############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data tidybulk ### ############################################################################## ############################################################################## * checking for file ‘tidybulk/DESCRIPTION’ ... OK * preparing ‘tidybulk’: * checking DESCRIPTION meta-information ... OK * installing the package to process help pages * building the PDF package manual Hmm ... looks like a package Converting Rd files to LaTeX ............ Creating pdf output from LaTeX ... This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode LaTeX2e <2020-02-02> patch level 2 L3 programming layer <2020-02-14> (./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2019/12/20 v1.4l Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (/home/biocbuild/bbs-3.13-bioc/R/share/texmf/tex/latex/Rd.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/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/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) Writing index file Rd2.idx (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def) No file Rd2.aux. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [2] Overfull \hbox (0.64713pt too wide) in paragraph at lines 101--102 []\T1/ptm/m/n/10 adjust_abundance() takes as in-put a `tbl` for-mat-ted as | | | (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [3] [4] Overfull \hbox (13.41685pt too wide) in paragraph at lines 250--251 []\T1/ptm/m/n/10 aggregate_duplicates() takes as in-put a `tbl` for-mat-ted as | | | [5] [6] Overfull \hbox (49.56651pt too wide) in paragraph at lines 342--347 []\T1/ptm/m/n/10 Underlying cus-tom method: data fil-ter(n_aggr > 1) group_by(! !.sample,!!.transcript) dplyr::mutate(!!.abundance [7] Overfull \hbox (4.18723pt too wide) in paragraph at lines 394--396 []\T1/ptm/m/n/10 <[`tidy-eval`][dplyr_tidy_eval]> Vari-ables, or func-tions or vari-ables. Use [desc()] [8] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) Overfull \hbox (41.25328pt too wide) in paragraph at lines 479--479 []\T1/zi4/m/n/9 tidybulk::se_mini %>% tidybulk() %>% select(feature, count) %> % head %>% as_matrix(rownames=feature)[] [9] [10] [11] [12] Underfull \vbox (badness 10000) has occurred while \output is active [13] [14] [15] [16] Underfull \vbox (badness 10000) has occurred while \output is active [17] [18] Overfull \hbox (159.74715pt too wide) in paragraph at lines 967--967 []\T1/zi4/m/n/9 tidybulk::se_mini %>% tidybulk() %>% filter(sample=="SRR174003 4") %>% deconvolve_cellularity(sample, feature, count, cores = 1)[] [19] [20] Overfull \hbox (10.85692pt too wide) in paragraph at lines 1104--1105 []\T1/ptm/m/n/10 ensembl_to_symbol() takes as in-put a `tbl` for-mat-ted as | < SAM-PLE> | | [21] [22] [23] [24] [25] [26] Overfull \hbox (7.27914pt too wide) in paragraph at lines 1451--1453 []\T1/ptm/m/n/10 When `.drop = TRUE`, empty groups are dropped. See [group_by_d rop_default()] [27] Overfull \hbox (1.76709pt too wide) in paragraph at lines 1487--1488 []\T1/ptm/m/n/10 identify_abundant() takes as in-put a `tbl` for-mat-ted as | < SAM-PLE> | | [28] Overfull \hbox (53.61636pt too wide) in paragraph at lines 1582--1589 []\T1/ptm/m/n/10 Underlying method: edgeR::filterByExpr( data, min.count = min- i-mum_counts, group = string_factor_of_interest, [29] [30] [31] [32] Overfull \hbox (81.74408pt too wide) in paragraph at lines 1761--1761 []\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble( ) %>% distinct(sample) %>% mutate(source = "AU")[] Overfull \hbox (81.74408pt