Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

BUILD report for tidybulk on malbec2

This page was generated on 2020-10-17 11:55:55 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE tidybulk PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1797/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tidybulk 1.0.2
Stefano Mangiola
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/tidybulk
Branch: RELEASE_3_11
Last Commit: bfa4dd1
Last Changed Date: 2020-06-08 00:40:18 -0400 (Mon, 08 Jun 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK [ OK ] WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: tidybulk
Version: 1.0.2
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data tidybulk
StartedAt: 2020-10-16 22:12:35 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 22:16:12 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 216.5 seconds
RetCode: 0
Status:  OK 
PackageFile: tidybulk_1.0.2.tar.gz
PackageFileSize: 3.541 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data tidybulk
###
##############################################################################
##############################################################################


* checking for file ‘tidybulk/DESCRIPTION’ ... OK
* preparing ‘tidybulk’:
* 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 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 33 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.11-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/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/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [1{/var/lib/texmf/fonts
/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
Overfull \hbox (3.42702pt too wide) in paragraph at lines 82--83
[]\T1/ptm/m/n/10 adjust_abundance() takes as im-put a `tbl` for-mat-ted as | <S
AM-PLE> | <TRAN-SCRIPT> | <COUNT>
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [2]
Underfull \vbox (badness 10000) has occurred while \output is active [3]
[4] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (16.19675pt too wide) in paragraph at lines 230--231
[]\T1/ptm/m/n/10 aggregate_duplicates() takes as im-put a `tbl` for-mat-ted as 
| <SAM-PLE> | <TRAN-SCRIPT> | <COUNT>
[5] [6] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (4.18723pt too wide) in paragraph at lines 390--392
[]\T1/ptm/m/n/10 <[`tidy-eval`][dplyr_tidy_eval]> Vari-ables, or func-tions or 
vari-ables. Use [desc()]
[7] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [8]
Overfull \hbox (18.77168pt too wide) in paragraph at lines 485--485
 []\T1/zi4/m/n/9 as_matrix(head(dplyr::select(tidybulk::counts_mini, transcript
, count)), rownames=transcript)[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [10]
Underfull \vbox (badness 10000) has occurred while \output is active [11]
Overfull \hbox (35.25021pt too wide) in paragraph at lines 702--702
 []    \T1/zi4/m/n/9 cluster_elements(tidybulk::counts_mini, sample, transcript
, count,centers = 2, method="kmeans")[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [12]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [13] [14] [15]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [16]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.63681pt too wide) in paragraph at lines 952--953
[]\T1/ptm/m/n/10 ensembl_to_symbol() takes as im-put a `tbl` for-mat-ted as | <
SAM-PLE> | <EN-SEMBL_ID> | <COUNT>
[17] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [18]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [20]
Overfull \hbox (7.27914pt too wide) in paragraph at lines 1192--1194
[]\T1/ptm/m/n/10 When `.drop = TRUE`, empty groups are dropped. See [group_by_d
rop_default()]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (7.31702pt too wide) in paragraph at lines 1228--1229
[]\T1/ptm/m/n/10 impute_abundance() takes as im-put a `tbl` for-mat-ted as | <S
AM-PLE> | <TRAN-SCRIPT> | <COUNT>
[21] [22] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [23]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [24] [25]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [26] [27]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [28]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [29] [30]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [32]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [33]
Overfull \hbox (9.18677pt too wide) in paragraph at lines 1969--1970
[]\T1/ptm/m/n/10 reduce_dimensions() takes as im-put a `tbl` for-mat-ted as | <
SAM-PLE> | <TRAN-SCRIPT> | <COUNT>
[34]
Underfull \vbox (badness 10000) has occurred while \output is active [35]
Overfull \hbox (66.75021pt too wide) in paragraph at lines 2125--2125
 []\T1/zi4/m/n/9 counts.MDS =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="MDS", .dims = 3)[] 

Overfull \hbox (66.75021pt too wide) in paragraph at lines 2128--2128
 []\T1/zi4/m/n/9 counts.PCA =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="PCA", .dims = 3)[] 
[36] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.16739pt too wide) in paragraph at lines 2143--2144
[]\T1/ptm/m/n/10 remove_redundancy() takes as im-put a `tbl` for-mat-ted as | <
SAM-PLE> | <TRAN-SCRIPT> | <COUNT>

Overfull \hbox (18.57648pt too wide) in paragraph at lines 2143--2144
\T1/ptm/m/n/10 | <...> | for cor-re-la-tion method or | <DI-MEN-SION 1> | <DI-M
EN-SION 2> | <...> | for re-duced_dimensions
[37]
Underfull \vbox (badness 10000) has occurred while \output is active [38]
[39]
Overfull \hbox (66.75021pt too wide) in paragraph at lines 2298--2298
 []\T1/zi4/m/n/9 counts.MDS =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="MDS", .dims = 3)[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [40]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [41] [42] [43]
Overfull \hbox (66.75021pt too wide) in paragraph at lines 2553--2553
 []\T1/zi4/m/n/9 counts.MDS =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="MDS", .dims = 3)[] 

