Back to Multiple platform build/check report for BioC 3.14
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-21 13:07:57 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD results for ISAnalytics on machv2


To the developers/maintainers of the ISAnalytics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ISAnalytics.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 956/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISAnalytics 1.4.3  (landing page)
Andrea Calabria
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/ISAnalytics
git_branch: RELEASE_3_14
git_last_commit: 51c47b9
git_last_commit_date: 2022-01-13 08:23:28 -0500 (Thu, 13 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ISAnalytics
Version: 1.4.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ISAnalytics
StartedAt: 2022-01-20 06:30:53 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 06:32:06 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 73.2 seconds
RetCode: 0
Status:   OK  
PackageFile: ISAnalytics_1.4.3.tar.gz
PackageFileSize: 4.209 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ISAnalytics
###
##############################################################################
##############################################################################


* checking for file ‘ISAnalytics/DESCRIPTION’ ... OK
* preparing ‘ISAnalytics’:
* 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 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/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/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.

)
Overfull \hbox (25.5492pt too wide) in paragraph at lines 88--92
\T1/ptm/m/n/10 group. For more de-tails on how to use this func-tion: \T1/zi4/m
/n/10 vignette("aggregate_function_usage",package
[2]
Overfull \hbox (83.22833pt too wide) in paragraph at lines 149--154
\T1/ptm/m/n/10 the spec-i-fied lambda. For more de-tails on how to use this fun
c-tion: \T1/zi4/m/n/10 vignette("aggregate_function_usage",package
[3] [4] (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
Overfull \hbox (87.43779pt too wide) in paragraph at lines 289--291
[]\T1/ptm/m/n/10 Either a sin-gle ma-trix or a list of ma-tri-ces, ide-ally ob-
tained via \T1/zi4/m/n/10 import_parallel_Vispa2Matrices()
[5] [6] [7]
Overfull \hbox (7.2896pt too wide) in paragraph at lines 446--450
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_
launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association
_file[][][]()\T1/ptm/m/n/10 ,
[8] [9]
Overfull \hbox (21.58893pt too wide) in paragraph at lines 567--570
[]\T1/ptm/m/n/10 Additional named ar-gu-ments to pass on to cho-sen de-vice, \T
1/zi4/m/n/10 circlize::circos.par()\T1/ptm/m/n/10 ,

Overfull \hbox (25.29086pt too wide) in paragraph at lines 567--570
\T1/zi4/m/n/10 circlize::circos.genomicDensity() \T1/ptm/m/n/10 and \T1/zi4/m/n
/10 circlize::circos.genomicLabels() 

Overfull \hbox (47.36969pt too wide) in paragraph at lines 592--599
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10 ,
[10]
Overfull \hbox (92.28088pt too wide) in paragraph at lines 626--633
\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][] 

Overfull \hbox (30.68967pt too wide) in paragraph at lines 702--714
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat
rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[11] [12] (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
Overfull \hbox (77.36969pt too wide) in paragraph at lines 850--857
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 HSC_population_
plot[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\
T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n
/10 ,
[13] [14]
Overfull \hbox (83.3352pt too wide) in paragraph at lines 923--927
[]\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained 
via [][]im-port_parallel_Vispa2Matrices_interactive[][][]
[15]
Overfull \hbox (1.63855pt too wide) in paragraph at lines 1008--1011
[]\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th
e \T1/zi4/m/n/10 mandatory_IS_vars()

Overfull \hbox (20.16898pt too wide) in paragraph at lines 1008--1011
\T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4
/m/n/10 aggregate_values_by_key()\T1/ptm/m/n/10 )
[16] [17]
Overfull \hbox (9.28818pt too wide) in paragraph at lines 1136--1148
\T1/ptm/m/n/10 data frame con-tains the ref-er-ence of pre-recalibration val-ue
s for \T1/zi4/m/n/10 chr\T1/ptm/m/n/10 , \T1/zi4/m/n/10 strand \T1/ptm/m/n/10 a
nd \T1/zi4/m/n/10 integration_locus
[18]
Overfull \hbox (50.20969pt too wide) in paragraph at lines 1257--1269
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_is[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (40.36096pt too wide) in paragraph at lines 1257--1269
[][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so
urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[19]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 1333--1345
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (40.36096pt too wide) in paragraph at lines 1333--1345
[][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so
urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[20]
Underfull \hbox (badness 10000) in paragraph at lines 1388--1388
[]\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/
m/it/10 pa-

Underfull \hbox (badness 10000) in paragraph at lines 1388--1388
\T1/ptm/m/it/10 ram-e-ter in \T1/zi4/m/n/10 import_association_file\T1/ptm/m/it
/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 1388--1388
\T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and
[21] [22] [23]
Overfull \hbox (29.30962pt too wide) in paragraph at lines 1573--1577
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]() 
[24]
Overfull \hbox (19.25786pt too wide) in paragraph at lines 1624--1629
[]\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for
 ex-am-ple c("CLOEXP", "PROJECT1100",

Overfull \hbox (59.30962pt too wide) in paragraph at lines 1639--1643
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]() 
[25]
Overfull \hbox (62.36969pt too wide) in paragraph at lines 1691--1698
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/
ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10
 ,
[26] [27]
Overfull \hbox (3.4271pt too wide) in paragraph at lines 1790--1792
[]\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match
-ing is case-insensitive. 