too wide) in paragraph at lines 1765--1765 []\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble( ) %>% distinct(sample) %>% mutate(source = "AU")[] Overfull \hbox (81.74408pt too wide) in paragraph at lines 1769--1769 []\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble( ) %>% distinct(sample) %>% mutate(source = "AU")[] [33] Underfull \vbox (badness 10000) has occurred while \output is active [34] Overfull \hbox (53.61636pt too wide) in paragraph at lines 1878--1885 []\T1/ptm/m/n/10 Underlying method: edgeR::filterByExpr( data, min.count = min- i-mum_counts, group = string_factor_of_interest, [35] [36] [37] Overfull \hbox (81.74408pt too wide) in paragraph at lines 2059--2059 []\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble( ) %>% distinct(sample) %>% mutate(source = "AU")[] [38] [39] [40] [41] [42] [43] Overfull \hbox (6.40688pt too wide) in paragraph at lines 2412--2413 []\T1/ptm/m/n/10 reduce_dimensions() takes as in-put a `tbl` for-mat-ted as | < SAM-PLE> | | [44] Underfull \vbox (badness 10000) has occurred while \output is active [45] [46] Overfull \hbox (10.3875pt too wide) in paragraph at lines 2602--2603 []\T1/ptm/m/n/10 remove_redundancy() takes as in-put a `tbl` for-mat-ted as | < SAM-PLE> | | Overfull \hbox (18.57648pt too wide) in paragraph at lines 2602--2603 \T1/ptm/m/n/10 | <...> | for cor-re-la-tion method or | | | <...> | for re-duced_dimensions [47] [48] Underfull \vbox (badness 10000) has occurred while \output is active [49] [50] [51] [52] Underfull \vbox (badness 10000) has occurred while \output is active [53] [54] Overfull \hbox (79.64253pt too wide) in paragraph at lines 2977--2977 []\T1/zi4/m/n/9 counts.MDS.rotated = rotate_dimensions(counts.MDS, \TS1/cmtt/ m/n/9 `\T1/zi4/m/n/9 Dim1\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , \TS1/cmtt/m/n/9 `\T1/ zi4/m/n/9 Dim2\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , rotation_degrees = 45, .element = sample)[] [55] [56] Overfull \hbox (41.07668pt too wide) in paragraph at lines 3122--3124 []\T1/ptm/m/n/10 Underlying method edgeR::calcNormFactors(.data, method = c("TM M","TMMwsp","RLE","upperquartile")) [57] [58] [59] Overfull \hbox (83.24715pt too wide) in paragraph at lines 3312--3312 []\T1/zi4/m/n/9 tidybulk::se_mini %>% tidybulk() %>% as_tibble() %>% symbol_to _entrez(.transcript = feature, .sample = sample)[] [60] [61] Underfull \vbox (badness 10000) has occurred while \output is active [62] Underfull \vbox (badness 10000) has occurred while \output is active [63] Overfull \hbox (40.04678pt too wide) in paragraph at lines 3476--3477 []\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther "edgeR_quasi_likelihood" (i.e., QLF), "edgeR_likelihood_ratio" Overfull \hbox (104.18698pt too wide) in paragraph at lines 3476--3477 \T1/ptm/m/n/10 (i.e., LRT), "edger_robust_likelihood_ratio", "DE-Seq2", "limma_ voom", "limma_voom_sample_weights" Overfull \hbox (58.60709pt too wide) in paragraph at lines 3480--3481 \T1/ptm/m/n/10 and limma-voom (i.e., edgeR::calcNormFactors; "TMM","TMMwsp","RL E","upperquartile"). Overfull \hbox (21.76895pt too wide) in paragraph at lines 3499--3501 \T1/zi4/m/n/10 btp616$[][]\T1/ptm/m/n/10 , limma-voom [][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1186 / gb-[]2014-[]15-[]2-[]r29$[][]\T1/ptm/m/n/10 , li mma_voom_sample_weights Overfull \hbox (28.64075pt too wide) in paragraph at lines 3499--3501 [][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1093 / nar / gkv412$[][] \T1/p tm/m/n/10 or DE-Seq2 [][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1186 / s1 3059-[]014-[]0550-[]8$[][] [64] Overfull \hbox (26.17642pt too wide) in paragraph at lines 3505--3511 []\T1/ptm/m/n/10 # Fil-ter keep_abundant( fac-tor_of_interest = !!