##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ngsReports
###
##############################################################################
##############################################################################
* checking for file ‘ngsReports/DESCRIPTION’ ... OK
* preparing ‘ngsReports’:
* 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 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-02-25>
(./Rd2.tex (/usr/local/texlive/2019/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2019/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/local/texlive/2019/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2019/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/local/texlive/2019/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2019/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty
)))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 378.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 378.
) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/inputenc.sty)
Writing index file Rd2.idx
(/usr/local/texlive/2019/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
No file Rd2.aux.
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2019/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/gettitlestring/gettitlestring.s
ty)) (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
[1{/usr/local/texlive/2019/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [2]
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1phv.fd
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 20.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 23.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 26.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 46.
) (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [3]
[4]
Overfull \hbox (2.23863pt too wide) in paragraph at lines 240--242
[]\T1/ptm/m/n/10 The un-der-ly-ing data from the Per_sequence_quality_scores mo
d-
Overfull \hbox (6.28877pt too wide) in paragraph at lines 255--257
[]\T1/ptm/m/n/10 The un-der-ly-ing data from the Se-quence_Duplication_Levels m
od-
Overfull \hbox (24.47815pt too wide) in paragraph at lines 265--267
[]\T1/ptm/m/n/10 Estimate taken from the plot data for Se-quence_Duplication_Le
vels.
[5] [6] [7] [8] [9] [10]
Overfull \hbox (63.11093pt too wide) in paragraph at lines 680--691
\T1/zi4/m/n/10 Summary\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Basic_Statistics\T1/ptm/m
/n/10 , \T1/zi4/m/n/10 Per_base_sequence_quality\T1/ptm/m/n/10 , \T1/zi4/m/n/10
Per_tile_sequence_quality\T1/ptm/m/n/10 ,
Overfull \hbox (68.59091pt too wide) in paragraph at lines 680--691
\T1/zi4/m/n/10 Per_sequence_quality_scores\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_b
ase_sequence_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_sequence_GC_content\T1/
ptm/m/n/10 ,
Overfull \hbox (58.59091pt too wide) in paragraph at lines 680--691
\T1/zi4/m/n/10 Per_base_N_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Lengt
h_Distribution\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Duplication_Levels\T1/pt
m/m/n/10 ,
Overfull \hbox (103.11093pt too wide) in paragraph at lines 680--691
\T1/zi4/m/n/10 Overrepresented_sequences\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Adapter
_Content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Kmer_Content\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 Total_Deduplicated_Percentage\T1/ptm/m/n/10 .
[11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24]
Overfull \hbox (23.0476pt too wide) in paragraph at lines 1555--1560
[]\T1/ptm/m/n/10 When act-ing on a \T1/zi4/m/n/10 FastqcDataList\T1/ptm/m/n/10
, this de-faults to a heatmap us-ing the mean Per_base_sequence_quality
[25] [26] [27]
Overfull \hbox (55.89735pt too wide) in paragraph at lines 1774--1777
[]\T1/zi4/m/n/10 character \T1/ptm/m/n/10 vec-tor con-tain-ing the de-sired Fas
tQC mod-ule (eg. c("Per_base_sequence_quality",
[28] [29] [30] [31] [32]
Overfull \hbox (43.32875pt too wide) in paragraph at lines 2074--2076
[]\T1/ptm/m/n/10 The colour palette. If the vec-tor sup-plied is less than n, \
T1/zi4/m/n/10 grDevices::colorRampPalette()
[33] [34] [35]
Overfull \hbox (37.21838pt too wide) in paragraph at lines 2295--2297
[]\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me
ric vec-tors of length 4. Passed to scale_*_continuous()
[36] [37] [38] [39]
Overfull \hbox (0.38704pt too wide) in paragraph at lines 2534--2538
\T1/ptm/m/n/10 plot-ting from mul-ti-ple re-ports. The in-di-vid-ual line plots
are able to be gen-er-ated by set-ting \T1/zi4/m/n/10 plotType
[40]
Overfull \hbox (6.82005pt too wide) in paragraph at lines 2627--2630
[]\T1/zi4/m/n/10 character\T1/ptm/m/n/10 . Can only take the val-ues \T1/zi4/m/
n/10 plotType = "heatmap" plotType = "line"
Overfull \hbox (27.78935pt too wide) in paragraph at lines 2631--2633
[]\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me
ric vec-tor of length 4. Passed to \T1/zi4/m/n/10 scale_x_discrete
[41] [42] [43] [44] [45] [46] [47] [48] [49] [50]
No file Rd2.ind.
