Back to the "Multiple platform build/check report" A [B] C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 73/658HostnameOS / ArchBUILDCHECKBUILD BIN
BiocParallel 0.0.12
Bioconductor Package Maintainer
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocParallel
Last Changed Rev: 73871 / Revision: 74774
Last Changed Date: 2013-03-01 17:45:14 -0800 (Fri, 01 Mar 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Leopard (10.5.8) / i386 [ OK ] WARNINGS  OK 

Summary

Package: BiocParallel
Version: 0.0.12
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BiocParallel
StartedAt: 2013-03-25 00:38:35 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 00:38:43 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 7.6 seconds
RetCode: 0
Status:  OK 
PackageFile: BiocParallel_0.0.12.tar.gz
PackageFileSize: 123.6 KiB

Command output

* checking for file 'BiocParallel/DESCRIPTION' ... OK
* preparing 'BiocParallel':
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* building the PDF package manual
Hmm ... looks like a package
Converting Rd files to LaTeX .
Creating pdf output from LaTeX ...

This is pdfTeX, Version 3.1415926-2.3-1.40.12 (TeX Live 2011)
 \write18 enabled.
entering extended mode
(/private/tmp/RtmpMtcVBZ/Rbuild6fbe7f43c10f/BiocParallel/.Rd2pdf28606/Rd2.tex
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2009-06-19, ngerman-x-2009-06-19, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, galician, german, ngerman, swissgerman, monogreek, greek, hungarian,
 icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, marathi, or
iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, kurmanji,
 lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, pol
ish, portuguese, romanian, russian, sanskrit, serbian, serbianc, slovak, sloven
ian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, welsh, loaded
.
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/url/url.sty) NOT loading ae
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/times.sty)
NOT loading lmodern
(/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2011/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2011/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2011/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2011/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/hyperref.cfg))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 356.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 356.

) (/usr/local/texlive/2011/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2011/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
ive/2011/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [3]
Overfull \hbox (8.34976pt too wide) in paragraph at lines 257--259
[]\T1/ptm/m/n/10 See \T1/fi4/m/n/10 showMethods{bplapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/fi4/m/n/10 method?bplapply("MulticoreParam")\T1/
ptm/m/n/10 . 
[4] (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [8]
Overfull \hbox (13.43846pt too wide) in paragraph at lines 624--629
[]\T1/fi4/m/n/10 logical(1) \T1/ptm/m/n/10 in-di-cat-ing whether forked chil-dr
en will be ter-mi-nated be-fore \T1/fi4/m/n/10 bplapply
[9] (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1.9087pt too wide) in paragraph at lines 712--715
[]\T1/ptm/m/n/10 Make this the de-fault \T1/fi4/m/n/10 BiocParallelParam \T1/pt
m/m/n/10 for sub-se-quent eval-u-a-tions? If \T1/fi4/m/n/10 FALSE\T1/ptm/m/n/10
 ,
[10] (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [11]
Overfull \hbox (4.73901pt too wide) in paragraph at lines 897--900
[]\T1/ptm/m/n/10 Use \T1/fi4/m/n/10 as(cl, "SnowParam") \T1/ptm/m/n/10 to co-er
ce a clus-ter cre-ated di-rectly by \T1/fi4/m/n/10 parallel::param \T1/ptm/m/n/
10 to a \T1/fi4/m/n/10 SnowParam
[12]
No file Rd2.ind.
[13] (./Rd2.aux)

Package rerunfilecheck Warning: File `Rd2.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.