Overfull \hbox (2.29784pt too wide) in paragraph at lines 1822--1831
\T1/ptm/m/n/10 orig-i-nal ma-trix are kept if the se-quence count value is grea
ter or equal than the \T1/zi4/m/n/10 seqCount_threshold
[28]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 1909--1912
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 
[29]
Overfull \hbox (115.40988pt too wide) in paragraph at lines 1933--1937
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][
][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]() 
[30]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 1996--1999
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 

Overfull \hbox (25.32918pt too wide) in paragraph at lines 2012--2014
[]\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t
ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file

Overfull \hbox (80.40988pt too wide) in paragraph at lines 2023--2027
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]() 
[31]
Overfull \hbox (64.31819pt too wide) in paragraph at lines 2085--2087
[]\T1/ptm/m/n/10 For more de-tails see the "How to use im-port func-tions" vi-g
nette: \T1/zi4/m/n/10 vignette("import_functions_howto",package

Overfull \hbox (100.40988pt too wide) in paragraph at lines 2094--2098
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][][]() 
[32]
Overfull \hbox (3.81735pt too wide) in paragraph at lines 2143--2146
\T1/ptm/m/n/10 el-e-ments rep-re-sent reg-u-lar ex-pres-sions. For de-faults se
e [][]de-fault_iss_file_prefixes[][][]. 

Overfull \hbox (5.10971pt too wide) in paragraph at lines 2155--2158
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 
[33] [34]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 2274--2281
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[35] [36]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2396--2408
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (55.36096pt too wide) in paragraph at lines 2396--2408
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[37]
Overfull \hbox (122.32698pt too wide) in paragraph at lines 2500--2505
[]\T1/ptm/m/n/10 The func-tion ac-cepts mul-ti-ple in-puts for dif-fer-ent sce-
nar-ios, please re-fer to the vi-gnette \T1/zi4/m/n/10 vignette("sharing_analys
es",package
[38]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2528--2540
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (55.36096pt too wide) in paragraph at lines 2528--2540
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss
_source[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[39]
Overfull \hbox (51.20859pt too wide) in paragraph at lines 2611--2613
[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma
tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2
Matrices_auto\T1/ptm/m/n/10 . 
[40]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 2716--2719
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 
[41] [42] [43] [44]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2973--2985
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (40.36096pt too wide) in paragraph at lines 2973--2985
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[45]
Overfull \hbox (118.70859pt too wide) in paragraph at lines 3008--3012
[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu
antification_type \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel
_vispa2Matrices_interactive

Overfull \hbox (16.08829pt too wide) in paragraph at lines 3057--3064
\T1/ptm/m/n/10 rea-son you re-moved the col-li-sions by pass-ing only the se-qu
ence count ma-trix to \T1/zi4/m/n/10 remove_collisions()\T1/ptm/m/n/10 ,
[46]
Overfull \hbox (25.75836pt too wide) in paragraph at lines 3074--3076
[]\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio
ns via \T1/zi4/m/n/10 remove_collisions() 

Overfull \hbox (33.86833pt too wide) in paragraph at lines 3084--3086
[]\T1/ptm/m/n/10 For more de-tails on how to use col-li-sion re-moval func-tion
-al-ity: \T1/zi4/m/n/10 vignette("collision_removal",package
[47] (/usr/local/texlive/2019/texmf-dist/tex/latex/base/t1cmtt.fd)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/ts1cmtt.fd) [48]
Overfull \hbox (19.7378pt too wide) in paragraph at lines 3226--3236
\T1/ptm/m/n/10 tails re-fer to the vi-gnette "Col-li-sion re-moval func-tion-al
-ity": \T1/zi4/m/n/10 vignette("collision_removal",package
[49]
Overfull \hbox (33.6188pt too wide) in paragraph at lines 3260--3262
[]\T1/ptm/m/n/10 The date col-umn that should be con-sid-ered. Must be one valu
e in \T1/zi4/m/n/10 date_columns_coll() 

Overfull \hbox (5.10971pt too wide) in paragraph at lines 3271--3274
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 
[50] [51]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 3376--3388
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (20.36096pt too wide) in paragraph at lines 3376--3388
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[52]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 3458--3470
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[53]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 3542--3549
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[54]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 3617--3624
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[55]
Overfull \hbox (3.36687pt too wide) in paragraph at lines 3677--3683
\T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and
 char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an
d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 .

Overfull \hbox (14.32507pt too wide) in paragraph at lines 3677--3683
\T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment 
by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com
parators
[56] [57]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 3848--3860
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[58]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 3964--3971
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[59]
Overfull \hbox (12.649pt too wide) in paragraph at lines 4000--4002
[]\T1/zi4/m/n/10 keep = "nothing" \T1/ptm/m/n/10 only keeps the manda-tory colu
mns (\T1/zi4/m/n/10 mandatory_IS_vars()\T1/ptm/m/n/10 ) plus the columns
[60]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 4047--4059
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[61]
Overfull \hbox (99.30962pt too wide) in paragraph at lines 4114--4118
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]() 
No file Rd2.ind.
[62]
(/private/tmp/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/Rd2.aux)

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

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

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

pdfTeX warning (dest): name{Rfn.import.Rul.parallel.Rul.Vispa2Matrices.Rul.auto
} has been referenced but does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.import.Rul.parallel.Rul.Vispa2Matrices.Rul.inte
ractive} has been referenced but does not exist, replaced by a fixed one

