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This page was generated on 2021-10-15 15:06:40 -0400 (Fri, 15 Oct 2021).
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. |
Package 944/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ISAnalytics 1.2.1 (landing page) Andrea Calabria
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: ISAnalytics |
Version: 1.2.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ISAnalytics |
StartedAt: 2021-10-14 12:47:17 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 12:48:27 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 70.1 seconds |
RetCode: 0 |
Status: OK |
PackageFile: ISAnalytics_1.2.1.tar.gz |
PackageFileSize: 3.156 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/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'. 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Found on input line 46. ) [2] [3] (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [4] [5] [6] Overfull \hbox (7.2896pt too wide) in paragraph at lines 386--390 []\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 , [7] Overfull \hbox (92.28088pt too wide) in paragraph at lines 459--466 \T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120 6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][] [8] Overfull \hbox (30.68967pt too wide) in paragraph at lines 521--529 []\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 , Overfull \hbox (18.34094pt too wide) in paragraph at lines 521--529 [][]\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 , [][]\T1/zi4/m/n/10 threshold_f ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]() [9] Overfull \hbox (29.76044pt too wide) in paragraph at lines 569--569 [] \T1/zi4/m/n/10 onco_db_file = system.file("extdata", "201806_uniprot-Proto -oncogene.tsv.xz", package[] [10] [11] [12] Overfull \hbox (83.3352pt too wide) in paragraph at lines 764--768 []\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[][][] Overfull \hbox (18.34094pt too wide) in paragraph at lines 791--799 [][]\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 , [][]\T1/zi4/m/n/10 threshold_f ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]() [13] Overfull \hbox (1.63855pt too wide) in paragraph at lines 844--847 []\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 844--847 \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 ) [14] Overfull \hbox (18.34094pt too wide) in paragraph at lines 877--885 [][]\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 , [][]\T1/zi4/m/n/10 threshold_f ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]() Overfull \hbox (0.26779pt too wide) in paragraph at lines 932--935 \T1/ptm/m/n/10 value columns cor-re-spond-ing to dif-fer-ent quan-tifi-ca-tion types (ob-tained via [][]com- [15] [16] [17] Overfull \hbox (70.20969pt too wide) in paragraph at lines 1097--1105 []\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 sample_statistics[][][]()\T1/ptm/m/n/10 , [18] Underfull \hbox (badness 10000) in paragraph at lines 1170--1170 []\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 1170--1170 \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 1170--1170 \T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and [19] [20] [21] Overfull \hbox (29.30962pt too wide) in paragraph at lines 1332--1336 []\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[][][]() [22] Overfull \hbox (19.25786pt too wide) in paragraph at lines 1383--1388 []\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 1398--1402 []\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[][][]() [23] [24] [25] Overfull \hbox (3.4271pt too wide) in paragraph at lines 1551--1553 []\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match -ing is case-insensitive. [26] [27] Underfull \hbox (badness 10000) in paragraph at lines 1690--1699 [28] Overfull \hbox (24.6883pt too wide) in paragraph at lines 1777--1779 []\T1/ptm/m/n/10 A vec-tor of re-quested quan-tifi-ca-tion_types. Must be one i n \T1/zi4/m/n/10 quantification_types() Overfull \hbox (25.32918pt too wide) in paragraph at lines 1799--1801 []\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 (61.1266pt too wide) in paragraph at lines 1805--1812 \T1/ptm/m/n/10 For more de-tails on how to prop-erly use these func-tions, re-f er to the vi-gnette - vi-gnette("how_to_import_functions") [29] Overfull \hbox (4.8009pt too wide) in paragraph at lines 1847--1849 [][][]\T1/zi4/m/n/10 matching_options[][][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / stringr . tidyverse . org / articles / regular-[]expressions . htm l$[][] Overfull \hbox (162.90988pt too wide) in paragraph at lines 1850--1855 []\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_interactive[][ ][]()\T1/ptm/m/n/10 , [30] Overfull \hbox (24.6883pt too wide) in paragraph at lines 1907--1909 []\T1/ptm/m/n/10 A vec-tor of re-quested quan-tifi-ca-tion_types. Must be one i n \T1/zi4/m/n/10 quantification_types() Overfull \hbox (25.32918pt too wide) in paragraph at lines 1923--1925 []\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 (61.1266pt too wide) in paragraph at lines 1929--1936 \T1/ptm/m/n/10 For more de-tails on how to prop-erly use these func-tions, re-f er to the vi-gnette - vi-gnette("how_to_import_functions") [31] Overfull \hbox (127.90988pt too wide) in paragraph at lines 1956--1961 []\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_auto[][][]()\T 1/ptm/m/n/10 , (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [32] Overfull \hbox (127.90988pt too wide) in paragraph at lines 2022--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_parallel_Vispa2Matrices_auto[][][]()\T 1/ptm/m/n/10 , Overfull \hbox (3.81735pt too wide) in paragraph at lines 2065--2068 \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 (18.38986pt too wide) in paragraph at lines 2087--2092 []\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice s_auto[][][]()\T1/ptm/m/n/10 , [33] [34] [35] Overfull \hbox (51.20859pt too wide) in paragraph at lines 2298--2300 []\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 . [36] [37] [38] Overfull \hbox (118.70859pt too wide) in paragraph at lines 2524--2528 []\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 [39] Overfull \hbox (15.75836pt too wide) in paragraph at lines 2589--2591 []\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 [40] [41] [42] Overfull \hbox (51.33856pt too wide) in paragraph at lines 2724--2730 \T1/ptm/m/n/10 tails on how to use col-li-sion re-moval func-tion-al-ity: \T1/z i4/m/n/10 vignette("Collision removal functionality",package [43] [44] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2840--2848 []\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 , [45] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2932--2940 []\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 , [46] Overfull \hbox (3.36687pt too wide) in paragraph at lines 3000--3006 \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 3000--3006 \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 [47] [48] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3171--3179 []\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 , [49] Overfull \hbox (12.649pt too wide) in paragraph at lines 3224--3226 []\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 [50] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3271--3279 []\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 (99.30962pt too wide) in paragraph at lines 3334--3338 []\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[][][]() [51] No file Rd2.ind. [52] (/private/tmp/Rtmp60PWuZ/Rbuild130e4fc257a7/ISAnalytics/.Rd2pdf78052/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 {/usr/local/texlive/2019/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us r/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/20 19/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t exlive/2019/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/ 2019/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf -dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/font s/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/ur w/times/utmri8a.pfb> Output written on Rd2.pdf (52 pages, 185031 bytes). 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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. 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Found on input line 46. ) (/private/tmp/Rtmp60PWuZ/Rbuild130e4fc257a7/ISAnalytics/.Rd2pdf78052/Rd2.toc [2]) [3] [4] (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [5] [6] [7] Overfull \hbox (7.2896pt too wide) in paragraph at lines 386--390 []\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] Overfull \hbox (92.28088pt too wide) in paragraph at lines 459--466 \T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120 6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][] [9] Overfull \hbox (30.68967pt too wide) in paragraph at lines 521--529 []\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 , Overfull \hbox (18.34094pt too wide) in paragraph at lines 521--529 [][]\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 , [][]\T1/zi4/m/n/10 threshold_f ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]() [10] Overfull \hbox (29.76044pt too wide) in paragraph at lines 569--569 [] \T1/zi4/m/n/10 onco_db_file = system.file("extdata", "201806_uniprot-Proto -oncogene.tsv.xz", package[] [11] [12] [13] Overfull \hbox (83.3352pt too wide) in paragraph at lines 764--768 []\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[][][] Overfull \hbox (18.34094pt too wide) in paragraph at lines 791--799 [][]\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 , [][]\T1/zi4/m/n/10 threshold_f ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]() [14] Overfull \hbox (1.63855pt too wide) in paragraph at lines 844--847 []\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 844--847 \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 ) [15] Overfull \hbox (18.34094pt too wide) in paragraph at lines 877--885 [][]\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 , [][]\T1/zi4/m/n/10 threshold_f ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]() Overfull \hbox (0.26779pt too wide) in paragraph at lines 932--935 \T1/ptm/m/n/10 value columns cor-re-spond-ing to dif-fer-ent quan-tifi-ca-tion types (ob-tained via [][]com- [16] [17] [18] Overfull \hbox (70.20969pt too wide) in paragraph at lines 1097--1105 []\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 sample_statistics[][][]()\T1/ptm/m/n/10 , [19] Underfull \hbox (badness 10000) in paragraph at lines 1170--1170 []\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 1170--1170 \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 1170--1170 \T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and [20] [21] [22] Overfull \hbox (29.30962pt too wide) in paragraph at lines 1332--1336 []\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[][][]() [23] Overfull \hbox (19.25786pt too wide) in paragraph at lines 1383--1388 []\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 1398--1402 []\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[][][]() [24] [25] [26] Overfull \hbox (3.4271pt too wide) in paragraph at lines 1551--1553 []\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match -ing is case-insensitive. [27] [28] Underfull \hbox (badness 10000) in paragraph at lines 1690--1699 [29] Overfull \hbox (24.6883pt too wide) in paragraph at lines 1777--1779 []\T1/ptm/m/n/10 A vec-tor of re-quested quan-tifi-ca-tion_types. Must be one i n \T1/zi4/m/n/10 quantification_types() Overfull \hbox (25.32918pt too wide) in paragraph at lines 1799--1801 []\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 (61.1266pt too wide) in paragraph at lines 1805--1812 \T1/ptm/m/n/10 For more de-tails on how to prop-erly use these func-tions, re-f er to the vi-gnette - vi-gnette("how_to_import_functions") [30] Overfull \hbox (4.8009pt too wide) in paragraph at lines 1847--1849 [][][]\T1/zi4/m/n/10 matching_options[][][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / stringr . tidyverse . org / articles / regular-[]expressions . htm l$[][] Overfull \hbox (162.90988pt too wide) in paragraph at lines 1850--1855 []\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_interactive[][ ][]()\T1/ptm/m/n/10 , [31] Overfull \hbox (24.6883pt too wide) in paragraph at lines 1907--1909 []\T1/ptm/m/n/10 A vec-tor of re-quested quan-tifi-ca-tion_types. Must be one i n \T1/zi4/m/n/10 quantification_types() Overfull \hbox (25.32918pt too wide) in paragraph at lines 1923--1925 []\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 (61.1266pt too wide) in paragraph at lines 1929--1936 \T1/ptm/m/n/10 For more de-tails on how to prop-erly use these func-tions, re-f er to the vi-gnette - vi-gnette("how_to_import_functions") [32] Overfull \hbox (127.90988pt too wide) in paragraph at lines 1956--1961 []\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_auto[][][]()\T 1/ptm/m/n/10 , (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [33] Overfull \hbox (127.90988pt too wide) in paragraph at lines 2022--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_parallel_Vispa2Matrices_auto[][][]()\T 1/ptm/m/n/10 , Overfull \hbox (3.81735pt too wide) in paragraph at lines 2065--2068 \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 (18.38986pt too wide) in paragraph at lines 2087--2092 []\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice s_auto[][][]()\T1/ptm/m/n/10 , [34] [35] [36] Overfull \hbox (51.20859pt too wide) in paragraph at lines 2298--2300 []\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 . [37] [38] [39] Overfull \hbox (118.70859pt too wide) in paragraph at lines 2524--2528 []\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 [40] Overfull \hbox (15.75836pt too wide) in paragraph at lines 2589--2591 []\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 [41] [42] [43] Overfull \hbox (51.33856pt too wide) in paragraph at lines 2724--2730 \T1/ptm/m/n/10 tails on how to use col-li-sion re-moval