Overfull \hbox (78.74715pt too wide) in paragraph at lines 2555--2555
 []\T1/zi4/m/n/9 counts.MDS.rotated =  rotate_dimensions(counts.MDS, \TS1/zi4/m
/n/9 `\T1/zi4/m/n/9 Dim1\TS1/zi4/m/n/9 `\T1/zi4/m/n/9 , \TS1/zi4/m/n/9 `\T1/zi4
/m/n/9 Dim2\TS1/zi4/m/n/9 `\T1/zi4/m/n/9 , rotation_degrees = 45, .element = sa
mple)[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [44]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [45]
Underfull \vbox (badness 10000) has occurred while \output is active [46]
[47] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [48] [49]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [50] [51]
Underfull \vbox (badness 10000) has occurred while \output is active [52]
Overfull \hbox (40.04678pt too wide) in paragraph at lines 3070--3071
[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther "edgeR_quasi_likelihood" (i.e., 
QLF), "edgeR_likelihood_ratio"
[53] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [54] [55]
Overfull \hbox (20.25635pt too wide) in paragraph at lines 3235--3235
 []\T1/zi4/m/n/9 df_entrez = symbol_to_entrez(tidybulk::counts_mini, .transcrip
t = transcript, .sample = sample)[] 

Overfull \hbox (173.23795pt too wide) in paragraph at lines 3236--3236
 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [56]
Overfull \hbox (20.25635pt too wide) in paragraph at lines 3313--3313
 []\T1/zi4/m/n/9 df_entrez = symbol_to_entrez(tidybulk::counts_mini, .transcrip
t = transcript, .sample = sample)[] 

Overfull \hbox (173.23795pt too wide) in paragraph at lines 3314--3314
 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] 

Overfull \hbox (17.25021pt too wide) in paragraph at lines 3315--3315
 []\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = transcript %in% c("TNF
RSF4", "PLCH2", "PADI4", "PAX7"))[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [57]
Overfull \hbox (5.09679pt too wide) in paragraph at lines 3336--3337
[]\T1/ptm/m/n/10 tidybulk() cre-ates a `tt` ob-ject from a `tbl` for-mat-ted as
 | <SAM-PLE> | <TRAN-SCRIPT> | <COUNT>
[58] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [59]
No file Rd2.ind.
[60] (/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/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/share/texlive/texmf-d
ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts
/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola
ta/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/inconsolata/In
consolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (60 pages, 173789 bytes).
Transcript written on Rd2.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 33 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.11-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/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/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
Writing index file Rd2.idx
(/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/Rd2.out)
(/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [1{/var/lib/texmf/fonts
/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/Rd2.toc [2])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
Overfull \hbox (3.42702pt too wide) in paragraph at lines 82--83
[]\T1/ptm/m/n/10 adjust_abundance() takes as im-put a `tbl` for-mat-ted as | <S
AM-PLE> | <TRAN-SCRIPT> | <COUNT>
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [3] [4]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (16.19675pt too wide) in paragraph at lines 230--231
[]\T1/ptm/m/n/10 aggregate_duplicates() takes as im-put a `tbl` for-mat-ted as 
| <SAM-PLE> | <TRAN-SCRIPT> | <COUNT>
[5] [6] [7] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (4.18723pt too wide) in paragraph at lines 390--392
[]\T1/ptm/m/n/10 <[`tidy-eval`][dplyr_tidy_eval]> Vari-ables, or func-tions or 
vari-ables. Use [desc()]
[8] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [9]
Overfull \hbox (18.77168pt too wide) in paragraph at lines 485--485
 []\T1/zi4/m/n/9 as_matrix(head(dplyr::select(tidybulk::counts_mini, transcript
, count)), rownames=transcript)[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [11]
Underfull \vbox (badness 10000) has occurred while \output is active [12]
Overfull \hbox (35.25021pt too wide) in paragraph at lines 702--702
 []    \T1/zi4/m/n/9 cluster_elements(tidybulk::counts_mini, sample, transcript
, count,centers = 2, method="kmeans")[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [13]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [14] [15] [16]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [17]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.63681pt too wide) in paragraph at lines 952--953
[]\T1/ptm/m/n/10 ensembl_to_symbol() takes as im-put a `tbl` for-mat-ted as | <
SAM-PLE> | <EN-SEMBL_ID> | <COUNT>
[18] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [20]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [21]
Overfull \hbox (7.27914pt too wide) in paragraph at lines 1192--1194
[]\T1/ptm/m/n/10 When `.drop = TRUE`, empty groups are dropped. See [group_by_d
rop_default()]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (7.31702pt too wide) in paragraph at lines 1228--1229
[]\T1/ptm/m/n/10 impute_abundance() takes as im-put a `tbl` for-mat-ted as | <S
AM-PLE> | <TRAN-SCRIPT> | <COUNT>
[22] [23] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [24]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [25] [26]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [27] [28]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [29]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [30] [31]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [32]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [33]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [34]
Overfull \hbox (9.18677pt too wide) in paragraph at lines 1969--1970
[]\T1/ptm/m/n/10 reduce_dimensions() takes as im-put a `tbl` for-mat-ted as | <
SAM-PLE> | <TRAN-SCRIPT> | <COUNT>
[35]
Underfull \vbox (badness 10000) has occurred while \output is active [36]
Overfull \hbox (66.75021pt too wide) in paragraph at lines 2125--2125
 []\T1/zi4/m/n/9 counts.MDS =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="MDS", .dims = 3)[] 

