##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data glmSparseNet
###
##############################################################################
##############################################################################
* checking for file ‘glmSparseNet/DESCRIPTION’ ... OK
* preparing ‘glmSparseNet’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘example_brca_logistic.Rmd’ using rmarkdown
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: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following object is masked from 'package:dplyr':
count
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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 objects are masked from 'package:base':
I, expand.grid, unname
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'TCGAutils'
The following object is masked from 'package:MultiAssayExperiment':
splitAssays
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Loading required package: glmnet
Loaded glmnet 4.1-3
snapshotDate(): 2021-10-19
Working on: BRCA_RNASeq2GeneNorm-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BRCA_colData-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BRCA_metadata-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: BRCA_sampleMap-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
harmonizing input:
removing 13161 sampleMap rows not in names(experiments)
removing 5 colData rownames not in sampleMap 'primary'
* Hostname www.ensembl.org was found in DNS cache
* Trying 193.62.193.83:443...
* TCP_NODELAY set
* Connected to www.ensembl.org (193.62.193.83) port 443 (#6)
* ALPN, offering h2
* ALPN, offering http/1.1
* successfully set certificate verify locations:
* CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs
* SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256
* ALPN, server did not agree to a protocol
* Server certificate:
* subject: OU=Domain Control Validated; CN=*.ensembl.org
* start date: May 6 13:36:20 2020 GMT
* expire date: May 18 08:32:01 2022 GMT
* issuer: C=US; ST=Arizona; L=Scottsdale; O=GoDaddy.com, Inc.; OU=http://certs.godaddy.com/repository/; CN=Go Daddy Secure Certificate Authority - G2
* SSL certificate verify ok.
> GET /biomart/martservice?type=registry&requestid=biomaRt&redirect=no HTTP/1.1
Host: www.ensembl.org
User-Agent: libcurl/7.68.0 r-curl/4.3.2 httr/1.4.2
Accept-Encoding: deflate, gzip, br
Accept: application/json, text/xml, application/xml, */*
Content-Type: text/plain
* Operation timed out after 10000 milliseconds with 0 bytes received
* Closing connection 6
* Trying 46.137.253.241:443...
* TCP_NODELAY set
* Connected to asia.ensembl.org (46.137.253.241) port 443 (#7)
* ALPN, offering h2
* ALPN, offering http/1.1
* successfully set certificate verify locations:
* CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs
* SSL connection using TLSv1.2 / ECDHE-RSA-AES256-GCM-SHA384
* ALPN, server did not agree to a protocol
* Server certificate:
* subject: OU=Domain Control Validated; CN=*.ensembl.org
* start date: May 6 13:36:20 2020 GMT
* expire date: May 18 08:32:01 2022 GMT
* issuer: C=US; ST=Arizona; L=Scottsdale; O=GoDaddy.com, Inc.; OU=http://certs.godaddy.com/repository/; CN=Go Daddy Secure Certificate Authority - G2
* SSL certificate verify result: unable to get local issuer certificate (20), continuing anyway.
> GET /biomart/martservice?type=registry&requestid=biomaRt&redirect=no HTTP/1.1
Host: asia.ensembl.org
User-Agent: libcurl/7.68.0 r-curl/4.3.2 httr/1.4.2
Accept-Encoding: deflate, gzip, br
Accept: application/json, text/xml, application/xml, */*
Content-Type: text/plain
* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< Date: Tue, 12 Apr 2022 08:41:19 GMT
< Server: Apache
< Connection: close
< Transfer-Encoding: chunked
< Content-Type: text/plain; charset=utf-8
<
* Closing connection 7
* Hostname www.ensembl.org was found in DNS cache
* Trying 193.62.193.83:443...
* TCP_NODELAY set
* Connected to www.ensembl.org (193.62.193.83) port 443 (#8)
* ALPN, offering h2
* ALPN, offering http/1.1
* successfully set certificate verify locations:
* CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs
* SSL re-using session ID
* SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256
* ALPN, server did not agree to a protocol
* Server certificate:
* subject: OU=Domain Control Validated; CN=*.ensembl.org
* start date: May 6 13:36:20 2020 GMT
* expire date: May 18 08:32:01 2022 GMT
* issuer: C=US; ST=Arizona; L=Scottsdale; O=GoDaddy.com, Inc.; OU=http://certs.godaddy.com/repository/; CN=Go Daddy Secure Certificate Authority - G2
* SSL certificate verify ok.
