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This page was generated on 2022-04-13 12:06:39 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD results for glmSparseNet on tokay2


To the developers/maintainers of the glmSparseNet package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/glmSparseNet.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 789/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
glmSparseNet 1.12.0  (landing page)
André Veríssimo
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/glmSparseNet
git_branch: RELEASE_3_14
git_last_commit: d305a80
git_last_commit_date: 2021-10-26 12:46:59 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: glmSparseNet
Version: 1.12.0
Command: chmod a+r glmSparseNet -R && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data glmSparseNet
StartedAt: 2022-04-12 11:02:44 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 11:11:40 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 535.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r glmSparseNet -R && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe 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

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")'.


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'
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