func-tion-al-ity: \T1/z i4/m/n/10 vignette("Collision removal functionality",package [44] [45] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2840--2848 []\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 , [46] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2932--2940 []\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 , [47] Overfull \hbox (3.36687pt too wide) in paragraph at lines 3000--3006 \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 3000--3006 \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 [48] [49] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3171--3179 []\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 , [50] Overfull \hbox (12.649pt too wide) in paragraph at lines 3224--3226 []\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 [51] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3271--3279 []\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 (99.30962pt too wide) in paragraph at lines 3334--3338 []\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[][][]() [52] No file Rd2.ind. [53] (/private/tmp/Rtmp60PWuZ/Rbuild130e4fc257a7/ISAnalytics/.Rd2pdf78052/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 {/usr/local/texlive/2019/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us r/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/20 19/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t exlive/2019/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/ 2019/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf -dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/font s/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/ur w/times/utmri8a.pfb> Output written on Rd2.pdf (53 pages, 190815 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (249 entries accepted, 2 rejected). Sorting entries.....done (2139 comparisons). Generating output file Rd2.ind....done (274 lines written, 5 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. 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Found on input line 46. ) (/private/tmp/Rtmp60PWuZ/Rbuild130e4fc257a7/ISAnalytics/.Rd2pdf78052/Rd2.toc [2]) [3] [4] (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [5] [6] [7] Overfull \hbox (7.2896pt too wide) in paragraph at lines 386--390 []\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] Overfull \hbox (92.28088pt too wide) in paragraph at lines 459--466 \T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120 6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][] [9] Overfull \hbox (30.68967pt too wide) in paragraph at lines 521--529 []\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 , Overfull \hbox (18.34094pt too wide) in paragraph at lines 521--529 [][]\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 , [][]\T1/zi4/m/n/10 threshold_f ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]() [10] Overfull \hbox (29.76044pt too wide) in paragraph at lines 569--569 [] \T1/zi4/m/n/10 onco_db_file = system.file("extdata", "201806_uniprot-Proto -oncogene.tsv.xz", package[] [11] [12] [13] Overfull \hbox (83.3352pt too wide) in paragraph at lines 764--768 []\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[][][] Overfull \hbox (18.34094pt too wide) in paragraph at lines 791--799 [][]\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 , [][]\T1/zi4/m/n/10 threshold_f ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]() [14] Overfull \hbox (1.63855pt too wide) in paragraph at lines 844--847 []\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 844--847 \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 ) [15] Overfull \hbox (18.34094pt too wide) in paragraph at lines 877--885 [][]\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 , [][]\T1/zi4/m/n/10 threshold_f ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]() Overfull \hbox (0.26779pt too wide) in paragraph at lines 932--935 \T1/ptm/m/n/10 value columns cor-re-spond-ing to dif-fer-ent quan-tifi-ca-tion types (ob-tained via [][]com- [16] [17] [18] Overfull \hbox (70.20969pt too wide) in paragraph at lines 1097--1105 []\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 sample_statistics[][][]()\T1/ptm/m/n/10 , [19] Underfull \hbox (badness 10000) in paragraph at lines 1170--1170 []\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 1170--1170 \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 1170--1170 \T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and [20] [21] [22] Overfull \hbox (29.30962pt too wide) in paragraph at lines 1332--1336 []\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[][][]() [23] Overfull \hbox (19.25786pt too wide) in paragraph at lines 1383--1388 []\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 1398--1402 []\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[][][]() [24] [25] [26] Overfull \hbox (3.4271pt too wide) in paragraph at lines 1551--1553 []\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match -ing is case-insensitive. [27] [28] Underfull \hbox (badness 10000) in paragraph at lines 1690--1699 [29] Overfull \hbox (24.6883pt too wide) in paragraph at lines 1777--1779 []\T1/ptm/m/n/10 A vec-tor of re-quested quan-tifi-ca-tion_types. Must be one i n \T1/zi4/m/n/10 quantification_types() Overfull \hbox (25.32918pt too wide) in paragraph at lines 1799--1801 []\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 (61.1266pt too wide) in paragraph at lines 1805--1812 \T1/ptm/m/n/10 For more de-tails on how to prop-erly use these func-tions, re-f er to the vi-gnette - vi-gnette("how_to_import_functions") [30] Overfull \hbox (4.8009pt too wide) in paragraph at lines 1847--1849 [][][]\T1/zi4/m/n/10 matching_options[][][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / stringr . tidyverse . org / articles / regular-[]expressions . htm l$[][] Overfull \hbox (162.90988pt too wide) in paragraph at lines 1850--1855 []\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_interactive[][ ][]()\T1/ptm/m/n/10 , [31] Overfull \hbox (24.6883pt too wide) in paragraph at lines 1907--1909 []\T1/ptm/m/n/10 A vec-tor of re-quested quan-tifi-ca-tion_types. Must be one i n \T1/zi4/m/n/10 quantification_types() Overfull \hbox (25.32918pt too wide) in paragraph at lines 1923--1925 []\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 (61.1266pt too wide) in paragraph at lines 1929--1936 \T1/ptm/m/n/10 For more de-tails on how to prop-erly use these func-tions, re-f er to the vi-gnette - vi-gnette("how_to_import_functions") [32] Overfull \hbox (127.90988pt too wide) in paragraph at lines 1956--1961 []\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_auto[][][]()\T 1/ptm/m/n/10 , (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [33] Overfull \hbox (127.90988pt too wide) in paragraph at lines 2022--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_parallel_Vispa2Matrices_auto[][][]()\T 1/ptm/m/n/10 , Overfull \hbox (3.81735pt too wide) in paragraph at lines 2065--2068 \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 (18.38986pt too wide) in paragraph at lines 2087--2092 []\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice s_auto[][][]()\T1/ptm/m/n/10 , [34] [35] [36] Overfull \hbox (51.20859pt too wide) in paragraph at lines 2298--2300 []\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 . [37] [38] [39] Overfull \hbox (118.70859pt too wide) in paragraph at lines 2524--2528 []\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 [40] Overfull \hbox (15.75836pt too wide) in paragraph at lines 2589--2591 []\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 [41] [42] [43] Overfull \hbox (51.33856pt too wide) in paragraph at lines 2724--2730 \T1/ptm/m/n/10 tails on how to use col-li-sion re-moval func-tion-al-ity: \T1/z i4/m/n/10 vignette("Collision removal functionality",package [44] [45] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2840--2848 []\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 , [46] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2932--2940 []\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 , [47] Overfull \hbox (3.36687pt too wide) in paragraph at lines 3000--3006 \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 3000--3006 \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 [48] [49] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3171--3179 []\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 , [50] Overfull \hbox (12.649pt too wide) in paragraph at lines 3224--3226 []\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 [51] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3271--3279 []\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 (99.30962pt too wide) in paragraph at lines 3334--3338 []\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[][][]() [52] (/private/tmp/Rtmp60PWuZ/Rbuild130e4fc257a7/ISAnalytics/.Rd2pdf78052/Rd2.ind [53] Overfull \hbox (8.3567pt too wide) in paragraph at lines 28--30 []| \T1/zi4/m/n/10 import_parallel_Vispa2Matrices_auto\T1/ptm/m/n/10 , Overfull \hbox (43.3567pt too wide) in paragraph at lines 30--32 []| \T1/zi4/m/n/10 import_parallel_Vispa2Matrices_interactive\T1/ptm/m/n/10 , Overfull \hbox (3.3567pt too wide) in paragraph at lines 40--42 []| \T1/zi4/m/n/10 clinical_relevant_suspicious_genes\T1/ptm/m/n/10 , [54] Overfull \hbox (23.3567pt too wide) in paragraph at lines 177--183 []\T1/zi4/m/n/10 