ldblock 1.17.1
VJ Carey
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/ldblock |
| Branch: master |
| Last Commit: 2a9fa63 |
| Last Changed Date: 2019-11-25 09:45:26 -0500 (Mon, 25 Nov 2019) |
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | [ OK ] | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ldblock
###
##############################################################################
##############################################################################
* checking for file ‘ldblock/DESCRIPTION’ ... OK
* preparing ‘ldblock’:
* 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 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2018-04-01> patch level 2
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./Rd2.tex (/usr/local/texlive/2018/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2018/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2018/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2018/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 377.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 377.
) (/usr/local/texlive/2018/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/inputenc.sty)
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2018/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1phv.fd)
Underfull \hbox (badness 10000) in paragraph at lines 40--40
[]\T1/ptm/m/it/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_title(\"#
1\")",
Underfull \hbox (badness 1342) in paragraph at lines 40--40
\T1/ptm/m/it/10 "ld-block")data struc-tures for link-age dis-e-qui-lib-rium mea
-sures in
Overfull \hbox (15.39606pt too wide) in paragraph at lines 45--47
[]\T1/ptm/m/n/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_descriptio
n(\"#1\")", "ld-block")Define data struc-
Overfull \hbox (25.26584pt too wide) in paragraph at lines 50--57
[]\T1/ptm/m/n/10 The DE-SCRIP-TION file: c("\Sexpr[results=rd,stage=build]tools
:::Rd_package_DESCRIPTION(\"#1\")",
Overfull \hbox (49.72574pt too wide) in paragraph at lines 50--57
\T1/ptm/m/n/10 rium mea-sures in pop-u-la-tions\cr Ver-sion: \tab 1.17.1\cr Au-
thor: \tab VJ Carey <stvjc@channing.harvard.edu>\cr
Overfull \hbox (56.36618pt too wide) in paragraph at lines 50--57
\T1/ptm/m/n/10 Rox-y-gen-Note: \tab 6.1.1\cr En-cod-ing: \tab UTF-8\cr git_url:
\tab https://git.bioconductor.org/packages/ldblock\cr
Overfull \hbox (63.84549pt too wide) in paragraph at lines 50--57
\T1/ptm/m/n/10 25\cr Date/Publication: \tab 2020-01-15\cr } c("\Sexpr[results=r
d,stage=build]tools:::Rd_package_indices(\"#1\")",
Overfull \hbox (8.41577pt too wide) in paragraph at lines 50--57
\T1/ptm/m/n/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_title(\"#1\"
)", "ld-block")data struc-tures for link-
Overfull \hbox (26.38489pt too wide) in paragraph at lines 50--57
\T1/ptm/m/n/10 age dis-e-qui-lib-rium mea-sures in pop-u-la-tions ld-mat use LD
-mat API from NCI LDlink ser-vice ldmat,ldstruct-
[1{/usr/local/texlive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (91.02522pt too wide) in paragraph at lines 60--62
[]\T1/ptm/m/n/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_author(\"#
1\")", "ld-block")VJ Carey <stvjc@channing.harvard.edu>
Overfull \hbox (4.40584pt too wide) in paragraph at lines 63--66
[]\T1/ptm/m/n/10 Maintainer: c("\Sexpr[results=rd,stage=build]tools:::Rd_packag
e_maintainer(\"#1\")", "ld-block")VJ
[2]
Overfull \hbox (173.10059pt too wide) in paragraph at lines 86--86
[] \T1/zi4/m/n/10 urlTemplate = "http://hapmap.ncbi.nlm.nih.gov/downloads/ld_
data/2009-02_phaseIII_r2/ld_%%CHRN%%_%%POPN%%.txt.gz",[]
[3]
Overfull \hbox (14.65924pt too wide) in paragraph at lines 198--201
[]\T1/ptm/m/n/10 name of gzipped text file as dis-tributed at [][]$\T1/zi4/m/n/
10 hapmap . ncbi . nlm . nih . gov / downloads /
[4] [5]
Overfull \hbox (47.51794pt too wide) in paragraph at lines 299--300
[]\T1/ptm/m/n/10 the API to-ken pro-vided by NCI, de-faults to value of en-vi-r
on-ment vari-able LDLINK_TOKEN
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [6]
[7]
No file Rd2.ind.
[8] (./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.TabixFile} has been referenced but does not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.ld} has been referenced but does not exist, rep
laced by a fixed one
pdfTeX warning (dest): name{Rfn.readVcf} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.genemodel} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.read.delim} has been referenced but does not ex
ist, replaced by a fixed one
{/usr/local/texlive/2018/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2018/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2018/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
18/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2018/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/
2018/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2018/texmf
-dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2018/texmf-dist/font
s/type1/urw/times/utmr8a.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/ur
w/times/utmri8a.pfb>
Output written on Rd2.pdf (8 pages, 104299 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (25 entries accepted, 1 rejected).
