BioC 3.5: BUILD report for PAnnBuilder on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data PAnnBuilder
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* checking for file ‘PAnnBuilder/DESCRIPTION’ ... OK
* preparing ‘PAnnBuilder’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: RSQLite
Loading required package: Biobase
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, cbind, colMeans, colSums, colnames, 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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

org.Hs.ipiGENEID         package:org.Hs.ipi.db         R Documentation

_M_a_p _p_r_o_t_e_i_n _i_d_e_n_t_i_f_i_e_r _t_o _E_n_t_r_e_z _g_e_n_e _i_d_e_n_t_i_f_i_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     org.Hs.ipiGENEID maps protein identifiers to Entrez Gene
     identifiers.

_D_e_t_a_i_l_s:

     Mappings were based on data provided by: IPI (<URL:
     ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.HUMAN.dat.gz>)
     on Homo sapiens 3.75, 19 Aug 2010

_E_x_a_m_p_l_e_s:

             x <- org.Hs.ipiGENEID
       # Get the protein identifiers that are mapped to Entrez gene identifier.
       mapped_proteins <- mappedkeys(x)
       # Convert to a list
       xx <- as.list(x[mapped_proteins])
             if(length(xx) > 0){
                     # Get the value of the first key
                     xx[[1]]
                     # Get the values for a few keys
                     if(length(xx) >= 3){
                             xx[1:3]
                     }
             }
     

trying URL 'http://gpcr2.biocomp.unibo.it/bacello/dataset.htm'
Content type 'text/html; charset=iso-8859-1' length 5062 bytes
==================================================
downloaded 5062 bytes

sh: wget: command not found
Warning in download.file(srcUrl, fileName, method = "wget", quiet = TRUE) :
  download had nonzero exit status
[filef409b203da0animals_dataset.zip]
  End-of-central-directory signature not found.  Either this file is not
  a zipfile, or it constitutes one disk of a multi-part archive.  In the
  latter case the central directory and zipfile comment will be found on
  the last disk(s) of this archive.
unzip:  cannot find zipfile directory in one of filef409b203da0animals_dataset.zip or
        filef409b203da0animals_dataset.zip.zip, and cannot find filef409b203da0animals_dataset.zip.ZIP, period.
Warning: running command '/usr/bin/unzip -q filef409b203da0animals_dataset.zip' had status 9
sh: wget: command not found
Warning in download.file(srcUrl, fileName, method = "wget", quiet = TRUE) :
  download had nonzero exit status
[filef40971add914fungi_dataset.zip]
  End-of-central-directory signature not found.  Either this file is not
  a zipfile, or it constitutes one disk of a multi-part archive.  In the
  latter case the central directory and zipfile comment will be found on
  the last disk(s) of this archive.
unzip:  cannot find zipfile directory in one of filef40971add914fungi_dataset.zip or
        filef40971add914fungi_dataset.zip.zip, and cannot find filef40971add914fungi_dataset.zip.ZIP, period.
Warning: running command '/usr/bin/unzip -q filef40971add914fungi_dataset.zip' had status 9
sh: wget: command not found
Warning in download.file(srcUrl, fileName, method = "wget", quiet = TRUE) :
  download had nonzero exit status
[filef4094c86ea5aplants_dataset.zip]
  End-of-central-directory signature not found.  Either this file is not
  a zipfile, or it constitutes one disk of a multi-part archive.  In the
  latter case the central directory and zipfile comment will be found on
  the last disk(s) of this archive.
unzip:  cannot find zipfile directory in one of filef4094c86ea5aplants_dataset.zip or
        filef4094c86ea5aplants_dataset.zip.zip, and cannot find filef4094c86ea5aplants_dataset.zip.ZIP, period.
Warning: running command '/usr/bin/unzip -q filef4094c86ea5aplants_dataset.zip' had status 9
Warning: Closing open result set, pending rows
Warning: Closing open result set, pending rows
Warning: Closing open result set, pending rows
Warning: Closing open result set, pending rows
Warning: Closing open result set, pending rows
Warning: Closing open result set, pending rows
Warning in rsqlite_disconnect(conn@ptr) :
  There are 1 result in use. The connection will be released when they are closed
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'PAnnBuilder.tex' failed.
LaTeX errors:
! Package auto-pst-pdf Error: 
    "shell escape" (or "write18") is not enabled:
    auto-pst-pdf will not work!
.

! Emergency stop.
 ...                                              
                                                  
l.134         Or turn off auto-pst-pdf.}
                                        %
!  ==> Fatal error occurred, no output PDF file produced!
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted
BioC 3.5: BUILD report for PAnnBuilder on oaxaca

Summary

Command output