{/usr/local/texlive/2019/texmf-dist/fonts/enc/dvips/cm-super/cm-super-ts1.enc}{
/usr/local/texlive/2019/texmf-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/201
9/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/te
xlive/2019/texmf-dist/fonts/type1/public/cm-super/sftt1000.pfb></usr/local/texl
ive/2019/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/201
9/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf-di
st/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/t
imes/utmri8a.pfb>
Output written on Rd2.pdf (62 pages, 213980 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 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/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/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/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/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/Rd2.out)
(/private/tmp/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/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/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/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/Rd2.toc
[2]) [3]
Overfull \hbox (25.5492pt too wide) in paragraph at lines 88--92
\T1/ptm/m/n/10 group. For more de-tails on how to use this func-tion: \T1/zi4/m
/n/10 vignette("aggregate_function_usage",package

Overfull \hbox (83.22833pt too wide) in paragraph at lines 149--154
\T1/ptm/m/n/10 the spec-i-fied lambda. For more de-tails on how to use this fun
c-tion: \T1/zi4/m/n/10 vignette("aggregate_function_usage",package
[4] [5] (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
Overfull \hbox (87.43779pt too wide) in paragraph at lines 289--291
[]\T1/ptm/m/n/10 Either a sin-gle ma-trix or a list of ma-tri-ces, ide-ally ob-
tained via \T1/zi4/m/n/10 import_parallel_Vispa2Matrices()
[6] [7] [8]
Overfull \hbox (7.2896pt too wide) in paragraph at lines 446--450
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_
launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association
_file[][][]()\T1/ptm/m/n/10 ,
[9] [10]
Overfull \hbox (21.58893pt too wide) in paragraph at lines 567--570
[]\T1/ptm/m/n/10 Additional named ar-gu-ments to pass on to cho-sen de-vice, \T
1/zi4/m/n/10 circlize::circos.par()\T1/ptm/m/n/10 ,

Overfull \hbox (25.29086pt too wide) in paragraph at lines 567--570
\T1/zi4/m/n/10 circlize::circos.genomicDensity() \T1/ptm/m/n/10 and \T1/zi4/m/n
/10 circlize::circos.genomicLabels() 

Overfull \hbox (47.36969pt too wide) in paragraph at lines 592--599
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10 ,
[11]
Overfull \hbox (92.28088pt too wide) in paragraph at lines 626--633
\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][] 

Overfull \hbox (30.68967pt too wide) in paragraph at lines 702--714
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat
rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[12] [13] (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
Overfull \hbox (77.36969pt too wide) in paragraph at lines 850--857
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 HSC_population_
plot[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\
T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n
/10 ,
[14] [15]
Overfull \hbox (83.3352pt too wide) in paragraph at lines 923--927
[]\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained 
via [][]im-port_parallel_Vispa2Matrices_interactive[][][]
[16]
Overfull \hbox (1.63855pt too wide) in paragraph at lines 1008--1011
[]\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th
e \T1/zi4/m/n/10 mandatory_IS_vars()

Overfull \hbox (20.16898pt too wide) in paragraph at lines 1008--1011
\T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4
/m/n/10 aggregate_values_by_key()\T1/ptm/m/n/10 )
[17] [18]
Overfull \hbox (9.28818pt too wide) in paragraph at lines 1136--1148
\T1/ptm/m/n/10 data frame con-tains the ref-er-ence of pre-recalibration val-ue
s for \T1/zi4/m/n/10 chr\T1/ptm/m/n/10 , \T1/zi4/m/n/10 strand \T1/ptm/m/n/10 a
nd \T1/zi4/m/n/10 integration_locus
[19]
Overfull \hbox (50.20969pt too wide) in paragraph at lines 1257--1269
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_is[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (40.36096pt too wide) in paragraph at lines 1257--1269
[][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so
urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[20]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 1333--1345
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (40.36096pt too wide) in paragraph at lines 1333--1345
[][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so
urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[21]
Underfull \hbox (badness 10000) in paragraph at lines 1388--1388
[]\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/
m/it/10 pa-

Underfull \hbox (badness 10000) in paragraph at lines 1388--1388
\T1/ptm/m/it/10 ram-e-ter in \T1/zi4/m/n/10 import_association_file\T1/ptm/m/it
/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 1388--1388
\T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and
[22] [23] [24]
Overfull \hbox (29.30962pt too wide) in paragraph at lines 1573--1577
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]() 
[25]
Overfull \hbox (19.25786pt too wide) in paragraph at lines 1624--1629
[]\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for
 ex-am-ple c("CLOEXP", "PROJECT1100",

Overfull \hbox (59.30962pt too wide) in paragraph at lines 1639--1643
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]() 
[26]
Overfull \hbox (62.36969pt too wide) in paragraph at lines 1691--1698
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/
ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10
 ,
[27] [28]
Overfull \hbox (3.4271pt too wide) in paragraph at lines 1790--1792
[]\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match
-ing is case-insensitive. 

Overfull \hbox (2.29784pt too wide) in paragraph at lines 1822--1831
\T1/ptm/m/n/10 orig-i-nal ma-trix are kept if the se-quence count value is grea
ter or equal than the \T1/zi4/m/n/10 seqCount_threshold
[29]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 1909--1912
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 
[30]
Overfull \hbox (115.40988pt too wide) in paragraph at lines 1933--1937
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][
][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]() 
[31]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 1996--1999
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 

Overfull \hbox (25.32918pt too wide) in paragraph at lines 2012--2014
[]\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t
ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file

Overfull \hbox (80.40988pt too wide) in paragraph at lines 2023--2027
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]() 
[32]
Overfull \hbox (64.31819pt too wide) in paragraph at lines 2085--2087
[]\T1/ptm/m/n/10 For more de-tails see the "How to use im-port func-tions" vi-g
nette: \T1/zi4/m/n/10 vignette("import_functions_howto",package

Overfull \hbox (100.40988pt too wide) in paragraph at lines 2094--2098
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][][]() 
[33]
Overfull \hbox (3.81735pt too wide) in paragraph at lines 2143--2146
\T1/ptm/m/n/10 el-e-ments rep-re-sent reg-u-lar ex-pres-sions. For de-faults se
e [][]de-fault_iss_file_prefixes[][][]. 