[51]
(/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/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){/usr/local/texlive/2019/te
xmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/local/texlive/2019/texmf-
dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive/2019/texmf-dist/fonts/enc/
dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/2019/texmf-dist/fonts/type1/p
ublic/inconsolata/Inconsolata-zi4r.pfb></usr/local/texlive/2019/texmf-dist/font
s/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1
/urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times
/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/utmr8a.pf
b></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (51 pages, 173814 bytes).
Transcript written on Rd2.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-02-25>
(./Rd2.tex (/usr/local/texlive/2019/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2019/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/local/texlive/2019/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2019/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/local/texlive/2019/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2019/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty
)))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 378.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 378.
) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/inputenc.sty)
Writing index file Rd2.idx
(/usr/local/texlive/2019/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/Rd2.aux)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2019/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/gettitlestring/gettitlestring.s
ty))
(/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/Rd2.out)
(/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/Rd2.out)
(/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1{/usr/loc
al/texlive/2019/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [2]
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1phv.fd
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 20.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 23.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 26.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 46.
) (/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/Rd2.toc
[3]) (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
[4]
Overfull \hbox (2.23863pt too wide) in paragraph at lines 240--242
[]\T1/ptm/m/n/10 The un-der-ly-ing data from the Per_sequence_quality_scores mo
d-
Overfull \hbox (6.28877pt too wide) in paragraph at lines 255--257
[]\T1/ptm/m/n/10 The un-der-ly-ing data from the Se-quence_Duplication_Levels m
od-
[5]
Overfull \hbox (24.47815pt too wide) in paragraph at lines 265--267
[]\T1/ptm/m/n/10 Estimate taken from the plot data for Se-quence_Duplication_Le
vels.
[6] [7] [8] [9] [10] [11]
Overfull \hbox (63.11093pt too wide) in paragraph at lines 680--691
\T1/zi4/m/n/10 Summary\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Basic_Statistics\T1/ptm/m
/n/10 , \T1/zi4/m/n/10 Per_base_sequence_quality\T1/ptm/m/n/10 , \T1/zi4/m/n/10
Per_tile_sequence_quality\T1/ptm/m/n/10 ,
Overfull \hbox (68.59091pt too wide) in paragraph at lines 680--691
\T1/zi4/m/n/10 Per_sequence_quality_scores\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_b
ase_sequence_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_sequence_GC_content\T1/
ptm/m/n/10 ,
Overfull \hbox (58.59091pt too wide) in paragraph at lines 680--691
\T1/zi4/m/n/10 Per_base_N_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Lengt
h_Distribution\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Duplication_Levels\T1/pt
m/m/n/10 ,
Overfull \hbox (103.11093pt too wide) in paragraph at lines 680--691
\T1/zi4/m/n/10 Overrepresented_sequences\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Adapter
_Content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Kmer_Content\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 Total_Deduplicated_Percentage\T1/ptm/m/n/10 .
