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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SingscoreAMLMutations
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* checking for file ‘SingscoreAMLMutations/DESCRIPTION’ ... OK
* preparing ‘SingscoreAMLMutations’:
* checking DESCRIPTION meta-information ...It is recommended to use ‘given’ instead of ‘middle’.
It is recommended to use ‘given’ instead of ‘middle’.
 OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘workflow_transcriptional_mut_sig.Rmd’ using rmarkdown
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-LAML
--------------------
oo Filtering results
--------------------
ooo By data.type
ooo By workflow.type
----------------
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-LAML
GDCdownload will download 151 files. A total of 38.93826 MB
Downloading as: Fri_Oct_16_09_25_07_2020.tar.gz
Starting to add information to samples
 => Add clinical information to samples
 => Adding TCGA molecular information from marker papers
 => Information will have prefix 'paper_' 
Accessing www.ensembl.org to get gene information
Downloading genome information (try:0) Using: Human genes (GRCh38.p13)
From the 60483 genes we couldn't map 4026
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_22/gencode.v22.annotation.gtf.gz'
Content type 'unknown' length 40933020 bytes (39.0 MB)
==================================
Warning in download.file(gencode_link, gencode_file, method = "libcurl") :
  downloaded length 28207716 != reported length 40933020
Warning in download.file(gencode_link, gencode_file, method = "libcurl") :
  URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_22/gencode.v22.annotation.gtf.gz': Timeout of 60 seconds was reached
Quitting from lines 238-246 (workflow_transcriptional_mut_sig.Rmd) 
Error: processing vignette 'workflow_transcriptional_mut_sig.Rmd' failed with diagnostics:
cannot open URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_22/gencode.v22.annotation.gtf.gz'
--- failed re-building ‘workflow_transcriptional_mut_sig.Rmd’

--- re-building ‘workflow_transcriptional_mut_sig_chinese.Rmd’ using rmarkdown
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-LAML
--------------------
oo Filtering results
--------------------
ooo By data.type
ooo By workflow.type
----------------
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-LAML
Of the 151 files for download 151 already exist.
All samples have been already downloaded
Starting to add information to samples
 => Add clinical information to samples
 => Adding TCGA molecular information from marker papers
 => Information will have prefix 'paper_' 
Accessing www.ensembl.org to get gene information
Downloading genome information (try:0) Using: Human genes (GRCh38.p13)
From the 60483 genes we couldn't map 4026
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_22/gencode.v22.annotation.gtf.gz'
Content type 'unknown' length 40933020 bytes (39.0 MB)
==================================================
'select()' returned 1:many mapping between keys and columns
trying URL 'http://software.broadinstitute.org/gsea/msigdb/download_geneset.jsp?geneSetName=VERHAAK_AML_WITH_NPM1_MUTATED_UP&fileType=xml'
downloaded 12 KB

trying URL 'http://software.broadinstitute.org/gsea/msigdb/download_geneset.jsp?geneSetName=VERHAAK_AML_WITH_NPM1_MUTATED_DN&fileType=xml'
downloaded 15 KB

Warning: Ignoring unknown aesthetics: text
Warning: Ignoring unknown aesthetics: text
Warning: Ignoring unknown aesthetics: text
trying URL 'http://software.broadinstitute.org/gsea/msigdb/download_geneset.jsp?geneSetName=ROSS_AML_WITH_MLL_FUSIONS&fileType=xml'
downloaded 6897 bytes

Warning in checkGenes(upSet, rownames(rankData)) :
  7 genes missing: 1066, 339005, 344, 51760, 55511, 653067, 9638
Warning in singleSingscore(rankData, upSet, downSet = downSet, subSamples = subSamples,  :
  'centerScore' is disabled for this setting
Warning: Ignoring unknown aesthetics: text
trying URL 'http://software.broadinstitute.org/gsea/msigdb/download_geneset.jsp?geneSetName=ROSS_AML_WITH_PML_RARA_FUSION&fileType=xml'
downloaded 6906 bytes

Warning in checkGenes(upSet, rownames(rankData)) :
  7 genes missing: 11209, 1280, 2258, 51285, 55855, 653145, 79605
Warning in singleSingscore(rankData, upSet, downSet = downSet, subSamples = subSamples,  :
  'centerScore' is disabled for this setting
Warning: Ignoring unknown aesthetics: text
--- finished re-building ‘workflow_transcriptional_mut_sig_chinese.Rmd’

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

Error: Vignette re-building failed.
Execution halted