Overfull \hbox (5.10971pt too wide) in paragraph at lines 2155--2158
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 
[34] [35]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 2274--2281
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[36] [37]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2396--2408
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (55.36096pt too wide) in paragraph at lines 2396--2408
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[38]
Overfull \hbox (122.32698pt too wide) in paragraph at lines 2500--2505
[]\T1/ptm/m/n/10 The func-tion ac-cepts mul-ti-ple in-puts for dif-fer-ent sce-
nar-ios, please re-fer to the vi-gnette \T1/zi4/m/n/10 vignette("sharing_analys
es",package
[39]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2528--2540
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (55.36096pt too wide) in paragraph at lines 2528--2540
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss
_source[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[40]
Overfull \hbox (51.20859pt too wide) in paragraph at lines 2611--2613
[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma
tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2
Matrices_auto\T1/ptm/m/n/10 . 
[41]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 2716--2719
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 
[42] [43] [44] [45]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2973--2985
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (40.36096pt too wide) in paragraph at lines 2973--2985
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[46]
Overfull \hbox (118.70859pt too wide) in paragraph at lines 3008--3012
[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu
antification_type \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel
_vispa2Matrices_interactive

Overfull \hbox (16.08829pt too wide) in paragraph at lines 3057--3064
\T1/ptm/m/n/10 rea-son you re-moved the col-li-sions by pass-ing only the se-qu
ence count ma-trix to \T1/zi4/m/n/10 remove_collisions()\T1/ptm/m/n/10 ,
[47]
Overfull \hbox (25.75836pt too wide) in paragraph at lines 3074--3076
[]\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio
ns via \T1/zi4/m/n/10 remove_collisions() 

Overfull \hbox (33.86833pt too wide) in paragraph at lines 3084--3086
[]\T1/ptm/m/n/10 For more de-tails on how to use col-li-sion re-moval func-tion
-al-ity: \T1/zi4/m/n/10 vignette("collision_removal",package
[48] (/usr/local/texlive/2019/texmf-dist/tex/latex/base/t1cmtt.fd)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/ts1cmtt.fd) [49]
Overfull \hbox (19.7378pt too wide) in paragraph at lines 3226--3236
\T1/ptm/m/n/10 tails re-fer to the vi-gnette "Col-li-sion re-moval func-tion-al
-ity": \T1/zi4/m/n/10 vignette("collision_removal",package
[50]
Overfull \hbox (33.6188pt too wide) in paragraph at lines 3260--3262
[]\T1/ptm/m/n/10 The date col-umn that should be con-sid-ered. Must be one valu
e in \T1/zi4/m/n/10 date_columns_coll() 

Overfull \hbox (5.10971pt too wide) in paragraph at lines 3271--3274
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 
[51] [52]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 3376--3388
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (20.36096pt too wide) in paragraph at lines 3376--3388
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[53]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 3458--3470
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[54]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 3542--3549
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[55]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 3617--3624
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[56]
Overfull \hbox (3.36687pt too wide) in paragraph at lines 3677--3683
\T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and
 char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an
d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 .

Overfull \hbox (14.32507pt too wide) in paragraph at lines 3677--3683
\T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment 
by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com
parators
[57] [58]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 3848--3860
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[59]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 3964--3971
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[60]
Overfull \hbox (12.649pt too wide) in paragraph at lines 4000--4002
[]\T1/zi4/m/n/10 keep = "nothing" \T1/ptm/m/n/10 only keeps the manda-tory colu
mns (\T1/zi4/m/n/10 mandatory_IS_vars()\T1/ptm/m/n/10 ) plus the columns
[61]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 4047--4059
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[62]
Overfull \hbox (99.30962pt too wide) in paragraph at lines 4114--4118
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]() 
No file Rd2.ind.
[63]
(/private/tmp/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/Rd2.aux) 
)
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.dynamic.Rdash.dots} has been referenced but does not exist, replaced by a 
fixed one

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

pdfTeX warning (dest): name{Rfn.import.Rul.parallel.Rul.Vispa2Matrices.Rul.auto
} has been referenced but does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.import.Rul.parallel.Rul.Vispa2Matrices.Rul.inte
ractive} has been referenced but does not exist, replaced by a fixed one

{/usr/local/texlive/2019/texmf-dist/fonts/enc/dvips/cm-super/cm-super-ts1.enc}{
/usr/local/texlive/2019/texmf-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/201
9/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/te
xlive/2019/texmf-dist/fonts/type1/public/cm-super/sftt1000.pfb></usr/local/texl
ive/2019/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/201
9/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf-di
st/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/t
imes/utmri8a.pfb>
Output written on Rd2.pdf (63 pages, 220836 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (374 entries accepted, 1 rejected).
Sorting entries......done (3393 comparisons).
Generating output file Rd2.ind....done (367 lines written, 4 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 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/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/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/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/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/Rd2.out)
(/private/tmp/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/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/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/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/Rd2.toc
[2]) [3]
Overfull \hbox (25.5492pt too wide) in paragraph at lines 88--92
\T1/ptm/m/n/10 group. For more de-tails on how to use this func-tion: \T1/zi4/m
/n/10 vignette("aggregate_function_usage",package

