-chunk-35-1.png"' execution failed with error code 4
gbm subtype information from:doi:10.1016/j.cell.2015.12.028
lgg subtype information from:doi:10.1016/j.cell.2015.12.028
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "TCGAWorkflow_files/figure-html/unnamed-chunk-36-1.png" -trim "TCGAWorkflow_files/figure-html/unnamed-chunk-36-1.png"' execution failed with error code 4
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'.
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "TCGAWorkflow_files/figure-html/unnamed-chunk-39-1.png" -trim "TCGAWorkflow_files/figure-html/unnamed-chunk-39-1.png"' execution failed with error code 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'.
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "TCGAWorkflow_files/figure-html/unnamed-chunk-40-1.png" -trim "TCGAWorkflow_files/figure-html/unnamed-chunk-40-1.png"' execution failed with error code 4
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 -------------------------------
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "TCGAWorkflow_files/figure-html/unnamed-chunk-44-1.png" -trim "TCGAWorkflow_files/figure-html/unnamed-chunk-44-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "TCGAWorkflow_files/figure-html/unnamed-chunk-45-1.png" -trim "TCGAWorkflow_files/figure-html/unnamed-chunk-45-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "TCGAWorkflow_files/figure-html/unnamed-chunk-46-1.png" -trim "TCGAWorkflow_files/figure-html/unnamed-chunk-46-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "TCGAWorkflow_files/figure-html/unnamed-chunk-47-1.png" -trim "TCGAWorkflow_files/figure-html/unnamed-chunk-47-1.png"' execution failed with error code 4
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'
The following object is masked from 'package:DelayedArray':
simplify
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 C:/Users/biocbuild/bbs-3.7-workflows/tmpdir/Rtmp6zWJid/Rbuild28d043985562/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'
The following object is masked from 'package:clusterProfiler':
simplify
The following object is masked from 'package:circlize':
degree
The following objects are masked from 'package:DelayedArray':
path, simplify
The following object is masked from 'package:GenomicRanges':
union
The following object is masked from 'package:IRanges':
union
The following object is masked from 'package:S4Vectors':
union
The following objects are masked from 'package:BiocGenerics':
normalize, path, union
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
==================== DATA Summary ====================
==================== END DATA Summary ====================
==================== T test results ====================
==================== END T test results ====================
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "TCGAWorkflow_files/figure-html/unnamed-chunk-52-1.png" -trim "TCGAWorkflow_files/figure-html/unnamed-chunk-52-1.png"' execution failed with error code 4
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'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Loading required package: BSgenome
Loading required package: rtracklayer
Attaching package: 'rtracklayer'
The following object is masked from 'package:igraph':
blocks
Loading required package: seqLogo
Loading required package: grImport
Loading required package: XML
Loading required package: MotIV
Attaching package: 'MotIV'
The following object is masked from 'package:rGADEM':
readPWMfile
The following object is masked from 'package:seqLogo':
makePWM
The following object is masked from 'package:igraph':
similarity
The following object is masked from 'package:stats':
filter
Loading required package: ade4
Attaching package: 'ade4'
The following object is masked from 'package:BSgenome':
score
The following object is masked from 'package:rtracklayer':
score
The following object is masked from 'package:Biostrings':
score
The following object is masked from 'package:GenomicRanges':
score
The following object is masked from 'package:IRanges':
score
The following object is masked from 'package:BiocGenerics':
score
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "TCGAWorkflow_files/figure-html/unnamed-chunk-55-1.png" -trim "TCGAWorkflow_files/figure-html/unnamed-chunk-55-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "TCGAWorkflow_files/figure-html/unnamed-chunk-56-1.png" -trim "TCGAWorkflow_files/figure-html/unnamed-chunk-56-1.png"' execution failed with error code 4
Found more than one class "textConnection" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'RJSONIO'
Found more than one class "textConnection" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'RJSONIO'
Found more than one class "textConnection" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'RJSONIO'
Downloading genome information (try:0) Using: Homo sapiens genes (GRCh37.p13)
o Fetching auxiliary information
oo Fetching probes genomic information
http://zwdzwd.io/InfiniumAnnotation/current/hm450/hm450.hg19.manifest.rds
trying URL 'http://zwdzwd.io/InfiniumAnnotation/current/hm450/hm450.hg19.manifest.rds'
Content type 'À=¦¬û' length 26177984 bytes (25.0 MB)
==================================================
downloaded 25.0 MB
oo Fetching TSS information
Downloading transcripts information. Using: Homo sapiens genes (GRCh37.p13)
o Mapping probes to nearest TSS
o Mapping results information
o Plotting figure
oo Adding names to genes
o Saving results
oo Saving significant results as: starburst_results.csv
oo It contains pair with changes both in the expression level of the nearest gene and in the DNA methylation level
ChIPseeker v1.16.1 For help: https://guangchuangyu.github.io/ChIPseeker
If you use ChIPseeker in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Qing-Yu He. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 2015, 31(14):2382-2383
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "TCGAWorkflow_files/figure-html/unnamed-chunk-63-1.png" -trim "TCGAWorkflow_files/figure-html/unnamed-chunk-63-1.png"' execution failed with error code 4
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "TCGAWorkflow_files/figure-html/unnamed-chunk-65-1.png" -trim "TCGAWorkflow_files/figure-html/unnamed-chunk-65-1.png"' execution failed with error code 4
Loading required package: ELMER.data
Downloading transcripts information. Using: Homo sapiens genes (GRCh37.p13)
Returning distal probes: 163576
Downloading genome information (try:0) Using: Homo sapiens genes (GRCh37.p13)
Loading from disk
Checking if samples have both DNA methylation and Gene expression and if they are in the same order...