Overfull \hbox (66.75021pt too wide) in paragraph at lines 2128--2128
 []\T1/zi4/m/n/9 counts.PCA =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="PCA", .dims = 3)[] 
[37] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.16739pt too wide) in paragraph at lines 2143--2144
[]\T1/ptm/m/n/10 remove_redundancy() takes as im-put a `tbl` for-mat-ted as | <
SAM-PLE> | <TRAN-SCRIPT> | <COUNT>

Overfull \hbox (18.57648pt too wide) in paragraph at lines 2143--2144
\T1/ptm/m/n/10 | <...> | for cor-re-la-tion method or | <DI-MEN-SION 1> | <DI-M
EN-SION 2> | <...> | for re-duced_dimensions
[38]
Underfull \vbox (badness 10000) has occurred while \output is active [39]
[40]
Overfull \hbox (66.75021pt too wide) in paragraph at lines 2298--2298
 []\T1/zi4/m/n/9 counts.MDS =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="MDS", .dims = 3)[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [41]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [42] [43] [44]
Overfull \hbox (66.75021pt too wide) in paragraph at lines 2553--2553
 []\T1/zi4/m/n/9 counts.MDS =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="MDS", .dims = 3)[] 

Overfull \hbox (78.74715pt too wide) in paragraph at lines 2555--2555
 []\T1/zi4/m/n/9 counts.MDS.rotated =  rotate_dimensions(counts.MDS, \TS1/zi4/m
/n/9 `\T1/zi4/m/n/9 Dim1\TS1/zi4/m/n/9 `\T1/zi4/m/n/9 , \TS1/zi4/m/n/9 `\T1/zi4
/m/n/9 Dim2\TS1/zi4/m/n/9 `\T1/zi4/m/n/9 , rotation_degrees = 45, .element = sa
mple)[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [45]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [46]
Underfull \vbox (badness 10000) has occurred while \output is active [47]
[48] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [49] [50]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [51] [52]
Underfull \vbox (badness 10000) has occurred while \output is active [53]
Overfull \hbox (40.04678pt too wide) in paragraph at lines 3070--3071
[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther "edgeR_quasi_likelihood" (i.e., 
QLF), "edgeR_likelihood_ratio"
[54] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [55] [56]
Overfull \hbox (20.25635pt too wide) in paragraph at lines 3235--3235
 []\T1/zi4/m/n/9 df_entrez = symbol_to_entrez(tidybulk::counts_mini, .transcrip
t = transcript, .sample = sample)[] 

Overfull \hbox (173.23795pt too wide) in paragraph at lines 3236--3236
 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [57]
Overfull \hbox (20.25635pt too wide) in paragraph at lines 3313--3313
 []\T1/zi4/m/n/9 df_entrez = symbol_to_entrez(tidybulk::counts_mini, .transcrip
t = transcript, .sample = sample)[] 

Overfull \hbox (173.23795pt too wide) in paragraph at lines 3314--3314
 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] 