Overfull \hbox (83.22833pt too wide) in paragraph at lines 149--154
\T1/ptm/m/n/10 the spec-i-fied lambda. For more de-tails on how to use this fun
c-tion: \T1/zi4/m/n/10 vignette("aggregate_function_usage",package
[4] [5] (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
Overfull \hbox (87.43779pt too wide) in paragraph at lines 289--291
[]\T1/ptm/m/n/10 Either a sin-gle ma-trix or a list of ma-tri-ces, ide-ally ob-
tained via \T1/zi4/m/n/10 import_parallel_Vispa2Matrices()
[6] [7] [8]
Overfull \hbox (7.2896pt too wide) in paragraph at lines 446--450
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_
launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association
_file[][][]()\T1/ptm/m/n/10 ,
[9] [10]
Overfull \hbox (21.58893pt too wide) in paragraph at lines 567--570
[]\T1/ptm/m/n/10 Additional named ar-gu-ments to pass on to cho-sen de-vice, \T
1/zi4/m/n/10 circlize::circos.par()\T1/ptm/m/n/10 ,

Overfull \hbox (25.29086pt too wide) in paragraph at lines 567--570
\T1/zi4/m/n/10 circlize::circos.genomicDensity() \T1/ptm/m/n/10 and \T1/zi4/m/n
/10 circlize::circos.genomicLabels() 

Overfull \hbox (47.36969pt too wide) in paragraph at lines 592--599
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10 ,
[11]
Overfull \hbox (92.28088pt too wide) in paragraph at lines 626--633
\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][] 

Overfull \hbox (30.68967pt too wide) in paragraph at lines 702--714
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat
rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[12] [13] (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
Overfull \hbox (77.36969pt too wide) in paragraph at lines 850--857
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 HSC_population_
plot[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\
T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n
/10 ,
[14] [15]
Overfull \hbox (83.3352pt too wide) in paragraph at lines 923--927
[]\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained 
via [][]im-port_parallel_Vispa2Matrices_interactive[][][]
[16]
Overfull \hbox (1.63855pt too wide) in paragraph at lines 1008--1011
[]\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th
e \T1/zi4/m/n/10 mandatory_IS_vars()

Overfull \hbox (20.16898pt too wide) in paragraph at lines 1008--1011
\T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4
/m/n/10 aggregate_values_by_key()\T1/ptm/m/n/10 )
[17] [18]
Overfull \hbox (9.28818pt too wide) in paragraph at lines 1136--1148
\T1/ptm/m/n/10 data frame con-tains the ref-er-ence of pre-recalibration val-ue
s for \T1/zi4/m/n/10 chr\T1/ptm/m/n/10 , \T1/zi4/m/n/10 strand \T1/ptm/m/n/10 a
nd \T1/zi4/m/n/10 integration_locus
[19]
Overfull \hbox (50.20969pt too wide) in paragraph at lines 1257--1269
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_is[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (40.36096pt too wide) in paragraph at lines 1257--1269
[][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so
urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[20]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 1333--1345
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (40.36096pt too wide) in paragraph at lines 1333--1345
[][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so
urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[21]
Underfull \hbox (badness 10000) in paragraph at lines 1388--1388
[]\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/
m/it/10 pa-

Underfull \hbox (badness 10000) in paragraph at lines 1388--1388
\T1/ptm/m/it/10 ram-e-ter in \T1/zi4/m/n/10 import_association_file\T1/ptm/m/it
/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 1388--1388
\T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and
[22] [23] [24]
Overfull \hbox (29.30962pt too wide) in paragraph at lines 1573--1577
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]() 
[25]
Overfull \hbox (19.25786pt too wide) in paragraph at lines 1624--1629
[]\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for
 ex-am-ple c("CLOEXP", "PROJECT1100",

Overfull \hbox (59.30962pt too wide) in paragraph at lines 1639--1643
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]() 
[26]
Overfull \hbox (62.36969pt too wide) in paragraph at lines 1691--1698
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/
ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10
 ,
[27] [28]
Overfull \hbox (3.4271pt too wide) in paragraph at lines 1790--1792
[]\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match
-ing is case-insensitive. 

Overfull \hbox (2.29784pt too wide) in paragraph at lines 1822--1831
\T1/ptm/m/n/10 orig-i-nal ma-trix are kept if the se-quence count value is grea
ter or equal than the \T1/zi4/m/n/10 seqCount_threshold
[29]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 1909--1912
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 
[30]
Overfull \hbox (115.40988pt too wide) in paragraph at lines 1933--1937
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][
][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]() 
[31]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 1996--1999
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 

Overfull \hbox (25.32918pt too wide) in paragraph at lines 2012--2014
[]\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t
ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file

Overfull \hbox (80.40988pt too wide) in paragraph at lines 2023--2027
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]() 
[32]
Overfull \hbox (64.31819pt too wide) in paragraph at lines 2085--2087
[]\T1/ptm/m/n/10 For more de-tails see the "How to use im-port func-tions" vi-g
nette: \T1/zi4/m/n/10 vignette("import_functions_howto",package

Overfull \hbox (100.40988pt too wide) in paragraph at lines 2094--2098
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][][]() 
[33]
Overfull \hbox (3.81735pt too wide) in paragraph at lines 2143--2146
\T1/ptm/m/n/10 el-e-ments rep-re-sent reg-u-lar ex-pres-sions. For de-faults se
e [][]de-fault_iss_file_prefixes[][][]. 