[12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24]
Overfull \hbox (23.0476pt too wide) in paragraph at lines 1555--1560
[]\T1/ptm/m/n/10 When act-ing on a \T1/zi4/m/n/10 FastqcDataList\T1/ptm/m/n/10
, this de-faults to a heatmap us-ing the mean Per_base_sequence_quality
[25] [26] [27] [28]
Overfull \hbox (55.89735pt too wide) in paragraph at lines 1774--1777
[]\T1/zi4/m/n/10 character \T1/ptm/m/n/10 vec-tor con-tain-ing the de-sired Fas
tQC mod-ule (eg. c("Per_base_sequence_quality",
[29] [30] [31] [32]
Overfull \hbox (43.32875pt too wide) in paragraph at lines 2074--2076
[]\T1/ptm/m/n/10 The colour palette. If the vec-tor sup-plied is less than n, \
T1/zi4/m/n/10 grDevices::colorRampPalette()
[33] [34] [35] [36]
Overfull \hbox (37.21838pt too wide) in paragraph at lines 2295--2297
[]\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me
ric vec-tors of length 4. Passed to scale_*_continuous()
[37] [38] [39]
Overfull \hbox (0.38704pt too wide) in paragraph at lines 2534--2538
\T1/ptm/m/n/10 plot-ting from mul-ti-ple re-ports. The in-di-vid-ual line plots
are able to be gen-er-ated by set-ting \T1/zi4/m/n/10 plotType
[40] [41]
Overfull \hbox (6.82005pt too wide) in paragraph at lines 2627--2630
[]\T1/zi4/m/n/10 character\T1/ptm/m/n/10 . Can only take the val-ues \T1/zi4/m/
n/10 plotType = "heatmap" plotType = "line"
Overfull \hbox (27.78935pt too wide) in paragraph at lines 2631--2633
[]\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me
ric vec-tor of length 4. Passed to \T1/zi4/m/n/10 scale_x_discrete
[42] [43] [44] [45] [46] [47] [48] [49] [50] [51]
No file Rd2.ind.
[52]
(/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/Rd2.aux) )
(see the transcript file for additional information){/usr/local/texlive/2019/te
xmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/local/texlive/2019/texmf-
dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive/2019/texmf-dist/fonts/enc/
dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/2019/texmf-dist/fonts/type1/p
ublic/inconsolata/Inconsolata-zi4r.pfb></usr/local/texlive/2019/texmf-dist/font
s/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1
/urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times
/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/utmr8a.pf
b></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (52 pages, 178288 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (145 entries accepted, 0 rejected).
Sorting entries....done (1210 comparisons).
Generating output file Rd2.ind....done (273 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-02-25>
(./Rd2.tex (/usr/local/texlive/2019/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2019/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/local/texlive/2019/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2019/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/local/texlive/2019/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2019/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty
)))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 378.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 378.
) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/inputenc.sty)
Writing index file Rd2.idx
(/usr/local/texlive/2019/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/Rd2.aux)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2019/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/gettitlestring/gettitlestring.s
ty))
(/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/Rd2.out)
(/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/Rd2.out)
(/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1{/usr/loc
al/texlive/2019/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [2]
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1phv.fd
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 20.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 23.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 26.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 46.
) (/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/Rd2.toc
[3]) (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
[4]
Overfull \hbox (2.23863pt too wide) in paragraph at lines 240--242
[]\T1/ptm/m/n/10 The un-der-ly-ing data from the Per_sequence_quality_scores mo
d-
Overfull \hbox (6.28877pt too wide) in paragraph at lines 255--257
[]\T1/ptm/m/n/10 The un-der-ly-ing data from the Se-quence_Duplication_Levels m
od-
[5]
Overfull \hbox (24.47815pt too wide) in paragraph at lines 265--267
[]\T1/ptm/m/n/10 Estimate taken from the plot data for Se-quence_Duplication_Le
vels.
[6] [7] [8] [9] [10] [11]
Overfull \hbox (63.11093pt too wide) in paragraph at lines 680--691
\T1/zi4/m/n/10 Summary\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Basic_Statistics\T1/ptm/m
/n/10 , \T1/zi4/m/n/10 Per_base_sequence_quality\T1/ptm/m/n/10 , \T1/zi4/m/n/10
Per_tile_sequence_quality\T1/ptm/m/n/10 ,
Overfull \hbox (68.59091pt too wide) in paragraph at lines 680--691
\T1/zi4/m/n/10 Per_sequence_quality_scores\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_b
ase_sequence_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_sequence_GC_content\T1/
ptm/m/n/10 ,
Overfull \hbox (58.59091pt too wide) in paragraph at lines 680--691
\T1/zi4/m/n/10 Per_base_N_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Lengt
h_Distribution\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Duplication_Levels\T1/pt
m/m/n/10 ,
Overfull \hbox (103.11093pt too wide) in paragraph at lines 680--691
\T1/zi4/m/n/10 Overrepresented_sequences\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Adapter
_Content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Kmer_Content\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 Total_Deduplicated_Percentage\T1/ptm/m/n/10 .