(as.symbol(pa rse_formula(.formula)[1])), min-i-mum_counts Overfull \hbox (24.77638pt too wide) in paragraph at lines 3512--3516 []\T1/ptm/m/n/10 # For-mat se-lect(!!.transcript,!!.sample,!!.abundance) spread (!!.sample,!!.abundance) as_matrix(rownames Overfull \hbox (81.21483pt too wide) in paragraph at lines 3517--3521 []\T1/ptm/m/n/10 # edgeR edgeR::DGEList(counts = .) edgeR::calcNormFactors(meth od = scal-ing_method) edgeR::estimateDisp(design) Overfull \hbox (3.26636pt too wide) in paragraph at lines 3522--3525 []\T1/ptm/m/n/10 # Fit edgeR::glmQLFit(design) edgeR::glmQLFTest(coef = 2, con- trast = my_contrasts) // or glmLRT Overfull \hbox (100.91638pt too wide) in paragraph at lines 3526--3532 []\T1/ptm/m/n/10 Underlying method for DE-Seq2 frame-work: keep_abundant( fac-t or_of_interest = !!as.symbol(parse_formula(.formula)[[1]]), [65] [66] Underfull \vbox (badness 10000) has occurred while \output is active [67] Overfull \hbox (22.20665pt too wide) in paragraph at lines 3689--3690 \T1/ptm/m/n/10 forms: mul-ti-vari-able (rec-om-mended) or uni-vari-able Re-spec -tively: \"fac-tor_of_interest Overfull \hbox (1.61646pt too wide) in paragraph at lines 3697--3698 []\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther \"ciber-sort\", \"epic\" or \"ll sr\". The re-gres-sion method Overfull \hbox (54.31668pt too wide) in paragraph at lines 3714--3725 \T1/ptm/m/n/10 script, !!.abun-dance, method=method, ref-er-ence = ref-er-ence, ac-tion="get", ... ) [..] betareg::betareg(.my_formula, Overfull \hbox (33.15706pt too wide) in paragraph at lines 3726--3738 \T1/ptm/m/n/10 !!.abun-dance, method=method, ref-er-ence = ref-er-ence, ac-tion ="get", ... ) [..] mu-tate(.proportion_0_corrected [68] [69] [70] Underfull \vbox (badness 10000) has occurred while \output is active [71] Overfull \hbox (104.10625pt too wide) in paragraph at lines 3929--3930 []\T1/ptm/m/n/10 This wrap-per ex-e-cutes en-sem-ble gene en-rich-ment anal-y-s es of the dataset us-ing EGSEA (DOI:0.12688/f1000research.12544.1) Overfull \hbox (16.85628pt too wide) in paragraph at lines 3939--3943 []\T1/ptm/m/n/10 # Make sure tran-script names are ad-ja-cent [...] as_matrix(r ownames = !!.en-trez) edgeR::DGEList(counts Overfull \hbox (20.2169pt too wide) in paragraph at lines 3944--3946 []\T1/ptm/m/n/10 idx = buil-dIdx(entrezIDs = row-names(dge), species = species, msigdb.gsets = msigdb.gsets, kegg.exclude [72] Overfull \hbox (137.23795pt too wide) in paragraph at lines 3981--3981 []\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini %>% tidybulk() %>% as_tibble() % >% symbol_to_entrez( .transcript = feature, .sample = sample)[] Overfull \hbox (173.23795pt too wide) in paragraph at lines 3982--3982 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] Overfull \hbox (126.71648pt too wide) in paragraph at lines 3993--3993 [] \T1/zi4/m/n/9 gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6" , "c7", "kegg_disease", "kegg_metabolism", "kegg_signaling"),[] [73] [74] [75] Overfull \hbox (137.23795pt too wide) in paragraph at lines 4139--4139 []\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini %>% tidybulk() %>% as_tibble() % >% symbol_to_entrez( .transcript = feature, .sample = sample)[] Overfull \hbox (173.23795pt too wide) in paragraph at lines 4140--4140 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] Overfull \hbox (3.75021pt too wide) in paragraph at lines 4141--4141 []\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = feature %in% c("TNFRSF 4", "PLCH2", "PADI4", "PAX7"))[] [76] Underfull \vbox (badness 10000) has occurred while \output is active [77] Overfull \hbox (31.37613pt too wide) in paragraph at lines 4270--4280 []\T1/ptm/m/n/10 # Ex-e-cute cal-cu-la-tion nest(data = -gs_cat) mu-tate(fit = map( data, ~ clus-ter-Pro-filer::GSEA( my_entrez_rank, Overfull \hbox (137.23795pt too wide) in paragraph at lines 4301--4301 []\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini %>% tidybulk() %>% as_tibble() % >% symbol_to_entrez( .transcript = feature, .sample = sample)[] Overfull \hbox (173.23795pt too wide) in paragraph at lines 4302--4302 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] Overfull \hbox (3.75021pt too wide) in paragraph at lines 4303--4303 []\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = feature %in% c("TNFRSF 4", "PLCH2", "PADI4", "PAX7"))[] [78] [79] Overfull \hbox (22.20665pt too wide) in paragraph at lines 4409--4410 \T1/ptm/m/n/10 forms: mul-ti-vari-able (rec-om-mended) or uni-vari-able Re-spec -tively: \"fac-tor_of_interest [80] Overfull \hbox (1.61646pt too wide) in paragraph at lines 4417--4418 []\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther \"ciber-sort\", \"epic\" or \"ll sr\". The re-gres-sion method [81] Overfull \hbox (5.09679pt too wide) in paragraph at lines 4494--4495 []\T1/ptm/m/n/10 tidybulk() cre-ates a `tt` ob-ject from a `tbl` for-mat-ted as | | | [82] [83] [84] [85] No file Rd2.ind. [86] (/tmp/RtmpeYe5YI/Rbuild386827695bc1d9/tidybulk/.Rd2pdf3696679/Rd2.aux) Package rerunfilecheck Warning: File `Rd2.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) {/usr/share/texlive/te xmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/ fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inco nsolata/i4-t1-0.enc} Output written on Rd2.pdf (86 pages, 202663 bytes). Transcript written on Rd2.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode LaTeX2e <2020-02-02> patch level 2 L3 programming layer <2020-02-14> (./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2019/12/20 v1.4l Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (/home/biocbuild/bbs-3.13-bioc/R/share/texmf/tex/latex/Rd.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/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/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) Writing index file Rd2.idx (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def) (/tmp/RtmpeYe5YI/Rbuild386827695bc1d9/tidybulk/.Rd2pdf3696679/Rd2.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/tmp/RtmpeYe5YI/Rbuild386827695bc1d9/tidybulk/.Rd2pdf3696679/Rd2.out) (/tmp/RtmpeYe5YI/Rbuild386827695bc1d9/tidybulk/.Rd2pdf3696679/Rd2.out) [1{/var/ lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (/tmp/RtmpeYe5YI/Rbuild386827695bc1d9/tidybulk/.Rd2pdf3696679/Rd2.toc [2] [3]) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) Overfull \hbox (0.64713pt too wide) in paragraph at lines 101--102 []\T1/ptm/m/n/10 adjust_abundance() takes as in-put a `tbl` for-mat-ted as | | | (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [4] [5] [6] Overfull \hbox (13.41685pt too wide) in paragraph at lines 250--251 []\T1/ptm/m/n/10 aggregate_duplicates() takes as in-put a `tbl` for-mat-ted as | | | [7] Overfull \hbox (49.56651pt too wide) in paragraph at lines 342--347 []\T1/ptm/m/n/10 Underlying cus-tom method: data fil-ter(n_aggr > 