> GET /biomart/martservice?redirect=no&type=version&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL HTTP/1.1
Host: www.ensembl.org
User-Agent: libcurl/7.68.0 r-curl/4.3.2 httr/1.4.2
Accept-Encoding: deflate, gzip, br
Accept: application/json, text/xml, application/xml, */*
Content-Type: text/plain
* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< Date: Tue, 12 Apr 2022 08:41:23 GMT
< Server: Apache
< Transfer-Encoding: chunked
< Content-Type: text/plain; charset=utf-8
<
* Connection #8 to host www.ensembl.org left intact
* Found bundle for host www.ensembl.org: 0x557c2709a9f0 [serially]
* Can not multiplex, even if we wanted to!
* Re-using existing connection! (#8) with host www.ensembl.org
* Connected to www.ensembl.org (193.62.193.83) port 443 (#8)
> GET /biomart/martservice?redirect=no&type=datasets&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL HTTP/1.1
Host: www.ensembl.org
User-Agent: libcurl/7.68.0 r-curl/4.3.2 httr/1.4.2
Accept-Encoding: deflate, gzip, br
Accept: application/json, text/xml, application/xml, */*
Content-Type: text/plain
* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< Date: Tue, 12 Apr 2022 08:41:29 GMT
< Server: Apache
< Transfer-Encoding: chunked
< Content-Type: text/plain; charset=utf-8
<
* Connection #8 to host www.ensembl.org left intact
* Found bundle for host www.ensembl.org: 0x557c2709a9f0 [serially]
* Can not multiplex, even if we wanted to!
* Re-using existing connection! (#8) with host www.ensembl.org
* Connected to www.ensembl.org (193.62.193.83) port 443 (#8)
> GET /biomart/martservice?redirect=no&type=attributes&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default HTTP/1.1
Host: www.ensembl.org
User-Agent: libcurl/7.68.0 r-curl/4.3.2 httr/1.4.2
Accept-Encoding: deflate, gzip, br
Accept: application/json, text/xml, application/xml, */*
Content-Type: text/plain
* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< Date: Tue, 12 Apr 2022 08:41:37 GMT
< Server: Apache
< Transfer-Encoding: chunked
< Content-Type: text/plain; charset=utf-8
<
* Operation timed out after 10000 milliseconds with 377159 bytes received
* Closing connection 8
* Hostname useast.ensembl.org was found in DNS cache
* Trying 107.22.174.6:443...
* TCP_NODELAY set
* Connected to useast.ensembl.org (107.22.174.6) port 443 (#9)
* ALPN, offering h2
* ALPN, offering http/1.1
* successfully set certificate verify locations:
* CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs
* SSL connection using TLSv1.2 / ECDHE-RSA-AES256-GCM-SHA384
* ALPN, server did not agree to a protocol
* Server certificate:
* subject: OU=Domain Control Validated; CN=*.ensembl.org
* start date: May 6 13:36:20 2020 GMT
* expire date: May 18 08:32:01 2022 GMT
* issuer: C=US; ST=Arizona; L=Scottsdale; O=GoDaddy.com, Inc.; OU=http://certs.godaddy.com/repository/; CN=Go Daddy Secure Certificate Authority - G2
* SSL certificate verify result: unable to get local issuer certificate (20), continuing anyway.
> GET /biomart/martservice?redirect=no&type=attributes&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default HTTP/1.1
Host: useast.ensembl.org
User-Agent: libcurl/7.68.0 r-curl/4.3.2 httr/1.4.2
Accept-Encoding: deflate, gzip, br
Accept: application/json, text/xml, application/xml, */*
Content-Type: text/plain
* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< Date: Tue, 12 Apr 2022 08:41:39 GMT
< Server: Apache
< Connection: close
< Transfer-Encoding: chunked
< Content-Type: text/plain; charset=utf-8
<
* Closing connection 9
* Hostname www.ensembl.org was found in DNS cache
* Trying 193.62.193.83:443...
* TCP_NODELAY set
* Connected to www.ensembl.org (193.62.193.83) port 443 (#10)
* ALPN, offering h2
* ALPN, offering http/1.1
* successfully set certificate verify locations:
* CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs
* SSL re-using session ID
* SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256
* ALPN, server did not agree to a protocol
* Server certificate:
* subject: OU=Domain Control Validated; CN=*.ensembl.org
* start date: May 6 13:36:20 2020 GMT
* expire date: May 18 08:32:01 2022 GMT
* issuer: C=US; ST=Arizona; L=Scottsdale; O=GoDaddy.com, Inc.; OU=http://certs.godaddy.com/repository/; CN=Go Daddy Secure Certificate Authority - G2
* SSL certificate verify ok.