Starting to add information to samples
=> Add clinical information to samples
Add FFPE information. More information at:
=> https://cancergenome.nih.gov/cancersselected/biospeccriteria
=> http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html
=> Adding subtype information to samples
gbm subtype information from:doi:10.1016/j.cell.2015.12.028
=> Adding subtype information to samples
lgg subtype information from:doi:10.1016/j.cell.2015.12.028
Creating MultiAssayExperiment
MAE saved as: mae.rda
Get diff methylated probes
ELMER will search for probes hypomethylated in group TCGA-GBM (n:10) compared to TCGA-LGG (n:10)
Number of probes: 2936
Saving results
Number of relevant probes found: 289
Get nearby genes
Searching for the 4 near genes
Get anti correlated probes-genes
Using pre-defined groups. U (unmethylated): TCGA-GBM, M (methylated): TCGA-LGG
-------------------
* Filtering probes
-------------------
For more information see function preAssociationProbeFiltering
Making sure we have at least 5% of beta values lesser than 0.3 and 5% of beta values greater 0.3.
Removing 2287 probes out of 2936
Calculating Pp (probe - gene) for all nearby genes
File created: elmer/hypo/getPair.hypo.all.pairs.statistic.csv
Downloading transcripts information. Using: Homo sapiens genes (GRCh37.p13)
Update the distance to gene to distance to the nearest TSS of the gene
Loading object: Probes.motif.hg19.450K
Retrieving TFClass family classification from ELMER.data.
Retrieving TFClass subfamily classification from ELMER.data.
------------------------------------
** Filtering motifs based on quality
------------------------------------
Number of enriched motifs with quality:
-----------
=> A: 15
=> B: 5
=> C: 6
=> D: 5
=> S: 0
-----------
Considering only motifs with quality from A up to DS: 31 motifs are enriched.
Using pre-defined groups. U (unmethylated): TCGA-GBM, M (methylated): TCGA-LGG
-------------------------------------------------------------------------------------------------------------------
** Downloading TF list from Lambert, Samuel A., et al. The human transcription factors. Cell 172.4 (2018): 650-665.
-------------------------------------------------------------------------------------------------------------------
Accessing TF families from TFClass database to indentify known potential TF
Retrieving TFClass family classification from ELMER.data.
Retrieving TFClass subfamily classification from ELMER.data.
Calculating the average methylation at all motif-adjacent probes
Performing Mann-Whitney U test
Finding potential TF and known potential TF
-----------------
** Creating plots
-----------------
TF rank plot highlighting TF in the same family (folder: elmer/hypo/TFrankPlot)
Retrieving TFClass family classification from ELMER.data.
Retrieving TFClass subfamily classification from ELMER.data.
Saving plot as: elmer/hypo/TFrankPlot/ETS1_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/KLF6_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ELF5_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ZN524_HUMAN.H11MO.0.D.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/FLI1_HUMAN.H11MO.1.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/EGR2_HUMAN.H11MO.1.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/FLI1_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/E2F4_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ELF2_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/E2F4_HUMAN.H11MO.1.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/PLAG1_HUMAN.H11MO.0.D.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ZFP82_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/GRHL1_HUMAN.H11MO.0.D.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/SP2_HUMAN.H11MO.1.B.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/PLAL1_HUMAN.H11MO.0.D.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ERG_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ZN341_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/SP4_HUMAN.H11MO.1.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ELK4_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ZN467_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/KLF14_HUMAN.H11MO.0.D.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/E2F3_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ZN331_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/FEV_HUMAN.H11MO.0.B.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/KLF15_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/KLF12_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/MBD2_HUMAN.H11MO.0.B.TFrankPlot.pdf