1) group_by(! !.sample,!!.transcript) dplyr::mutate(!!.abundance [8] Overfull \hbox (4.18723pt too wide) in paragraph at lines 394--396 []\T1/ptm/m/n/10 <[`tidy-eval`][dplyr_tidy_eval]> Vari-ables, or func-tions or vari-ables. Use [desc()] [9] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) Overfull \hbox (41.25328pt too wide) in paragraph at lines 479--479 []\T1/zi4/m/n/9 tidybulk::se_mini %>% tidybulk() %>% select(feature, count) %> % head %>% as_matrix(rownames=feature)[] [10] [11] [12] [13] [14] [15] [16] [17] Underfull \vbox (badness 10000) has occurred while \output is active [18] [19] Overfull \hbox (159.74715pt too wide) in paragraph at lines 967--967 []\T1/zi4/m/n/9 tidybulk::se_mini %>% tidybulk() %>% filter(sample=="SRR174003 4") %>% deconvolve_cellularity(sample, feature, count, cores = 1)[] [20] [21] Overfull \hbox (10.85692pt too wide) in paragraph at lines 1104--1105 []\T1/ptm/m/n/10 ensembl_to_symbol() takes as in-put a `tbl` for-mat-ted as | < SAM-PLE> | | [22] [23] [24] [25] [26] [27] Overfull \hbox (7.27914pt too wide) in paragraph at lines 1451--1453 []\T1/ptm/m/n/10 When `.drop = TRUE`, empty groups are dropped. See [group_by_d rop_default()] [28] Overfull \hbox (1.76709pt too wide) in paragraph at lines 1487--1488 []\T1/ptm/m/n/10 identify_abundant() takes as in-put a `tbl` for-mat-ted as | < SAM-PLE> | | [29] Overfull \hbox (53.61636pt too wide) in paragraph at lines 1582--1589 []\T1/ptm/m/n/10 Underlying method: edgeR::filterByExpr( data, min.count = min- i-mum_counts, group = string_factor_of_interest, [30] [31] [32] [33] Overfull \hbox (81.74408pt too wide) in paragraph at lines 1761--1761 []\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble( ) %>% distinct(sample) %>% mutate(source = "AU")[] Overfull \hbox (81.74408pt too wide) in paragraph at lines 1765--1765 []\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble( ) %>% distinct(sample) %>% mutate(source = "AU")[] Overfull \hbox (81.74408pt too wide) in paragraph at lines 1769--1769 []\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble( ) %>% distinct(sample) %>% mutate(source = "AU")[] [34] Underfull \vbox (badness 10000) has occurred while \output is active [35] Overfull \hbox (53.61636pt too wide) in paragraph at lines 1878--1885 []\T1/ptm/m/n/10 Underlying method: edgeR::filterByExpr( data, min.count = min- i-mum_counts, group = string_factor_of_interest, [36] [37] [38] Overfull \hbox (81.74408pt too wide) in paragraph at lines 2059--2059 []\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble( ) %>% distinct(sample) %>% mutate(source = "AU")[] [39] [40] [41] [42] [43] [44] Overfull \hbox (6.40688pt too wide) in paragraph at lines 2412--2413 []\T1/ptm/m/n/10 reduce_dimensions() takes as in-put a `tbl` for-mat-ted as | < SAM-PLE> | | [45] Underfull \vbox (badness 10000) has occurred while \output is active [46] [47] Overfull \hbox (10.3875pt too wide) in paragraph at lines 2602--2603 []\T1/ptm/m/n/10 remove_redundancy() takes as in-put a `tbl` for-mat-ted as | < SAM-PLE> | | Overfull \hbox (18.57648pt too wide) in paragraph at lines 2602--2603 \T1/ptm/m/n/10 | <...> | for cor-re-la-tion method or | | | <...