Overfull \hbox (17.25021pt too wide) in paragraph at lines 3315--3315
 []\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = transcript %in% c("TNF
RSF4", "PLCH2", "PADI4", "PAX7"))[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [58]
Overfull \hbox (5.09679pt too wide) in paragraph at lines 3336--3337
[]\T1/ptm/m/n/10 tidybulk() cre-ates a `tt` ob-ject from a `tbl` for-mat-ted as
 | <SAM-PLE> | <TRAN-SCRIPT> | <COUNT>
[59] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [60]
No file Rd2.ind.
[61] (/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/Rd2.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts
/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola
ta/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/inconsolata/In
consolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (61 pages, 179428 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (162 entries accepted, 0 rejected).
Sorting entries....done (1286 comparisons).
Generating output file Rd2.ind....done (302 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 33 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.11-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/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/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
Writing index file Rd2.idx
(/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/Rd2.out)
(/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [1{/var/lib/texmf/fonts
/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/Rd2.toc [2])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
Overfull \hbox (3.42702pt too wide) in paragraph at lines 82--83
[]\T1/ptm/m/n/10 adjust_abundance() takes as im-put a `tbl` for-mat-ted as | <S
AM-PLE> | <TRAN-SCRIPT> | <COUNT>
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [3] [4]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (16.19675pt too wide) in paragraph at lines 230--231
[]\T1/ptm/m/n/10 aggregate_duplicates() takes as im-put a `tbl` for-mat-ted as 
| <SAM-PLE> | <TRAN-SCRIPT> | <COUNT>
[5] [6] [7] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (4.18723pt too wide) in paragraph at lines 390--392
[]\T1/ptm/m/n/10 <[`tidy-eval`][dplyr_tidy_eval]> Vari-ables, or func-tions or 
vari-ables. Use [desc()]
[8] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [9]
Overfull \hbox (18.77168pt too wide) in paragraph at lines 485--485
 []\T1/zi4/m/n/9 as_matrix(head(dplyr::select(tidybulk::counts_mini, transcript
, count)), rownames=transcript)[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [11]
Underfull \vbox (badness 10000) has occurred while \output is active [12]
Overfull \hbox (35.25021pt too wide) in paragraph at lines 702--702
 []    \T1/zi4/m/n/9 cluster_elements(tidybulk::counts_mini, sample, transcript
, count,centers = 2, method="kmeans")[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [13]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [14] [15] [16]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [17]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.63681pt too wide) in paragraph at lines 952--953
[]\T1/ptm/m/n/10 ensembl_to_symbol() takes as im-put a `tbl` for-mat-ted as | <
SAM-PLE> | <EN-SEMBL_ID> | <COUNT>
[18] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [20]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [21]
Overfull \hbox (7.27914pt too wide) in paragraph at lines 1192--1194
[]\T1/ptm/m/n/10 When `.drop = TRUE`, empty groups are dropped. See [group_by_d
rop_default()]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (7.31702pt too wide) in paragraph at lines 1228--1229
[]\T1/ptm/m/n/10 impute_abundance() takes as im-put a `tbl` for-mat-ted as | <S
AM-PLE> | <TRAN-SCRIPT> | <COUNT>
[22] [23] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [24]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [25] [26]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [27] [28]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [29]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [30] [31]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [32]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [33]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [34]
Overfull \hbox (9.18677pt too wide) in paragraph at lines 1969--1970
[]\T1/ptm/m/n/10 reduce_dimensions() takes as im-put a `tbl` for-mat-ted as | <
SAM-PLE> | <TRAN-SCRIPT> | <COUNT>
[35]
Underfull \vbox (badness 10000) has occurred while \output is active [36]
Overfull \hbox (66.75021pt too wide) in paragraph at lines 2125--2125
 []\T1/zi4/m/n/9 counts.MDS =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="MDS", .dims = 3)[] 

Overfull \hbox (66.75021pt too wide) in paragraph at lines 2128--2128
 []\T1/zi4/m/n/9 counts.PCA =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="PCA", .dims = 3)[] 
[37] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.16739pt too wide) in paragraph at lines 2143--2144
[]\T1/ptm/m/n/10 remove_redundancy() takes as im-put a `tbl` for-mat-ted as | <
SAM-PLE> | <TRAN-SCRIPT> | <COUNT>

Overfull \hbox (18.57648pt too wide) in paragraph at lines 2143--2144
\T1/ptm/m/n/10 | <...> | for cor-re-la-tion method or | <DI-MEN-SION 1> | <DI-M
EN-SION 2> | <...> | for re-duced_dimensions
[38]
Underfull \vbox (badness 10000) has occurred while \output is active [39]
[40]
Overfull \hbox (66.75021pt too wide) in paragraph at lines 2298--2298
 []\T1/zi4/m/n/9 counts.MDS =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="MDS", .dims = 3)[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [41]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [42] [43] [44]
Overfull \hbox (66.75021pt too wide) in paragraph at lines 2553--2553
 []\T1/zi4/m/n/9 counts.MDS =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="MDS", .dims = 3)[] 

Overfull \hbox (78.74715pt too wide) in paragraph at lines 2555--2555
 []\T1/zi4/m/n/9 counts.MDS.rotated =  rotate_dimensions(counts.MDS, \TS1/zi4/m
/n/9 `\T1/zi4/m/n/9 Dim1\TS1/zi4/m/n/9 `\T1/zi4/m/n/9 , \TS1/zi4/m/n/9 `\T1/zi4
/m/n/9 Dim2\TS1/zi4/m/n/9 `\T1/zi4/m/n/9 , rotation_degrees = 45, .element = sa
mple)[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [45]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [46]
Underfull \vbox (badness 10000) has occurred while \output is active [47]
[48] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [49] [50]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [51] [52]
Underfull \vbox (badness 10000) has occurred while \output is active [53]
Overfull \hbox (40.04678pt too wide) in paragraph at lines 3070--3071
[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther "edgeR_quasi_likelihood" (i.e., 
QLF), "edgeR_likelihood_ratio"
[54] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [55] [56]
Overfull \hbox (20.25635pt too wide) in paragraph at lines 3235--3235
 []\T1/zi4/m/n/9 df_entrez = symbol_to_entrez(tidybulk::counts_mini, .transcrip
t = transcript, .sample = sample)[] 

Overfull \hbox (173.23795pt too wide) in paragraph at lines 3236--3236
 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [57]
Overfull \hbox (20.25635pt too wide) in paragraph at lines 3313--3313
 []\T1/zi4/m/n/9 df_entrez = symbol_to_entrez(tidybulk::counts_mini, .transcrip
t = transcript, .sample = sample)[] 

Overfull \hbox (173.23795pt too wide) in paragraph at lines 3314--3314
 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] 

Overfull \hbox (17.25021pt too wide) in paragraph at lines 3315--3315
 []\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = transcript %in% c("TNF
RSF4", "PLCH2", "PADI4", "PAX7"))[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [58]
Overfull \hbox (5.09679pt too wide) in paragraph at lines 3336--3337
[]\T1/ptm/m/n/10 tidybulk() cre-ates a `tt` ob-ject from a `tbl` for-mat-ted as
 | <SAM-PLE> | <TRAN-SCRIPT> | <COUNT>
[59] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [60]
(/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/Rd2.ind [61]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 25.