Sorting entries....done (120 comparisons).
Generating output file Rd2.ind....done (55 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2018-04-01> patch level 2
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./Rd2.tex (/usr/local/texlive/2018/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2018/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2018/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2018/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 377.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 377.
) (/usr/local/texlive/2018/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/inputenc.sty)
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2018/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc)
Underfull \hbox (badness 10000) in paragraph at lines 40--40
[]\T1/ptm/m/it/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_title(\"#
1\")",
Underfull \hbox (badness 1342) in paragraph at lines 40--40
\T1/ptm/m/it/10 "ld-block")data struc-tures for link-age dis-e-qui-lib-rium mea
-sures in
[1{/usr/local/texlive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (15.39606pt too wide) in paragraph at lines 45--47
[]\T1/ptm/m/n/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_descriptio
n(\"#1\")", "ld-block")Define data struc-
Overfull \hbox (25.26584pt too wide) in paragraph at lines 50--57
[]\T1/ptm/m/n/10 The DE-SCRIP-TION file: c("\Sexpr[results=rd,stage=build]tools
:::Rd_package_DESCRIPTION(\"#1\")",
Overfull \hbox (49.72574pt too wide) in paragraph at lines 50--57
\T1/ptm/m/n/10 rium mea-sures in pop-u-la-tions\cr Ver-sion: \tab 1.17.1\cr Au-
thor: \tab VJ Carey <stvjc@channing.harvard.edu>\cr
Overfull \hbox (56.36618pt too wide) in paragraph at lines 50--57
\T1/ptm/m/n/10 Rox-y-gen-Note: \tab 6.1.1\cr En-cod-ing: \tab UTF-8\cr git_url:
\tab https://git.bioconductor.org/packages/ldblock\cr
Overfull \hbox (63.84549pt too wide) in paragraph at lines 50--57
\T1/ptm/m/n/10 25\cr Date/Publication: \tab 2020-01-15\cr } c("\Sexpr[results=r
d,stage=build]tools:::Rd_package_indices(\"#1\")",
Overfull \hbox (8.41577pt too wide) in paragraph at lines 50--57
\T1/ptm/m/n/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_title(\"#1\"
)", "ld-block")data struc-tures for link-
Overfull \hbox (26.38489pt too wide) in paragraph at lines 50--57
\T1/ptm/m/n/10 age dis-e-qui-lib-rium mea-sures in pop-u-la-tions ld-mat use LD
-mat API from NCI LDlink ser-vice ldmat,ldstruct-
Overfull \hbox (91.02522pt too wide) in paragraph at lines 60--62
[]\T1/ptm/m/n/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_author(\"#
1\")", "ld-block")VJ Carey <stvjc@channing.harvard.edu>
Overfull \hbox (4.40584pt too wide) in paragraph at lines 63--66
[]\T1/ptm/m/n/10 Maintainer: c("\Sexpr[results=rd,stage=build]tools:::Rd_packag
e_maintainer(\"#1\")", "ld-block")VJ
[2]
Overfull \hbox (173.10059pt too wide) in paragraph at lines 86--86
[] \T1/zi4/m/n/10 urlTemplate = "http://hapmap.ncbi.nlm.nih.gov/downloads/ld_
data/2009-02_phaseIII_r2/ld_%%CHRN%%_%%POPN%%.txt.gz",[]
[3]
Overfull \hbox (14.65924pt too wide) in paragraph at lines 198--201
[]\T1/ptm/m/n/10 name of gzipped text file as dis-tributed at [][]$\T1/zi4/m/n/
10 hapmap . ncbi . nlm . nih . gov / downloads /
[4] [5]
Overfull \hbox (47.51794pt too wide) in paragraph at lines 299--300
[]\T1/ptm/m/n/10 the API to-ken pro-vided by NCI, de-faults to value of en-vi-r
on-ment vari-able LDLINK_TOKEN
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [6]
[7] (./Rd2.ind [8]
LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font) using `T1/zi4/m/n' instead on input line 33.
[9]) (./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.TabixFile} has been referenced but does not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.ld} has been referenced but does not exist, rep
laced by a fixed one
pdfTeX warning (dest): name{Rfn.readVcf} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.genemodel} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.read.delim} has been referenced but does not ex
ist, replaced by a fixed one
{/usr/local/texlive/2018/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2018/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2018/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
18/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2018/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/te
xlive/2018/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2
018/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2018/texmf-
dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2018/texmf-dist/fonts
/type1/urw/times/utmr8a.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/urw
/times/utmri8a.pfb>
Output written on Rd2.pdf (9 pages, 114541 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (25 entries accepted, 1 rejected).