 )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.parLapply} has been referenced but does not exist, replaced by a fixed one


pdfTeX warning (dest): name{Rfn.makeCluster} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pvec} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.mclapply} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lapply} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.DoparParam} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.parallel} has been referenced but does not exis
t, replaced by a fixed one

{/usr/local/texlive/2011/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2011/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2011/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2011/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/20
11/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2011/texmf-d
ist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2011/texmf-dist/fonts/
type1/urw/times/utmr8a.pfb></usr/local/texlive/2011/texmf-dist/fonts/type1/urw/
times/utmri8a.pfb>
Output written on Rd2.pdf (13 pages, 94236 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2011] (kpathsea + Thai support).
Scanning input file ./Rd2.idx....done (122 entries accepted, 1 rejected).
Sorting entries....done (953 comparisons).
Generating output file ./Rd2.ind....done (186 lines written, 0 warnings).
Output written in ./Rd2.ind.
Transcript written in ./Rd2.ilg.
This is pdfTeX, Version 3.1415926-2.3-1.40.12 (TeX Live 2011)
 \write18 enabled.
entering extended mode
(/private/tmp/RtmpMtcVBZ/Rbuild6fbe7f43c10f/BiocParallel/.Rd2pdf28606/Rd2.tex
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2009-06-19, ngerman-x-2009-06-19, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, galician, german, ngerman, swissgerman, monogreek, greek, hungarian,
 icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, marathi, or
iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, kurmanji,
 lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, pol
ish, portuguese, romanian, russian, sanskrit, serbian, serbianc, slovak, sloven
ian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, welsh, loaded
.
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/url/url.sty) NOT loading ae
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/times.sty)
NOT loading lmodern
(/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2011/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2011/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2011/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2011/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/hyperref.cfg))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 356.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 356.

) (/usr/local/texlive/2011/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2011/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
ive/2011/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [2] [3]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (8.34976pt too wide) in paragraph at lines 257--259
[]\T1/ptm/m/n/10 See \T1/fi4/m/n/10 showMethods{bplapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/fi4/m/n/10 method?bplapply("MulticoreParam")\T1/
ptm/m/n/10 . 
[4] (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [8]
Overfull \hbox (13.43846pt too wide) in paragraph at lines 624--629
[]\T1/fi4/m/n/10 logical(1) \T1/ptm/m/n/10 in-di-cat-ing whether forked chil-dr
en will be ter-mi-nated be-fore \T1/fi4/m/n/10 bplapply
[9] (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1.9087pt too wide) in paragraph at lines 712--715
[]\T1/ptm/m/n/10 Make this the de-fault \T1/fi4/m/n/10 BiocParallelParam \T1/pt
m/m/n/10 for sub-se-quent eval-u-a-tions? If \T1/fi4/m/n/10 FALSE\T1/ptm/m/n/10
 ,
[10] (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [11]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (4.73901pt too wide) in paragraph at lines 897--900
[]\T1/ptm/m/n/10 Use \T1/fi4/m/n/10 as(cl, "SnowParam") \T1/ptm/m/n/10 to co-er
ce a clus-ter cre-ated di-rectly by \T1/fi4/m/n/10 parallel::param \T1/ptm/m/n/
10 to a \T1/fi4/m/n/10 SnowParam
[12] (./Rd2.ind [13]

LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined
(Font)              using `T1/fi4/m/n' instead on input line 20.


Overfull \hbox (0.8567pt too wide) in paragraph at lines 28--30
[]\T1/fi4/m/it/10 bparallelize,ANY,MulticoreParam-method 

Overfull \hbox (10.8567pt too wide) in paragraph at lines 42--44
[]\T1/fi4/m/it/10 bpbackend<-,SnowParam,SOCKcluster-method 
[14] [15]) (./Rd2.aux)

Package rerunfilecheck Warning: File `Rd2.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.


LaTeX Font Warning: Some font shapes were not available, defaults substituted.

 )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.parLapply} has been referenced but does not exist, replaced by a fixed one


pdfTeX warning (dest): name{Rfn.makeCluster} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pvec} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.mclapply} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lapply} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.DoparParam} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.parallel} has been referenced but does not exis
t, replaced by a fixed one