Overfull \hbox (60.8567pt too wide) in paragraph at lines 25--27
[]\T1/zi4/m/n/10 adjust_abundance,RangedSummarizedExperiment-method 

Overfull \hbox (30.8567pt too wide) in paragraph at lines 29--31
[]\T1/zi4/m/it/10 adjust_abundance,SummarizedExperiment-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 36--38
[]\T1/zi4/m/it/10 aggregate_duplicates,RangedSummarizedExperiment-method 

Overfull \hbox (5.8567pt too wide) in paragraph at lines 38--40
[]\T1/zi4/m/it/10 aggregate_duplicates,spec_tbl_df-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 40--42
[]\T1/zi4/m/it/10 aggregate_duplicates,SummarizedExperiment-method 

Overfull \hbox (60.8567pt too wide) in paragraph at lines 65--67
[]\T1/zi4/m/it/10 cluster_elements,RangedSummarizedExperiment-method 

Overfull \hbox (30.8567pt too wide) in paragraph at lines 69--71
[]\T1/zi4/m/it/10 cluster_elements,SummarizedExperiment-method 

Overfull \hbox (90.8567pt too wide) in paragraph at lines 82--84
[]\T1/zi4/m/it/10 deconvolve_cellularity,RangedSummarizedExperiment-method 

Overfull \hbox (15.8567pt too wide) in paragraph at lines 84--86
[]\T1/zi4/m/it/10 deconvolve_cellularity,spec_tbl_df-method 

Overfull \hbox (60.8567pt too wide) in paragraph at lines 86--88
[]\T1/zi4/m/it/10 deconvolve_cellularity,SummarizedExperiment-method 

Overfull \hbox (0.8567pt too wide) in paragraph at lines 90--92
[]\T1/zi4/m/it/10 deconvolve_cellularity,tidybulk-method 
[62]
Overfull \hbox (60.8567pt too wide) in paragraph at lines 121--123
[]\T1/zi4/m/it/10 impute_abundance,RangedSummarizedExperiment-method 

Overfull \hbox (30.8567pt too wide) in paragraph at lines 125--127
[]\T1/zi4/m/it/10 impute_abundance,SummarizedExperiment-method 

Overfull \hbox (45.8567pt too wide) in paragraph at lines 136--138
[]\T1/zi4/m/it/10 keep_abundant,RangedSummarizedExperiment-method 

Overfull \hbox (15.8567pt too wide) in paragraph at lines 140--142
[]\T1/zi4/m/it/10 keep_abundant,SummarizedExperiment-method 

Overfull \hbox (45.8567pt too wide) in paragraph at lines 147--149
[]\T1/zi4/m/it/10 keep_variable,RangedSummarizedExperiment-method 

Overfull \hbox (15.8567pt too wide) in paragraph at lines 151--153
[]\T1/zi4/m/it/10 keep_variable,SummarizedExperiment-method 

Overfull \hbox (65.8567pt too wide) in paragraph at lines 193--195
[]\T1/zi4/m/it/10 reduce_dimensions,RangedSummarizedExperiment-method 

Overfull \hbox (35.8567pt too wide) in paragraph at lines 197--199
[]\T1/zi4/m/it/10 reduce_dimensions,SummarizedExperiment-method 

Overfull \hbox (65.8567pt too wide) in paragraph at lines 204--206
[]\T1/zi4/m/it/10 remove_redundancy,RangedSummarizedExperiment-method 

Overfull \hbox (35.8567pt too wide) in paragraph at lines 208--210
[]\T1/zi4/m/it/10 remove_redundancy,SummarizedExperiment-method 

Overfull \hbox (65.8567pt too wide) in paragraph at lines 220--222
[]\T1/zi4/m/it/10 rotate_dimensions,RangedSummarizedExperiment-method 

Overfull \hbox (35.8567pt too wide) in paragraph at lines 224--226
[]\T1/zi4/m/it/10 rotate_dimensions,SummarizedExperiment-method 

Overfull \hbox (55.8567pt too wide) in paragraph at lines 235--237
[]\T1/zi4/m/it/10 scale_abundance,RangedSummarizedExperiment-method 

Overfull \hbox (25.8567pt too wide) in paragraph at lines 239--241
[]\T1/zi4/m/it/10 scale_abundance,SummarizedExperiment-method 
[63]
Overfull \hbox (115.8567pt too wide) in paragraph at lines 256--258
[]\T1/zi4/m/it/10 test_differential_abundance,RangedSummarizedExperiment-method
 