import_parallel_Vispa2Matrices_interactive\T1/ptm/m/n/10 , [55]) (/private/tmp/Rtmp60PWuZ/Rbuild130e4fc257a7/ISAnalytics/.Rd2pdf78052/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 {/usr/local/texlive/2019/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us r/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/20 19/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t exlive/2019/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/te xlive/2019/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2 019/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf- dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts /type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw /times/utmri8a.pfb> Output written on Rd2.pdf (55 pages, 210045 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (249 entries accepted, 2 rejected). Sorting entries.....done (2139 comparisons). Generating output file Rd2.ind....done (274 lines written, 5 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. 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Found on input line 46. ) (/private/tmp/Rtmp60PWuZ/Rbuild130e4fc257a7/ISAnalytics/.Rd2pdf78052/Rd2.toc [2]) [3] [4] (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [5] [6] [7] Overfull \hbox (7.2896pt too wide) in paragraph at lines 386--390 []\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] Overfull \hbox (92.28088pt too wide) in paragraph at lines 459--466 \T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120 6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][] [9] Overfull \hbox (30.68967pt too wide) in paragraph at lines 521--529 []\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 , Overfull \hbox (18.34094pt too wide) in paragraph at lines 521--529 [][]\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 , [][]\T1/zi4/m/n/10 threshold_f ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]() [10] Overfull \hbox (29.76044pt too wide) in paragraph at lines 569--569 [] \T1/zi4/m/n/10 onco_db_file = system.file("extdata", "201806_uniprot-Proto -oncogene.tsv.xz", package[] [11] [12] [13] Overfull \hbox (83.3352pt too wide) in paragraph at lines 764--768 []\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[][][] Overfull \hbox (18.34094pt too wide) in paragraph at lines 791--799 [][]\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 , [][]\T1/zi4/m/n/10 threshold_f ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]() [14] Overfull \hbox (1.63855pt too wide) in paragraph at lines 844--847 []\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 844--847 \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 ) [15] Overfull \hbox (18.34094pt too wide) in paragraph at lines 877--885 [][]\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 , [][]\T1/zi4/m/n/10 threshold_f ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]() Overfull \hbox (0.26779pt too wide) in paragraph at lines 932--935 \T1/ptm/m/n/10 value columns cor-re-spond-ing to dif-fer-ent quan-tifi-ca-tion types (ob-tained via [][]com- [16] [17] [18] Overfull \hbox (70.20969pt too wide) in paragraph at lines 1097--1105 []\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 sample_statistics[][][]()\T1/ptm/m/n/10 , [19] Underfull \hbox (badness 10000) in paragraph at lines 1170--1170 []\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 1170--1170 \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 1170--1170 \T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and [20] [21] [22] Overfull \hbox (29.30962pt too wide) in paragraph at lines 1332--1336 []\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[][][]() [23] Overfull \hbox (19.25786pt too wide) in paragraph at lines 1383--1388 []\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 1398--1402 []\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[][][]() [24] [25] [26] Overfull \hbox (3.4271pt too wide) in paragraph at lines 1551--1553 []\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match -ing is case-insensitive. [27] [28] Underfull \hbox (badness 10000) in paragraph at lines 1690--1699 [29] Overfull \hbox (24.6883pt too wide) in paragraph at lines 1777--1779 []\T1/ptm/m/n/10 A vec-tor of re-quested quan-tifi-ca-tion_types. Must be one i n \T1/zi4/m/n/10 quantification_types() Overfull \hbox (25.32918pt too wide) in paragraph at lines 1799--1801 []\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 (61.1266pt too wide) in paragraph at lines 1805--1812 \T1/ptm/m/n/10 For more de-tails on how to prop-erly use these func-tions, re-f er to the vi-gnette - vi-gnette("how_to_import_functions") [30] Overfull \hbox (4.8009pt too wide) in paragraph at lines 1847--1849 [][][]\T1/zi4/m/n/10 