{/usr/local/texlive/2011/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2011/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2011/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2011/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texl
ive/2011/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/201
1/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2011/texmf-di
st/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2011/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb></usr/local/texlive/2011/texmf-dist/fonts/type1/urw/t
imes/utmri8a.pfb>
Output written on Rd2.pdf (15 pages, 111514 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2011] (kpathsea + Thai support).
Scanning input file ./Rd2.idx....done (122 entries accepted, 1 rejected).
Sorting entries....done (943 comparisons).
Generating output file ./Rd2.ind....done (187 lines written, 0 warnings).
Output written in ./Rd2.ind.
Transcript written in ./Rd2.ilg.
This is pdfTeX, Version 3.1415926-2.3-1.40.12 (TeX Live 2011)
 \write18 enabled.
entering extended mode
(/private/tmp/RtmpMtcVBZ/Rbuild6fbe7f43c10f/BiocParallel/.Rd2pdf28606/Rd2.tex
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2009-06-19, ngerman-x-2009-06-19, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, galician, german, ngerman, swissgerman, monogreek, greek, hungarian,
 icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, marathi, or
iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, kurmanji,
 lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, pol
ish, portuguese, romanian, russian, sanskrit, serbian, serbianc, slovak, sloven
ian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, welsh, loaded
.
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/url/url.sty) NOT loading ae
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/times.sty)
NOT loading lmodern
(/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2011/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2011/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2011/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2011/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/hyperref.cfg))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 356.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 356.

) (/usr/local/texlive/2011/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2011/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
ive/2011/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [2] [3]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (8.34976pt too wide) in paragraph at lines 257--259
[]\T1/ptm/m/n/10 See \T1/fi4/m/n/10 showMethods{bplapply} \T1/ptm/m/n/10 for ad
-di-tional meth-ods, e.g., \T1/fi4/m/n/10 method?bplapply("MulticoreParam")\T1/
ptm/m/n/10 . 
[4] (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [8]
Overfull \hbox (13.43846pt too wide) in paragraph at lines 624--629
[]\T1/fi4/m/n/10 logical(1) \T1/ptm/m/n/10 in-di-cat-ing whether forked chil-dr
en will be ter-mi-nated be-fore \T1/fi4/m/n/10 bplapply
[9] (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1.9087pt too wide) in paragraph at lines 712--715
[]\T1/ptm/m/n/10 Make this the de-fault \T1/fi4/m/n/10 BiocParallelParam \T1/pt
m/m/n/10 for sub-se-quent eval-u-a-tions? If \T1/fi4/m/n/10 FALSE\T1/ptm/m/n/10
 ,
[10] (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [11]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (4.73901pt too wide) in paragraph at lines 897--900
[]\T1/ptm/m/n/10 Use \T1/fi4/m/n/10 as(cl, "SnowParam") \T1/ptm/m/n/10 to co-er
ce a clus-ter cre-ated di-rectly by \T1/fi4/m/n/10 parallel::param \T1/ptm/m/n/
10 to a \T1/fi4/m/n/10 SnowParam
[12] (./Rd2.ind [13]

LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined
(Font)              using `T1/fi4/m/n' instead on input line 20.


Overfull \hbox (0.8567pt too wide) in paragraph at lines 28--30
[]\T1/fi4/m/it/10 bparallelize,ANY,MulticoreParam-method 

Overfull \hbox (10.8567pt too wide) in paragraph at lines 42--44
[]\T1/fi4/m/it/10 bpbackend<-,SnowParam,SOCKcluster-method 
[14] [15]) (./Rd2.aux)

LaTeX Font Warning: Some font shapes were not available, defaults substituted.

 )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.parLapply} has been referenced but does not exist, replaced by a fixed one


pdfTeX warning (dest): name{Rfn.makeCluster} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pvec} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.mclapply} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lapply} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.DoparParam} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.parallel} has been referenced but does not exis
t, replaced by a fixed one

{/usr/local/texlive/2011/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2011/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2011/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2011/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texl
ive/2011/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/201
1/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2011/texmf-di
st/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2011/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb></usr/local/texlive/2011/texmf-dist/fonts/type1/urw/t
imes/utmri8a.pfb>
Output written on Rd2.pdf (15 pages, 112215 bytes).
Transcript written on Rd2.log.
Saving output to '/private/tmp/RtmpMtcVBZ/Rbuild6fbe7f43c10f/BiocParallel/build/BiocParallel.pdf' ...
Done
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'BiocParallel_0.0.12.tar.gz'