Overfull \hbox (40.8567pt too wide) in paragraph at lines 258--260
[]\T1/zi4/m/it/10 test_differential_abundance,spec_tbl_df-method 

Overfull \hbox (85.8567pt too wide) in paragraph at lines 260--262
[]\T1/zi4/m/it/10 test_differential_abundance,SummarizedExperiment-method 

Overfull \hbox (15.8567pt too wide) in paragraph at lines 262--264
[]\T1/zi4/m/it/10 test_differential_abundance,tbl_df-method 

Overfull \hbox (25.8567pt too wide) in paragraph at lines 264--266
[]\T1/zi4/m/it/10 test_differential_abundance,tidybulk-method 

Overfull \hbox (5.8567pt too wide) in paragraph at lines 267--269
[]\T1/zi4/m/it/10 test_gene_enrichment,spec_tbl_df-method 

Overfull \hbox (45.8567pt too wide) in paragraph at lines 274--276
[]\T1/zi4/m/it/10 test_gene_overrepresentation,spec_tbl_df-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 276--278
[]\T1/zi4/m/it/10 test_gene_overrepresentation,tbl_df-method 

Overfull \hbox (30.8567pt too wide) in paragraph at lines 278--280
[]\T1/zi4/m/it/10 test_gene_overrepresentation,tidybulk-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 281--283
[]\T1/zi4/m/it/10 tidybulk,RangedSummarizedExperiment-method 

Overfull \hbox (25.8567pt too wide) in paragraph at lines 290--292
[]\T1/zi4/m/it/10 tidybulk_SAM_BAM,character,character-method 
[64]) (/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/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/share/texlive/texmf-d
ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts
/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola
ta/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/inconsolata/In
consolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb
></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on Rd2.pdf (64 pages, 196400 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (162 entries accepted, 0 rejected).
Sorting entries....done (1286 comparisons).
Generating output file Rd2.ind....done (302 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 33 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.11-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/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/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
Writing index file Rd2.idx
(/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/Rd2.out)
(/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [1{/var/lib/texmf/fonts
/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/Rd2.toc [2])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
Overfull \hbox (3.42702pt too wide) in paragraph at lines 82--83
[]\T1/ptm/m/n/10 adjust_abundance() takes as im-put a `tbl` for-mat-ted as | <S
AM-PLE> | <TRAN-SCRIPT> | <COUNT>
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [3] [4]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (16.19675pt too wide) in paragraph at lines 230--231
[]\T1/ptm/m/n/10 aggregate_duplicates() takes as im-put a `tbl` for-mat-ted as 
| <SAM-PLE> | <TRAN-SCRIPT> | <COUNT>
[5] [6] [7] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (4.18723pt too wide) in paragraph at lines 390--392
[]\T1/ptm/m/n/10 <[`tidy-eval`][dplyr_tidy_eval]> Vari-ables, or func-tions or 
vari-ables. Use [desc()]
[8] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [9]
Overfull \hbox (18.77168pt too wide) in paragraph at lines 485--485
 []\T1/zi4/m/n/9 as_matrix(head(dplyr::select(tidybulk::counts_mini, transcript
, count)), rownames=transcript)[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [11]
Underfull \vbox (badness 10000) has occurred while \output is active [12]
Overfull \hbox (35.25021pt too wide) in paragraph at lines 702--702
 []    \T1/zi4/m/n/9 cluster_elements(tidybulk::counts_mini, sample, transcript
, count,centers = 2, method="kmeans")[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [13]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [14] [15] [16]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [17]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.63681pt too wide) in paragraph at lines 952--953
[]\T1/ptm/m/n/10 ensembl_to_symbol() takes as im-put a `tbl` for-mat-ted as | <
SAM-PLE> | <EN-SEMBL_ID> | <COUNT>
[18] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [20]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [21]
Overfull \hbox (7.27914pt too wide) in paragraph at lines 1192--1194
[]\T1/ptm/m/n/10 When `.drop = TRUE`, empty groups are dropped. See [group_by_d
rop_default()]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (7.31702pt too wide) in paragraph at lines 1228--1229
[]\T1/ptm/m/n/10 impute_abundance() takes as im-put a `tbl` for-mat-ted as | <S
AM-PLE> | <TRAN-SCRIPT> | <COUNT>
[22] [23] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [24]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [25] [26]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [27] [28]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [29]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [30] [31]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [32]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [33]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [34]
Overfull \hbox (9.18677pt too wide) in paragraph at lines 1969--1970
[]\T1/ptm/m/n/10 reduce_dimensions() takes as im-put a `tbl` for-mat-ted as | <
SAM-PLE> | <TRAN-SCRIPT> | <COUNT>
[35]
Underfull \vbox (badness 10000) has occurred while \output is active [36]
Overfull \hbox (66.75021pt too wide) in paragraph at lines 2125--2125
 []\T1/zi4/m/n/9 counts.MDS =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="MDS", .dims = 3)[] 