Overfull \hbox (5.10971pt too wide) in paragraph at lines 2155--2158
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 
[34] [35]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 2274--2281
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[36] [37]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2396--2408
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (55.36096pt too wide) in paragraph at lines 2396--2408
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[38]
Overfull \hbox (122.32698pt too wide) in paragraph at lines 2500--2505
[]\T1/ptm/m/n/10 The func-tion ac-cepts mul-ti-ple in-puts for dif-fer-ent sce-
nar-ios, please re-fer to the vi-gnette \T1/zi4/m/n/10 vignette("sharing_analys
es",package
[39]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2528--2540
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (55.36096pt too wide) in paragraph at lines 2528--2540
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss
_source[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[40]
Overfull \hbox (51.20859pt too wide) in paragraph at lines 2611--2613
[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma
tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2
Matrices_auto\T1/ptm/m/n/10 . 
[41]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 2716--2719
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 
[42] [43] [44] [45]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2973--2985
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (40.36096pt too wide) in paragraph at lines 2973--2985
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[46]
Overfull \hbox (118.70859pt too wide) in paragraph at lines 3008--3012
[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu
antification_type \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel
_vispa2Matrices_interactive

Overfull \hbox (16.08829pt too wide) in paragraph at lines 3057--3064
\T1/ptm/m/n/10 rea-son you re-moved the col-li-sions by pass-ing only the se-qu
ence count ma-trix to \T1/zi4/m/n/10 remove_collisions()\T1/ptm/m/n/10 ,
[47]
Overfull \hbox (25.75836pt too wide) in paragraph at lines 3074--3076
[]\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio
ns via \T1/zi4/m/n/10 remove_collisions() 

Overfull \hbox (33.86833pt too wide) in paragraph at lines 3084--3086
[]\T1/ptm/m/n/10 For more de-tails on how to use col-li-sion re-moval func-tion
-al-ity: \T1/zi4/m/n/10 vignette("collision_removal",package
[48] (/usr/local/texlive/2019/texmf-dist/tex/latex/base/t1cmtt.fd)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/ts1cmtt.fd) [49]
Overfull \hbox (19.7378pt too wide) in paragraph at lines 3226--3236
\T1/ptm/m/n/10 tails re-fer to the vi-gnette "Col-li-sion re-moval func-tion-al
-ity": \T1/zi4/m/n/10 vignette("collision_removal",package
[50]
Overfull \hbox (33.6188pt too wide) in paragraph at lines 3260--3262
[]\T1/ptm/m/n/10 The date col-umn that should be con-sid-ered. Must be one valu
e in \T1/zi4/m/n/10 date_columns_coll() 

Overfull \hbox (5.10971pt too wide) in paragraph at lines 3271--3274
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 
[51] [52]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 3376--3388
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (20.36096pt too wide) in paragraph at lines 3376--3388
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[53]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 3458--3470
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[54]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 3542--3549
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[55]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 3617--3624
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[56]
Overfull \hbox (3.36687pt too wide) in paragraph at lines 3677--3683
\T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and
 char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an
d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 .

Overfull \hbox (14.32507pt too wide) in paragraph at lines 3677--3683
\T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment 
by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com
parators
[57] [58]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 3848--3860
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[59]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 3964--3971
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[60]
Overfull \hbox (12.649pt too wide) in paragraph at lines 4000--4002
[]\T1/zi4/m/n/10 keep = "nothing" \T1/ptm/m/n/10 only keeps the manda-tory colu
mns (\T1/zi4/m/n/10 mandatory_IS_vars()\T1/ptm/m/n/10 ) plus the columns
[61]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 4047--4059
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[62]
Overfull \hbox (99.30962pt too wide) in paragraph at lines 4114--4118
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]() 
(/private/tmp/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/Rd2.ind
[63]
Overfull \hbox (3.3567pt too wide) in paragraph at lines 43--45
[]| \T1/zi4/m/n/10 clinical_relevant_suspicious_genes\T1/ptm/m/n/10 , 
[64]
Overfull \hbox (23.3567pt too wide) in paragraph at lines 216--219
[]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices_interactive\T1/ptm/m/n/10 , 

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 294.

[65])
(/private/tmp/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/Rd2.aux)

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


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

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

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

pdfTeX warning (dest): name{Rfn.import.Rul.parallel.Rul.Vispa2Matrices.Rul.auto
} has been referenced but does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.import.Rul.parallel.Rul.Vispa2Matrices.Rul.inte
ractive} has been referenced but does not exist, replaced by a fixed one

{/usr/local/texlive/2019/texmf-dist/fonts/enc/dvips/cm-super/cm-super-ts1.enc}{
/usr/local/texlive/2019/texmf-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/201
9/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/te
xlive/2019/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/tex
live/2019/texmf-dist/fonts/type1/public/cm-super/sftt1000.pfb></usr/local/texli
ve/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-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/ty
pe1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/ti
mes/utmri8a.pfb>
Output written on Rd2.pdf (65 pages, 243626 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (374 entries accepted, 1 rejected).
Sorting entries......done (3393 comparisons).
Generating output file Rd2.ind....done (367 lines written, 4 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 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/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/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/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/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/Rd2.out)
(/private/tmp/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/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/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/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/Rd2.toc
[2]) [3]
Overfull \hbox (25.5492pt too wide) in paragraph at lines 88--92
\T1/ptm/m/n/10 group. For more de-tails on how to use this func-tion: \T1/zi4/m
/n/10 vignette("aggregate_function_usage",package