Sorting entries....done (120 comparisons).
Generating output file Rd2.ind....done (55 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2018-04-01> patch level 2
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./Rd2.tex (/usr/local/texlive/2018/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2018/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2018/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2018/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 377.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 377.
) (/usr/local/texlive/2018/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/inputenc.sty)
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2018/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc)
[1{/usr/local/texlive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
Underfull \hbox (badness 10000) in paragraph at lines 40--40
[]\T1/ptm/m/it/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_title(\"#
1\")",
Underfull \hbox (badness 1342) in paragraph at lines 40--40
\T1/ptm/m/it/10 "ld-block")data struc-tures for link-age dis-e-qui-lib-rium mea
-sures in
Overfull \hbox (15.39606pt too wide) in paragraph at lines 45--47
[]\T1/ptm/m/n/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_descriptio
n(\"#1\")", "ld-block")Define data struc-
Overfull \hbox (25.26584pt too wide) in paragraph at lines 50--57
[]\T1/ptm/m/n/10 The DE-SCRIP-TION file: c("\Sexpr[results=rd,stage=build]tools
:::Rd_package_DESCRIPTION(\"#1\")",
Overfull \hbox (49.72574pt too wide) in paragraph at lines 50--57
\T1/ptm/m/n/10 rium mea-sures in pop-u-la-tions\cr Ver-sion: \tab 1.17.1\cr Au-
thor: \tab VJ Carey <stvjc@channing.harvard.edu>\cr
Overfull \hbox (56.36618pt too wide) in paragraph at lines 50--57
\T1/ptm/m/n/10 Rox-y-gen-Note: \tab 6.1.1\cr En-cod-ing: \tab UTF-8\cr git_url:
\tab https://git.bioconductor.org/packages/ldblock\cr
Overfull \hbox (63.84549pt too wide) in paragraph at lines 50--57
\T1/ptm/m/n/10 25\cr Date/Publication: \tab 2020-01-15\cr } c("\Sexpr[results=r
d,stage=build]tools:::Rd_package_indices(\"#1\")",
Overfull \hbox (8.41577pt too wide) in paragraph at lines 50--57
\T1/ptm/m/n/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_title(\"#1\"
)", "ld-block")data struc-tures for link-
Overfull \hbox (26.38489pt too wide) in paragraph at lines 50--57
\T1/ptm/m/n/10 age dis-e-qui-lib-rium mea-sures in pop-u-la-tions ld-mat use LD
-mat API from NCI LDlink ser-vice ldmat,ldstruct-
Overfull \hbox (91.02522pt too wide) in paragraph at lines 60--62
[]\T1/ptm/m/n/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_author(\"#
1\")", "ld-block")VJ Carey <stvjc@channing.harvard.edu>
Overfull \hbox (4.40584pt too wide) in paragraph at lines 63--66
[]\T1/ptm/m/n/10 Maintainer: c("\Sexpr[results=rd,stage=build]tools:::Rd_packag
e_maintainer(\"#1\")", "ld-block")VJ
[2]
Overfull \hbox (173.10059pt too wide) in paragraph at lines 86--86
[] \T1/zi4/m/n/10 urlTemplate = "http://hapmap.ncbi.nlm.nih.gov/downloads/ld_
data/2009-02_phaseIII_r2/ld_%%CHRN%%_%%POPN%%.txt.gz",[]
[3]
Overfull \hbox (14.65924pt too wide) in paragraph at lines 198--201
[]\T1/ptm/m/n/10 name of gzipped text file as dis-tributed at [][]$\T1/zi4/m/n/
10 hapmap . ncbi . nlm . nih . gov / downloads /
[4] [5]
Overfull \hbox (47.51794pt too wide) in paragraph at lines 299--300
[]\T1/ptm/m/n/10 the API to-ken pro-vided by NCI, de-faults to value of en-vi-r
on-ment vari-able LDLINK_TOKEN
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [6]
[7] (./Rd2.ind [8]
LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font) using `T1/zi4/m/n' instead on input line 33.
[9]) (./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.TabixFile} has been referenced but does not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.ld} has been referenced but does not exist, rep
laced by a fixed one
pdfTeX warning (dest): name{Rfn.readVcf} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.genemodel} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.read.delim} has been referenced but does not ex
ist, replaced by a fixed one
{/usr/local/texlive/2018/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2018/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2018/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
18/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2018/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/te
xlive/2018/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2
018/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2018/texmf-
dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2018/texmf-dist/fonts
/type1/urw/times/utmr8a.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/urw
/times/utmri8a.pfb>
Output written on Rd2.pdf (9 pages, 114796 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/RtmpFoR9Lp/Rbuild143da689eef67/ldblock/build/ldblock.pdf’ ...
Done
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘ldblock_1.17.1.tar.gz’