Overfull \hbox (66.75021pt too wide) in paragraph at lines 2128--2128
 []\T1/zi4/m/n/9 counts.PCA =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="PCA", .dims = 3)[] 
[37] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.16739pt too wide) in paragraph at lines 2143--2144
[]\T1/ptm/m/n/10 remove_redundancy() takes as im-put a `tbl` for-mat-ted as | <
SAM-PLE> | <TRAN-SCRIPT> | <COUNT>

Overfull \hbox (18.57648pt too wide) in paragraph at lines 2143--2144
\T1/ptm/m/n/10 | <...> | for cor-re-la-tion method or | <DI-MEN-SION 1> | <DI-M
EN-SION 2> | <...> | for re-duced_dimensions
[38]
Underfull \vbox (badness 10000) has occurred while \output is active [39]
[40]
Overfull \hbox (66.75021pt too wide) in paragraph at lines 2298--2298
 []\T1/zi4/m/n/9 counts.MDS =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="MDS", .dims = 3)[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [41]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [42] [43] [44]
Overfull \hbox (66.75021pt too wide) in paragraph at lines 2553--2553
 []\T1/zi4/m/n/9 counts.MDS =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="MDS", .dims = 3)[] 

Overfull \hbox (78.74715pt too wide) in paragraph at lines 2555--2555
 []\T1/zi4/m/n/9 counts.MDS.rotated =  rotate_dimensions(counts.MDS, \TS1/zi4/m
/n/9 `\T1/zi4/m/n/9 Dim1\TS1/zi4/m/n/9 `\T1/zi4/m/n/9 , \TS1/zi4/m/n/9 `\T1/zi4
/m/n/9 Dim2\TS1/zi4/m/n/9 `\T1/zi4/m/n/9 , rotation_degrees = 45, .element = sa
mple)[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [45]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [46]
Underfull \vbox (badness 10000) has occurred while \output is active [47]
[48] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [49] [50]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [51] [52]
Underfull \vbox (badness 10000) has occurred while \output is active [53]
Overfull \hbox (40.04678pt too wide) in paragraph at lines 3070--3071
[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther "edgeR_quasi_likelihood" (i.e., 
QLF), "edgeR_likelihood_ratio"
[54] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [55] [56]
Overfull \hbox (20.25635pt too wide) in paragraph at lines 3235--3235
 []\T1/zi4/m/n/9 df_entrez = symbol_to_entrez(tidybulk::counts_mini, .transcrip
t = transcript, .sample = sample)[] 

Overfull \hbox (173.23795pt too wide) in paragraph at lines 3236--3236
 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [57]
Overfull \hbox (20.25635pt too wide) in paragraph at lines 3313--3313
 []\T1/zi4/m/n/9 df_entrez = symbol_to_entrez(tidybulk::counts_mini, .transcrip
t = transcript, .sample = sample)[] 

Overfull \hbox (173.23795pt too wide) in paragraph at lines 3314--3314
 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] 

Overfull \hbox (17.25021pt too wide) in paragraph at lines 3315--3315
 []\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = transcript %in% c("TNF
RSF4", "PLCH2", "PADI4", "PAX7"))[] 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [58]
Overfull \hbox (5.09679pt too wide) in paragraph at lines 3336--3337
[]\T1/ptm/m/n/10 tidybulk() cre-ates a `tt` ob-ject from a `tbl` for-mat-ted as
 | <SAM-PLE> | <TRAN-SCRIPT> | <COUNT>
[59] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [60]
(/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/Rd2.ind [61]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 25.


Overfull \hbox (60.8567pt too wide) in paragraph at lines 25--27
[]\T1/zi4/m/n/10 adjust_abundance,RangedSummarizedExperiment-method 

Overfull \hbox (30.8567pt too wide) in paragraph at lines 29--31
[]\T1/zi4/m/it/10 adjust_abundance,SummarizedExperiment-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 36--38
[]\T1/zi4/m/it/10 aggregate_duplicates,RangedSummarizedExperiment-method 

Overfull \hbox (5.8567pt too wide) in paragraph at lines 38--40
[]\T1/zi4/m/it/10 aggregate_duplicates,spec_tbl_df-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 40--42
[]\T1/zi4/m/it/10 aggregate_duplicates,SummarizedExperiment-method 

Overfull \hbox (60.8567pt too wide) in paragraph at lines 65--67
[]\T1/zi4/m/it/10 cluster_elements,RangedSummarizedExperiment-method 

Overfull \hbox (30.8567pt too wide) in paragraph at lines 69--71
[]\T1/zi4/m/it/10 cluster_elements,SummarizedExperiment-method 

Overfull \hbox (90.8567pt too wide) in paragraph at lines 82--84
[]\T1/zi4/m/it/10 deconvolve_cellularity,RangedSummarizedExperiment-method 

Overfull \hbox (15.8567pt too wide) in paragraph at lines 84--86
[]\T1/zi4/m/it/10 deconvolve_cellularity,spec_tbl_df-method 