matching_options[][][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / stringr . tidyverse . org / articles / regular-[]expressions . htm l$[][] Overfull \hbox (162.90988pt too wide) in paragraph at lines 1850--1855 []\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_interactive[][ ][]()\T1/ptm/m/n/10 , [31] Overfull \hbox (24.6883pt too wide) in paragraph at lines 1907--1909 []\T1/ptm/m/n/10 A vec-tor of re-quested quan-tifi-ca-tion_types. Must be one i n \T1/zi4/m/n/10 quantification_types() Overfull \hbox (25.32918pt too wide) in paragraph at lines 1923--1925 []\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 (61.1266pt too wide) in paragraph at lines 1929--1936 \T1/ptm/m/n/10 For more de-tails on how to prop-erly use these func-tions, re-f er to the vi-gnette - vi-gnette("how_to_import_functions") [32] Overfull \hbox (127.90988pt too wide) in paragraph at lines 1956--1961 []\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_auto[][][]()\T 1/ptm/m/n/10 , (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [33] Overfull \hbox (127.90988pt too wide) in paragraph at lines 2022--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_parallel_Vispa2Matrices_auto[][][]()\T 1/ptm/m/n/10 , Overfull \hbox (3.81735pt too wide) in paragraph at lines 2065--2068 \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 (18.38986pt too wide) in paragraph at lines 2087--2092 []\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice s_auto[][][]()\T1/ptm/m/n/10 , [34] [35] [36] Overfull \hbox (51.20859pt too wide) in paragraph at lines 2298--2300 []\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 . [37] [38] [39] Overfull \hbox (118.70859pt too wide) in paragraph at lines 2524--2528 []\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 [40] Overfull \hbox (15.75836pt too wide) in paragraph at lines 2589--2591 []\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 [41] [42] [43] Overfull \hbox (51.33856pt too wide) in paragraph at lines 2724--2730 \T1/ptm/m/n/10 tails on how to use col-li-sion re-moval func-tion-al-ity: \T1/z i4/m/n/10 vignette("Collision removal functionality",package [44] [45] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2840--2848 []\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 , [46] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2932--2940 []\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 , [47] Overfull \hbox (3.36687pt too wide) in paragraph at lines 3000--3006 \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 3000--3006 \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 [48] [49] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3171--3179 []\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 , [50] Overfull \hbox (12.649pt too wide) in paragraph at lines 3224--3226 []\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 [51] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3271--3279 []\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 (99.30962pt too wide) in paragraph at lines 3334--3338 []\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[][][]() [52] (/private/tmp/Rtmp60PWuZ/Rbuild130e4fc257a7/ISAnalytics/.Rd2pdf78052/Rd2.ind [53] Overfull \hbox (8.3567pt too wide) in paragraph at lines 28--30 []| \T1/zi4/m/n/10 import_parallel_Vispa2Matrices_auto\T1/ptm/m/n/10 , Overfull \hbox (43.3567pt too wide) in paragraph at lines 30--32 []| \T1/zi4/m/n/10 import_parallel_Vispa2Matrices_interactive\T1/ptm/m/n/10 , Overfull \hbox (3.3567pt too wide) in paragraph at lines 40--42 []| \T1/zi4/m/n/10 clinical_relevant_suspicious_genes\T1/ptm/m/n/10 , [54] Overfull \hbox (23.3567pt too wide) in paragraph at lines 177--183 []\T1/zi4/m/n/10 import_parallel_Vispa2Matrices_interactive\T1/ptm/m/n/10 , [55]) (/private/tmp/Rtmp60PWuZ/Rbuild130e4fc257a7/ISAnalytics/.Rd2pdf78052/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 {/usr/local/texlive/2019/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us r/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/20 19/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t exlive/2019/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/te xlive/2019/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2 019/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf- dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts /type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw /times/utmri8a.pfb> Output written on Rd2.pdf (55 pages, 210648 bytes). Transcript written on Rd2.log. Saving output to ‘/private/tmp/Rtmp60PWuZ/Rbuild130e4fc257a7/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 Omitted ‘LazyData’ from DESCRIPTION * building ‘ISAnalytics_1.2.1.tar.gz’