Overfull \hbox (83.22833pt too wide) in paragraph at lines 149--154
\T1/ptm/m/n/10 the spec-i-fied lambda. For more de-tails on how to use this fun
c-tion: \T1/zi4/m/n/10 vignette("aggregate_function_usage",package
[4] [5] (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
Overfull \hbox (87.43779pt too wide) in paragraph at lines 289--291
[]\T1/ptm/m/n/10 Either a sin-gle ma-trix or a list of ma-tri-ces, ide-ally ob-
tained via \T1/zi4/m/n/10 import_parallel_Vispa2Matrices()
[6] [7] [8]
Overfull \hbox (7.2896pt too wide) in paragraph at lines 446--450
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_
launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association
_file[][][]()\T1/ptm/m/n/10 ,
[9] [10]
Overfull \hbox (21.58893pt too wide) in paragraph at lines 567--570
[]\T1/ptm/m/n/10 Additional named ar-gu-ments to pass on to cho-sen de-vice, \T
1/zi4/m/n/10 circlize::circos.par()\T1/ptm/m/n/10 ,

Overfull \hbox (25.29086pt too wide) in paragraph at lines 567--570
\T1/zi4/m/n/10 circlize::circos.genomicDensity() \T1/ptm/m/n/10 and \T1/zi4/m/n
/10 circlize::circos.genomicLabels() 

Overfull \hbox (47.36969pt too wide) in paragraph at lines 592--599
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10 ,
[11]
Overfull \hbox (92.28088pt too wide) in paragraph at lines 626--633
\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][] 

Overfull \hbox (30.68967pt too wide) in paragraph at lines 702--714
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat
rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[12] [13] (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
Overfull \hbox (77.36969pt too wide) in paragraph at lines 850--857
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 HSC_population_
plot[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\
T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n
/10 ,
[14] [15]
Overfull \hbox (83.3352pt too wide) in paragraph at lines 923--927
[]\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained 
via [][]im-port_parallel_Vispa2Matrices_interactive[][][]
[16]
Overfull \hbox (1.63855pt too wide) in paragraph at lines 1008--1011
[]\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th
e \T1/zi4/m/n/10 mandatory_IS_vars()

Overfull \hbox (20.16898pt too wide) in paragraph at lines 1008--1011
\T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4
/m/n/10 aggregate_values_by_key()\T1/ptm/m/n/10 )
[17] [18]
Overfull \hbox (9.28818pt too wide) in paragraph at lines 1136--1148
\T1/ptm/m/n/10 data frame con-tains the ref-er-ence of pre-recalibration val-ue
s for \T1/zi4/m/n/10 chr\T1/ptm/m/n/10 , \T1/zi4/m/n/10 strand \T1/ptm/m/n/10 a
nd \T1/zi4/m/n/10 integration_locus
[19]
Overfull \hbox (50.20969pt too wide) in paragraph at lines 1257--1269
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_is[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (40.36096pt too wide) in paragraph at lines 1257--1269
[][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so
urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[20]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 1333--1345
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (40.36096pt too wide) in paragraph at lines 1333--1345
[][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so
urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[21]
Underfull \hbox (badness 10000) in paragraph at lines 1388--1388
[]\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/
m/it/10 pa-

Underfull \hbox (badness 10000) in paragraph at lines 1388--1388
\T1/ptm/m/it/10 ram-e-ter in \T1/zi4/m/n/10 import_association_file\T1/ptm/m/it
/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 1388--1388
\T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and
[22] [23] [24]
Overfull \hbox (29.30962pt too wide) in paragraph at lines 1573--1577
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]() 
[25]
Overfull \hbox (19.25786pt too wide) in paragraph at lines 1624--1629
[]\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for
 ex-am-ple c("CLOEXP", "PROJECT1100",

Overfull \hbox (59.30962pt too wide) in paragraph at lines 1639--1643
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]() 
[26]
Overfull \hbox (62.36969pt too wide) in paragraph at lines 1691--1698
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/
ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10
 ,
[27] [28]
Overfull \hbox (3.4271pt too wide) in paragraph at lines 1790--1792
[]\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match
-ing is case-insensitive. 

Overfull \hbox (2.29784pt too wide) in paragraph at lines 1822--1831
\T1/ptm/m/n/10 orig-i-nal ma-trix are kept if the se-quence count value is grea
ter or equal than the \T1/zi4/m/n/10 seqCount_threshold
[29]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 1909--1912
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 
[30]
Overfull \hbox (115.40988pt too wide) in paragraph at lines 1933--1937
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][
][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]() 
[31]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 1996--1999
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 

Overfull \hbox (25.32918pt too wide) in paragraph at lines 2012--2014
[]\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t
ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file

Overfull \hbox (80.40988pt too wide) in paragraph at lines 2023--2027
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]() 
[32]
Overfull \hbox (64.31819pt too wide) in paragraph at lines 2085--2087
[]\T1/ptm/m/n/10 For more de-tails see the "How to use im-port func-tions" vi-g
nette: \T1/zi4/m/n/10 vignette("import_functions_howto",package

Overfull \hbox (100.40988pt too wide) in paragraph at lines 2094--2098
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][][]() 
[33]
Overfull \hbox (3.81735pt too wide) in paragraph at lines 2143--2146
\T1/ptm/m/n/10 el-e-ments rep-re-sent reg-u-lar ex-pres-sions. For de-faults se
e [][]de-fault_iss_file_prefixes[][][]. 