[12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24]
Overfull \hbox (23.0476pt too wide) in paragraph at lines 1555--1560
[]\T1/ptm/m/n/10 When act-ing on a \T1/zi4/m/n/10 FastqcDataList\T1/ptm/m/n/10
, this de-faults to a heatmap us-ing the mean Per_base_sequence_quality
[25] [26] [27] [28]
Overfull \hbox (55.89735pt too wide) in paragraph at lines 1774--1777
[]\T1/zi4/m/n/10 character \T1/ptm/m/n/10 vec-tor con-tain-ing the de-sired Fas
tQC mod-ule (eg. c("Per_base_sequence_quality",
[29] [30] [31] [32]
Overfull \hbox (43.32875pt too wide) in paragraph at lines 2074--2076
[]\T1/ptm/m/n/10 The colour palette. If the vec-tor sup-plied is less than n, \
T1/zi4/m/n/10 grDevices::colorRampPalette()
[33] [34] [35] [36]
Overfull \hbox (37.21838pt too wide) in paragraph at lines 2295--2297
[]\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me
ric vec-tors of length 4. Passed to scale_*_continuous()
[37] [38] [39]
Overfull \hbox (0.38704pt too wide) in paragraph at lines 2534--2538
\T1/ptm/m/n/10 plot-ting from mul-ti-ple re-ports. The in-di-vid-ual line plots
are able to be gen-er-ated by set-ting \T1/zi4/m/n/10 plotType
[40] [41]
Overfull \hbox (6.82005pt too wide) in paragraph at lines 2627--2630
[]\T1/zi4/m/n/10 character\T1/ptm/m/n/10 . Can only take the val-ues \T1/zi4/m/
n/10 plotType = "heatmap" plotType = "line"
Overfull \hbox (27.78935pt too wide) in paragraph at lines 2631--2633
[]\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me
ric vec-tor of length 4. Passed to \T1/zi4/m/n/10 scale_x_discrete
[42] [43] [44] [45] [46] [47] [48] [49] [50] [51]
(/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/Rd2.ind
[52]
LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font) using `T1/zi4/m/n' instead on input line 6.
Overfull \hbox (55.01662pt too wide) in paragraph at lines 6--8
\T1/ptm/m/it/10 (\T1/zi4/m/n/10 [,FastqcDataList,numeric,missing-method\T1/ptm/
m/it/10 )\T1/ptm/m/n/10 ,
Overfull \hbox (15.8567pt too wide) in paragraph at lines 8--10
[]\T1/zi4/m/it/10 [,FastqcDataList,character,missing-method
Overfull \hbox (55.01662pt too wide) in paragraph at lines 8--10
\T1/ptm/m/it/10 (\T1/zi4/m/it/10 [,FastqcDataList,numeric,missing-method\T1/ptm
/m/it/10 )\T1/ptm/m/n/10 ,
Overfull \hbox (5.8567pt too wide) in paragraph at lines 10--12
[]\T1/zi4/m/it/10 [,FastqcDataList,logical,missing-method
Overfull \hbox (55.01662pt too wide) in paragraph at lines 10--12
\T1/ptm/m/it/10 (\T1/zi4/m/it/10 [,FastqcDataList,numeric,missing-method\T1/ptm
/m/it/10 )\T1/ptm/m/n/10 ,
Overfull \hbox (8.3567pt too wide) in paragraph at lines 12--14
[]\T1/zi4/m/it/10 [,FastqcDataList,numeric,missing-method\T1/ptm/m/n/10 ,
Overfull \hbox (5.01662pt too wide) in paragraph at lines 77--79
\T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 )
\T1/ptm/m/n/10 ,
Overfull \hbox (5.01662pt too wide) in paragraph at lines 80--82
\T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 )
\T1/ptm/m/n/10 ,
Overfull \hbox (5.01662pt too wide) in paragraph at lines 82--84
\T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 )
\T1/ptm/m/n/10 ,
Overfull \hbox (5.01662pt too wide) in paragraph at lines 84--86
\T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 )
\T1/ptm/m/n/10 ,
[53]
Overfull \hbox (10.8567pt too wide) in paragraph at lines 126--128
[]\T1/zi4/m/it/10 plotAdapterContent,FastqcDataList-method
Overfull \hbox (10.8567pt too wide) in paragraph at lines 214--216
[]\T1/zi4/m/it/10 plotSeqLengthDistn,FastqcDataList-method
[54] [55])
(/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/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){/usr/local/texlive/2019/te
xmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/local/texlive/2019/texmf-
dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive/2019/texmf-dist/fonts/enc/
dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/2019/texmf-dist/fonts/type1/p
ublic/inconsolata/Inconsolata-zi4r.pfb></usr/local/texlive/2019/texmf-dist/font
s/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texlive/2019/texmf-dist/fonts
/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/
urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/
utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/utmr8a.pfb
></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (55 pages, 195733 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (145 entries accepted, 0 rejected).