> GET /biomart/martservice?redirect=no&type=filters&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default HTTP/1.1
Host: www.ensembl.org
User-Agent: libcurl/7.68.0 r-curl/4.3.2 httr/1.4.2
Accept-Encoding: deflate, gzip, br
Accept: application/json, text/xml, application/xml, */*
Content-Type: text/plain
* Operation timed out after 10000 milliseconds with 0 bytes received
* Closing connection 10
* Hostname useast.ensembl.org was found in DNS cache
* Trying 107.22.174.6:443...
* TCP_NODELAY set
* Connected to useast.ensembl.org (107.22.174.6) port 443 (#11)
* ALPN, offering h2
* ALPN, offering http/1.1
* successfully set certificate verify locations:
* CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs
* SSL re-using session ID
* SSL connection using TLSv1.2 / ECDHE-RSA-AES256-GCM-SHA384
* ALPN, server did not agree to a protocol
* Server certificate:
* subject: OU=Domain Control Validated; CN=*.ensembl.org
* start date: May 6 13:36:20 2020 GMT
* expire date: May 18 08:32:01 2022 GMT
* issuer: C=US; ST=Arizona; L=Scottsdale; O=GoDaddy.com, Inc.; OU=http://certs.godaddy.com/repository/; CN=Go Daddy Secure Certificate Authority - G2
* SSL certificate verify result: unable to get local issuer certificate (20), continuing anyway.
> GET /biomart/martservice?redirect=no&type=filters&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default HTTP/1.1
Host: useast.ensembl.org
User-Agent: libcurl/7.68.0 r-curl/4.3.2 httr/1.4.2
Accept-Encoding: deflate, gzip, br
Accept: application/json, text/xml, application/xml, */*
Content-Type: text/plain
* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< Date: Tue, 12 Apr 2022 08:41:50 GMT
< Server: Apache
< Connection: close
< Transfer-Encoding: chunked
< Content-Type: text/plain; charset=utf-8
<
* Closing connection 11
Quitting from lines 133-134 (example_brca_logistic.Rmd)
Error: processing vignette 'example_brca_logistic.Rmd' failed with diagnostics:
Problem while computing `..1 = value > 0`.
Caused by error:
! object 'value' not found
--- failed re-building ‘example_brca_logistic.Rmd’
--- re-building ‘example_brca_protein-protein-interactions_survival.Rmd’ using rmarkdown
Loading required package: grid
Warning: Problem while computing `Days.to.Last.Contact =
as.integer(Days.to.Date.of.Last.Contact)`.
ℹ NAs introduced by coercion
Warning in gsub("~m", msg, message, fixed = TRUE) :
argument 'replacement' has length > 1 and only the first element will be used
--- finished re-building ‘example_brca_protein-protein-interactions_survival.Rmd’
--- re-building ‘example_brca_survival.Rmd’ using rmarkdown
Warning: Problem while computing `Days.to.Last.Contact =
as.integer(Days.to.Date.of.Last.Contact)`.
ℹ NAs introduced by coercion
Quitting from lines 164-165 (example_brca_survival.Rmd)
Error: processing vignette 'example_brca_survival.Rmd' failed with diagnostics:
Problem while computing `..1 = value > 0`.
Caused by error:
! object 'value' not found
--- failed re-building ‘example_brca_survival.Rmd’
--- re-building ‘example_prad_survival.Rmd’ using rmarkdown
Quitting from lines 161-162 (example_prad_survival.Rmd)
Error: processing vignette 'example_prad_survival.Rmd' failed with diagnostics:
Problem while computing `..1 = value > 0`.
Caused by error:
! object 'value' not found
--- failed re-building ‘example_prad_survival.Rmd’
--- re-building ‘example_skcm_survival.Rmd’ using rmarkdown
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 122.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 123.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 138.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 162.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 332.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 376.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 400.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 414.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 438.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 122.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 123.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 138.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 162.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 332.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 376.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 400.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 414.
Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm
= TRUE)`.
ℹ no non-missing arguments to max; returning -Inf
ℹ The warning occurred in row 438.
Quitting from lines 170-171 (example_skcm_survival.Rmd)
Error: processing vignette 'example_skcm_survival.Rmd' failed with diagnostics:
Problem while computing `..1 = value > 0`.
Caused by error:
! object 'value' not found
--- failed re-building ‘example_skcm_survival.Rmd’
--- re-building ‘separate2GroupsCox.Rmd’ using rmarkdown
--- finished re-building ‘separate2GroupsCox.Rmd’
SUMMARY: processing the following files failed:
‘example_brca_logistic.Rmd’ ‘example_brca_survival.Rmd’
‘example_prad_survival.Rmd’ ‘example_skcm_survival.Rmd’
Error: Vignette re-building failed.
Execution halted