Overfull \hbox (60.8567pt too wide) in paragraph at lines 86--88
[]\T1/zi4/m/it/10 deconvolve_cellularity,SummarizedExperiment-method 

Overfull \hbox (0.8567pt too wide) in paragraph at lines 90--92
[]\T1/zi4/m/it/10 deconvolve_cellularity,tidybulk-method 
[62]
Overfull \hbox (60.8567pt too wide) in paragraph at lines 121--123
[]\T1/zi4/m/it/10 impute_abundance,RangedSummarizedExperiment-method 

Overfull \hbox (30.8567pt too wide) in paragraph at lines 125--127
[]\T1/zi4/m/it/10 impute_abundance,SummarizedExperiment-method 

Overfull \hbox (45.8567pt too wide) in paragraph at lines 136--138
[]\T1/zi4/m/it/10 keep_abundant,RangedSummarizedExperiment-method 

Overfull \hbox (15.8567pt too wide) in paragraph at lines 140--142
[]\T1/zi4/m/it/10 keep_abundant,SummarizedExperiment-method 

Overfull \hbox (45.8567pt too wide) in paragraph at lines 147--149
[]\T1/zi4/m/it/10 keep_variable,RangedSummarizedExperiment-method 

Overfull \hbox (15.8567pt too wide) in paragraph at lines 151--153
[]\T1/zi4/m/it/10 keep_variable,SummarizedExperiment-method 

Overfull \hbox (65.8567pt too wide) in paragraph at lines 193--195
[]\T1/zi4/m/it/10 reduce_dimensions,RangedSummarizedExperiment-method 

Overfull \hbox (35.8567pt too wide) in paragraph at lines 197--199
[]\T1/zi4/m/it/10 reduce_dimensions,SummarizedExperiment-method 

Overfull \hbox (65.8567pt too wide) in paragraph at lines 204--206
[]\T1/zi4/m/it/10 remove_redundancy,RangedSummarizedExperiment-method 

Overfull \hbox (35.8567pt too wide) in paragraph at lines 208--210
[]\T1/zi4/m/it/10 remove_redundancy,SummarizedExperiment-method 

Overfull \hbox (65.8567pt too wide) in paragraph at lines 220--222
[]\T1/zi4/m/it/10 rotate_dimensions,RangedSummarizedExperiment-method 

Overfull \hbox (35.8567pt too wide) in paragraph at lines 224--226
[]\T1/zi4/m/it/10 rotate_dimensions,SummarizedExperiment-method 

Overfull \hbox (55.8567pt too wide) in paragraph at lines 235--237
[]\T1/zi4/m/it/10 scale_abundance,RangedSummarizedExperiment-method 

Overfull \hbox (25.8567pt too wide) in paragraph at lines 239--241
[]\T1/zi4/m/it/10 scale_abundance,SummarizedExperiment-method 
[63]
Overfull \hbox (115.8567pt too wide) in paragraph at lines 256--258
[]\T1/zi4/m/it/10 test_differential_abundance,RangedSummarizedExperiment-method
 

Overfull \hbox (40.8567pt too wide) in paragraph at lines 258--260
[]\T1/zi4/m/it/10 test_differential_abundance,spec_tbl_df-method 

Overfull \hbox (85.8567pt too wide) in paragraph at lines 260--262
[]\T1/zi4/m/it/10 test_differential_abundance,SummarizedExperiment-method 

Overfull \hbox (15.8567pt too wide) in paragraph at lines 262--264
[]\T1/zi4/m/it/10 test_differential_abundance,tbl_df-method 

Overfull \hbox (25.8567pt too wide) in paragraph at lines 264--266
[]\T1/zi4/m/it/10 test_differential_abundance,tidybulk-method 

Overfull \hbox (5.8567pt too wide) in paragraph at lines 267--269
[]\T1/zi4/m/it/10 test_gene_enrichment,spec_tbl_df-method 

Overfull \hbox (45.8567pt too wide) in paragraph at lines 274--276
[]\T1/zi4/m/it/10 test_gene_overrepresentation,spec_tbl_df-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 276--278
[]\T1/zi4/m/it/10 test_gene_overrepresentation,tbl_df-method 

Overfull \hbox (30.8567pt too wide) in paragraph at lines 278--280
[]\T1/zi4/m/it/10 test_gene_overrepresentation,tidybulk-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 281--283
[]\T1/zi4/m/it/10 tidybulk,RangedSummarizedExperiment-method 

Overfull \hbox (25.8567pt too wide) in paragraph at lines 290--292
[]\T1/zi4/m/it/10 tidybulk_SAM_BAM,character,character-method 
[64]) (/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/.Rd2pdf23210/Rd2.aux)

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

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts
/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola
ta/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/inconsolata/In
consolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb
></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on Rd2.pdf (64 pages, 196870 bytes).
Transcript written on Rd2.log.
Saving output to ‘/tmp/RtmpbynNKD/Rbuild5aaa399cc5a9/tidybulk/build/tidybulk.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 ‘tidybulk_1.0.2.tar.gz’