Sorting entries....done (1210 comparisons).
Generating output file Rd2.ind....done (273 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-02-25>
(./Rd2.tex (/usr/local/texlive/2019/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2019/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/local/texlive/2019/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2019/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/local/texlive/2019/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2019/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty
)))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 378.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 378.
) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/inputenc.sty)
Writing index file Rd2.idx
(/usr/local/texlive/2019/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/Rd2.aux)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2019/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/gettitlestring/gettitlestring.s
ty))
(/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/Rd2.out)
(/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/Rd2.out)
(/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1{/usr/loc
al/texlive/2019/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [2]
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1phv.fd
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 20.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 23.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 26.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 46.
) (/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/Rd2.toc
[3]) (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
[4]
Overfull \hbox (2.23863pt too wide) in paragraph at lines 240--242
[]\T1/ptm/m/n/10 The un-der-ly-ing data from the Per_sequence_quality_scores mo
d-
Overfull \hbox (6.28877pt too wide) in paragraph at lines 255--257
[]\T1/ptm/m/n/10 The un-der-ly-ing data from the Se-quence_Duplication_Levels m
od-
[5]
Overfull \hbox (24.47815pt too wide) in paragraph at lines 265--267
[]\T1/ptm/m/n/10 Estimate taken from the plot data for Se-quence_Duplication_Le
vels.
[6] [7] [8] [9] [10] [11]
Overfull \hbox (63.11093pt too wide) in paragraph at lines 680--691
\T1/zi4/m/n/10 Summary\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Basic_Statistics\T1/ptm/m
/n/10 , \T1/zi4/m/n/10 Per_base_sequence_quality\T1/ptm/m/n/10 , \T1/zi4/m/n/10
Per_tile_sequence_quality\T1/ptm/m/n/10 ,
Overfull \hbox (68.59091pt too wide) in paragraph at lines 680--691
\T1/zi4/m/n/10 Per_sequence_quality_scores\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_b
ase_sequence_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_sequence_GC_content\T1/
ptm/m/n/10 ,
Overfull \hbox (58.59091pt too wide) in paragraph at lines 680--691
\T1/zi4/m/n/10 Per_base_N_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Lengt
h_Distribution\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Duplication_Levels\T1/pt
m/m/n/10 ,
Overfull \hbox (103.11093pt too wide) in paragraph at lines 680--691
\T1/zi4/m/n/10 Overrepresented_sequences\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Adapter
_Content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Kmer_Content\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 Total_Deduplicated_Percentage\T1/ptm/m/n/10 .
