glmSparseNet 1.1.0
André Veríssimo
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/glmSparseNet |
| Branch: master |
| Last Commit: 9604319 |
| Last Changed Date: 2018-10-30 11:54:40 -0400 (Tue, 30 Oct 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | ERROR | skipped | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | [ ERROR ] | skipped | skipped | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### chmod a+r glmSparseNet -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data glmSparseNet
###
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* 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
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, colMeans, colSums, 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, rowMeans,
rowSums, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:dplyr':
first, rename
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following objects are masked from 'package:dplyr':
collapse, desc, slice
The following object is masked from 'package:grDevices':
windows
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
The following object is masked from 'package:dplyr':
count
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, rowsum
Registered S3 method overwritten by 'rvest':
method from
read_xml.response xml2
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Loading required package: glmnet
Loading required package: foreach
Loaded glmnet 2.0-16
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_brca_logistic_files/figure-html/results-1.png" -trim "example_brca_logistic_files/figure-html/results-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_brca_logistic_files/figure-html/hallmarks-1.png" -trim "example_brca_logistic_files/figure-html/hallmarks-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_brca_logistic_files/figure-html/predict-1.png" -trim "example_brca_logistic_files/figure-html/predict-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_brca_logistic_files/figure-html/roc-1.png" -trim "example_brca_logistic_files/figure-html/roc-1.png"' execution failed with error code 4
--- finished re-building 'example_brca_logistic.Rmd'
--- re-building 'example_brca_protein-protein-interactions_survival.Rmd' using rmarkdown
Loading required package: grid
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_brca_protein-protein-interactions_survival_files/figure-html/unnamed-chunk-7-1.png" -trim "example_brca_protein-protein-interactions_survival_files/figure-html/unnamed-chunk-7-1.png"' execution failed with error code 4
Warning: NAs introduced by coercion
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_brca_protein-protein-interactions_survival_files/figure-html/unnamed-chunk-11-1.png" -trim "example_brca_protein-protein-interactions_survival_files/figure-html/unnamed-chunk-11-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_brca_protein-protein-interactions_survival_files/figure-html/unnamed-chunk-15-1.png" -trim "example_brca_protein-protein-interactions_survival_files/figure-html/unnamed-chunk-15-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_brca_protein-protein-interactions_survival_files/figure-html/unnamed-chunk-17-1.png" -trim "example_brca_protein-protein-interactions_survival_files/figure-html/unnamed-chunk-17-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_brca_protein-protein-interactions_survival_files/figure-html/unnamed-chunk-19-1.png" -trim "example_brca_protein-protein-interactions_survival_files/figure-html/unnamed-chunk-19-1.png"' execution failed with error code 4
Warning in gsub("˜m", msg, message, fixed = TRUE) :
argument 'replacement' has length > 1 and only the first element will be used
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_brca_protein-protein-interactions_survival_files/figure-html/unnamed-chunk-20-1.png" -trim "example_brca_protein-protein-interactions_survival_files/figure-html/unnamed-chunk-20-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_brca_protein-protein-interactions_survival_files/figure-html/unnamed-chunk-21-1.png" -trim "example_brca_protein-protein-interactions_survival_files/figure-html/unnamed-chunk-21-1.png"' execution failed with error code 4
--- finished re-building 'example_brca_protein-protein-interactions_survival.Rmd'
--- re-building 'example_brca_survival.Rmd' using rmarkdown
Warning: NAs introduced by coercion
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_brca_survival_files/figure-html/results-1.png" -trim "example_brca_survival_files/figure-html/results-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_brca_survival_files/figure-html/hallmarks-1.png" -trim "example_brca_survival_files/figure-html/hallmarks-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_brca_survival_files/figure-html/unnamed-chunk-2-1.png" -trim "example_brca_survival_files/figure-html/unnamed-chunk-2-1.png"' execution failed with error code 4
--- finished re-building 'example_brca_survival.Rmd'
--- re-building 'example_prad_survival.Rmd' using rmarkdown
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_prad_survival_files/figure-html/results-1.png" -trim "example_prad_survival_files/figure-html/results-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_prad_survival_files/figure-html/hallmarks-1.png" -trim "example_prad_survival_files/figure-html/hallmarks-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_prad_survival_files/figure-html/unnamed-chunk-2-1.png" -trim "example_prad_survival_files/figure-html/unnamed-chunk-2-1.png"' execution failed with error code 4
--- finished re-building 'example_prad_survival.Rmd'
--- re-building 'example_skcm_survival.Rmd' using rmarkdown
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "example_skcm_survival_files/figure-html/results-1.png" -trim "example_skcm_survival_files/figure-html/results-1.png"' execution failed with error code 4
Quitting from lines 161-162 (example_skcm_survival.Rmd)
Error: processing vignette 'example_skcm_survival.Rmd' failed with diagnostics:
object 'variable' not found
--- failed re-building 'example_skcm_survival.Rmd'
SUMMARY: processing the following file failed:
'example_skcm_survival.Rmd'
Error: Vignette re-building failed.
Execution halted