############################################################################## ############################################################################## ### ### 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