[12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24]
Overfull \hbox (23.0476pt too wide) in paragraph at lines 1555--1560
[]\T1/ptm/m/n/10 When act-ing on a \T1/zi4/m/n/10 FastqcDataList\T1/ptm/m/n/10
, this de-faults to a heatmap us-ing the mean Per_base_sequence_quality
[25] [26] [27] [28]
Overfull \hbox (55.89735pt too wide) in paragraph at lines 1774--1777
[]\T1/zi4/m/n/10 character \T1/ptm/m/n/10 vec-tor con-tain-ing the de-sired Fas
tQC mod-ule (eg. c("Per_base_sequence_quality",
[29] [30] [31] [32]
Overfull \hbox (43.32875pt too wide) in paragraph at lines 2074--2076
[]\T1/ptm/m/n/10 The colour palette. If the vec-tor sup-plied is less than n, \
T1/zi4/m/n/10 grDevices::colorRampPalette()
[33] [34] [35] [36]
Overfull \hbox (37.21838pt too wide) in paragraph at lines 2295--2297
[]\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me
ric vec-tors of length 4. Passed to scale_*_continuous()
[37] [38] [39]
Overfull \hbox (0.38704pt too wide) in paragraph at lines 2534--2538
\T1/ptm/m/n/10 plot-ting from mul-ti-ple re-ports. The in-di-vid-ual line plots
are able to be gen-er-ated by set-ting \T1/zi4/m/n/10 plotType
[40] [41]
Overfull \hbox (6.82005pt too wide) in paragraph at lines 2627--2630
[]\T1/zi4/m/n/10 character\T1/ptm/m/n/10 . Can only take the val-ues \T1/zi4/m/
n/10 plotType = "heatmap" plotType = "line"
Overfull \hbox (27.78935pt too wide) in paragraph at lines 2631--2633
[]\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me
ric vec-tor of length 4. Passed to \T1/zi4/m/n/10 scale_x_discrete
[42] [43] [44] [45] [46] [47] [48] [49] [50] [51]
(/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/Rd2.ind
[52]
LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font) using `T1/zi4/m/n' instead on input line 6.
Overfull \hbox (55.01662pt too wide) in paragraph at lines 6--8
\T1/ptm/m/it/10 (\T1/zi4/m/n/10 [,FastqcDataList,numeric,missing-method\T1/ptm/
m/it/10 )\T1/ptm/m/n/10 ,
Overfull \hbox (15.8567pt too wide) in paragraph at lines 8--10
[]\T1/zi4/m/it/10 [,FastqcDataList,character,missing-method
Overfull \hbox (55.01662pt too wide) in paragraph at lines 8--10
\T1/ptm/m/it/10 (\T1/zi4/m/it/10 [,FastqcDataList,numeric,missing-method\T1/ptm
/m/it/10 )\T1/ptm/m/n/10 ,
Overfull \hbox (5.8567pt too wide) in paragraph at lines 10--12
[]\T1/zi4/m/it/10 [,FastqcDataList,logical,missing-method
Overfull \hbox (55.01662pt too wide) in paragraph at lines 10--12
\T1/ptm/m/it/10 (\T1/zi4/m/it/10 [,FastqcDataList,numeric,missing-method\T1/ptm
/m/it/10 )\T1/ptm/m/n/10 ,
Overfull \hbox (8.3567pt too wide) in paragraph at lines 12--14
[]\T1/zi4/m/it/10 [,FastqcDataList,numeric,missing-method\T1/ptm/m/n/10 ,
Overfull \hbox (5.01662pt too wide) in paragraph at lines 77--79
\T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 )
\T1/ptm/m/n/10 ,
Overfull \hbox (5.01662pt too wide) in paragraph at lines 80--82
\T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 )
\T1/ptm/m/n/10 ,
Overfull \hbox (5.01662pt too wide) in paragraph at lines 82--84
\T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 )
\T1/ptm/m/n/10 ,
Overfull \hbox (5.01662pt too wide) in paragraph at lines 84--86
\T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 )
\T1/ptm/m/n/10 ,
[53]
Overfull \hbox (10.8567pt too wide) in paragraph at lines 126--128
[]\T1/zi4/m/it/10 plotAdapterContent,FastqcDataList-method
Overfull \hbox (10.8567pt too wide) in paragraph at lines 214--216
[]\T1/zi4/m/it/10 plotSeqLengthDistn,FastqcDataList-method
[54] [55])
(/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/.Rd2pdf99045/Rd2.aux)
LaTeX Font Warning: Some font shapes were not available, defaults substituted.
)
(see the transcript file for additional information){/usr/local/texlive/2019/te
xmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/local/texlive/2019/texmf-
dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive/2019/texmf-dist/fonts/enc/
dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/2019/texmf-dist/fonts/type1/p
ublic/inconsolata/Inconsolata-zi4r.pfb></usr/local/texlive/2019/texmf-dist/font
s/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texlive/2019/texmf-dist/fonts
/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/
urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/
utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/utmr8a.pfb
></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (55 pages, 196456 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/Rtmp3ugnah/Rbuild182e56fef7076/ngsReports/build/ngsReports.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 ‘ngsReports_1.10.0.tar.gz’