Overfull \hbox (5.10971pt too wide) in paragraph at lines 2155--2158
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 
[34] [35]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 2274--2281
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[36] [37]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2396--2408
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (55.36096pt too wide) in paragraph at lines 2396--2408
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[38]
Overfull \hbox (122.32698pt too wide) in paragraph at lines 2500--2505
[]\T1/ptm/m/n/10 The func-tion ac-cepts mul-ti-ple in-puts for dif-fer-ent sce-
nar-ios, please re-fer to the vi-gnette \T1/zi4/m/n/10 vignette("sharing_analys
es",package
[39]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2528--2540
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (55.36096pt too wide) in paragraph at lines 2528--2540
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss
_source[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[40]
Overfull \hbox (51.20859pt too wide) in paragraph at lines 2611--2613
[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma
tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2
Matrices_auto\T1/ptm/m/n/10 . 
[41]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 2716--2719
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 
[42] [43] [44] [45]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2973--2985
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (40.36096pt too wide) in paragraph at lines 2973--2985
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[46]
Overfull \hbox (118.70859pt too wide) in paragraph at lines 3008--3012
[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu
antification_type \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel
_vispa2Matrices_interactive

Overfull \hbox (16.08829pt too wide) in paragraph at lines 3057--3064
\T1/ptm/m/n/10 rea-son you re-moved the col-li-sions by pass-ing only the se-qu
ence count ma-trix to \T1/zi4/m/n/10 remove_collisions()\T1/ptm/m/n/10 ,
[47]
Overfull \hbox (25.75836pt too wide) in paragraph at lines 3074--3076
[]\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio
ns via \T1/zi4/m/n/10 remove_collisions() 

Overfull \hbox (33.86833pt too wide) in paragraph at lines 3084--3086
[]\T1/ptm/m/n/10 For more de-tails on how to use col-li-sion re-moval func-tion
-al-ity: \T1/zi4/m/n/10 vignette("collision_removal",package
[48] (/usr/local/texlive/2019/texmf-dist/tex/latex/base/t1cmtt.fd)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/ts1cmtt.fd) [49]
Overfull \hbox (19.7378pt too wide) in paragraph at lines 3226--3236
\T1/ptm/m/n/10 tails re-fer to the vi-gnette "Col-li-sion re-moval func-tion-al
-ity": \T1/zi4/m/n/10 vignette("collision_removal",package
[50]
Overfull \hbox (33.6188pt too wide) in paragraph at lines 3260--3262
[]\T1/ptm/m/n/10 The date col-umn that should be con-sid-ered. Must be one valu
e in \T1/zi4/m/n/10 date_columns_coll() 

Overfull \hbox (5.10971pt too wide) in paragraph at lines 3271--3274
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . 
[51] [52]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 3376--3388
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (20.36096pt too wide) in paragraph at lines 3376--3388
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[53]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 3458--3470
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[54]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 3542--3549
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[55]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 3617--3624
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[56]
Overfull \hbox (3.36687pt too wide) in paragraph at lines 3677--3683
\T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and
 char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an
d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 .

Overfull \hbox (14.32507pt too wide) in paragraph at lines 3677--3683
\T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment 
by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com
parators
[57] [58]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 3848--3860
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[59]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 3964--3971
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[60]
Overfull \hbox (12.649pt too wide) in paragraph at lines 4000--4002
[]\T1/zi4/m/n/10 keep = "nothing" \T1/ptm/m/n/10 only keeps the manda-tory colu
mns (\T1/zi4/m/n/10 mandatory_IS_vars()\T1/ptm/m/n/10 ) plus the columns
[61]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 4047--4059
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[62]
Overfull \hbox (99.30962pt too wide) in paragraph at lines 4114--4118
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]() 
(/private/tmp/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/Rd2.ind
[63]
Overfull \hbox (3.3567pt too wide) in paragraph at lines 43--45
[]| \T1/zi4/m/n/10 clinical_relevant_suspicious_genes\T1/ptm/m/n/10 , 
[64]
Overfull \hbox (23.3567pt too wide) in paragraph at lines 216--219
[]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices_interactive\T1/ptm/m/n/10 , 

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 294.

[65])
(/private/tmp/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/.Rd2pdf86039/Rd2.aux)

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

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

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

pdfTeX warning (dest): name{Rfn.import.Rul.parallel.Rul.Vispa2Matrices.Rul.auto
} has been referenced but does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.import.Rul.parallel.Rul.Vispa2Matrices.Rul.inte
ractive} has been referenced but does not exist, replaced by a fixed one

{/usr/local/texlive/2019/texmf-dist/fonts/enc/dvips/cm-super/cm-super-ts1.enc}{
/usr/local/texlive/2019/texmf-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/201
9/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/te
xlive/2019/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/tex
live/2019/texmf-dist/fonts/type1/public/cm-super/sftt1000.pfb></usr/local/texli
ve/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-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/ty
pe1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/ti
mes/utmri8a.pfb>
Output written on Rd2.pdf (65 pages, 244388 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/RtmpJZlYhj/Rbuild1501755dff430/ISAnalytics/build/ISAnalytics.pdf’ ...
Done
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘ISAnalytics_1.4.3.tar.gz’