Package: genphen

Version: 1.8.0

Command: chmod a+r genphen -R && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data genphen

StartedAt: 2018-10-16 23:03:42 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:05:37 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 114.6 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r genphen -R && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data genphen
###
##############################################################################
##############################################################################


* checking for file 'genphen/DESCRIPTION' ... OK
* preparing 'genphen':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: genphen
Loading required package: e1071
Loading required package: Biostrings
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: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, lengths, 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
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: rstan
Loading required package: ggplot2
Loading required package: StanHeaders
rstan (Version 2.17.4, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Loading required package: ranger
Loading required package: foreach
Loading required package: doParallel
Loading required package: iterators
Loading required package: knitr
Loading required package: ggrepel
Loading required package: reshape2
Loading required package: ape

Attaching package: 'ape'

The following object is masked from 'package:Biostrings':

    complement

Loading required package: xtable
Warning in stan_model(file = f.pkg, model_name = "model") :
  StanHeaders version is ahead of rstan version; update to latest rstan
Warning in system(cmd, intern = !verbose) :
  running command 'C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64/R CMD SHLIB file13586ccc75c4.cpp 2> file13586ccc75c4.cpp.err.txt' had status 1

Error: processing vignette 'genphenManual.Rnw' failed with diagnostics:
 chunk 1 
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/config.hpp:39:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/math/tools/config.hpp:13,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/StanHeaders/include/stan/math/rev/core/var.hpp:7,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/StanHeaders/include/stan/math/rev/core/gevv_vvv_vari.hpp:5,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:12,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/StanHeaders/include/stan/math.hpp:4,
                 from C:
Execution halted