> | for re-duced_dimensions [48] [49] Underfull \vbox (badness 10000) has occurred while \output is active [50] [51] [52] [53] Underfull \vbox (badness 10000) has occurred while \output is active [54] [55] Overfull \hbox (79.64253pt too wide) in paragraph at lines 2977--2977 []\T1/zi4/m/n/9 counts.MDS.rotated = rotate_dimensions(counts.MDS, \TS1/cmtt/ m/n/9 `\T1/zi4/m/n/9 Dim1\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , \TS1/cmtt/m/n/9 `\T1/ zi4/m/n/9 Dim2\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , rotation_degrees = 45, .element = sample)[] [56] [57] Overfull \hbox (41.07668pt too wide) in paragraph at lines 3122--3124 []\T1/ptm/m/n/10 Underlying method edgeR::calcNormFactors(.data, method = c("TM M","TMMwsp","RLE","upperquartile")) [58] [59] [60] Overfull \hbox (83.24715pt too wide) in paragraph at lines 3312--3312 []\T1/zi4/m/n/9 tidybulk::se_mini %>% tidybulk() %>% as_tibble() %>% symbol_to _entrez(.transcript = feature, .sample = sample)[] [61] [62] Underfull \vbox (badness 10000) has occurred while \output is active [63] Underfull \vbox (badness 10000) has occurred while \output is active [64] Overfull \hbox (40.04678pt too wide) in paragraph at lines 3476--3477 []\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther "edgeR_quasi_likelihood" (i.e., QLF), "edgeR_likelihood_ratio" Overfull \hbox (104.18698pt too wide) in paragraph at lines 3476--3477 \T1/ptm/m/n/10 (i.e., LRT), "edger_robust_likelihood_ratio", "DE-Seq2", "limma_ voom", "limma_voom_sample_weights" Overfull \hbox (58.60709pt too wide) in paragraph at lines 3480--3481 \T1/ptm/m/n/10 and limma-voom (i.e., edgeR::calcNormFactors; "TMM","TMMwsp","RL E","upperquartile"). Overfull \hbox (21.76895pt too wide) in paragraph at lines 3499--3501 \T1/zi4/m/n/10 btp616$[][]\T1/ptm/m/n/10 , limma-voom [][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1186 / gb-[]2014-[]15-[]2-[]r29$[][]\T1/ptm/m/n/10 , li mma_voom_sample_weights Overfull \hbox (28.64075pt too wide) in paragraph at lines 3499--3501 [][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1093 / nar / gkv412$[][] \T1/p tm/m/n/10 or DE-Seq2 [][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1186 / s1 3059-[]014-[]0550-[]8$[][] [65] Overfull \hbox (26.17642pt too wide) in paragraph at lines 3505--3511 []\T1/ptm/m/n/10 # Fil-ter keep_abundant( fac-tor_of_interest = !!(as.symbol(pa rse_formula(.formula)[1])), min-i-mum_counts Overfull \hbox (24.77638pt too wide) in paragraph at lines 3512--3516 []\T1/ptm/m/n/10 # For-mat se-lect(!!.transcript,!!.sample,!!.abundance) spread (!!.sample,!!.abundance) as_matrix(rownames Overfull \hbox (81.21483pt too wide) in paragraph at lines 3517--3521 []\T1/ptm/m/n/10 # edgeR edgeR::DGEList(counts = .) edgeR::calcNormFactors(meth od = scal-ing_method) edgeR::estimateDisp(design) Overfull \hbox (3.26636pt too wide) in paragraph at lines 3522--3525 []\T1/ptm/m/n/10 # Fit edgeR::glmQLFit(design) edgeR::glmQLFTest(coef = 2, con- trast = my_contrasts) // or glmLRT Overfull \hbox (100.91638pt too wide) in paragraph at lines 3526--3532 []\T1/ptm/m/n/10 Underlying method for DE-Seq2 frame-work: keep_abundant( fac-t or_of_interest = !!as.symbol(parse_formula(.formula)[[1]]), [66] [67] Underfull \vbox (badness 10000) has occurred while \output is active [68] Overfull \hbox (22.20665pt too wide) in paragraph at lines 3689--3690 \T1/ptm/m/n/10 forms: mul-ti-vari-able (rec-om-mended) or uni-vari-able Re-spec -tively: \"fac-tor_of_interest Overfull \hbox (1.61646pt too wide) in paragraph at lines 3697--3698 []\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther \"ciber-sort\", \"epic\" or \"ll sr\". The re-gres-sion method Overfull \hbox (54.31668pt too wide) in paragraph at lines 3714--3725 \T1/ptm/m/n/10 script, !!.abun-dance, method=method, ref-er-ence = ref-er-ence, ac-tion="get", ... ) [..] betareg::betareg(.my_formula, Overfull \hbox (33.15706pt too wide) in paragraph at lines 3726--3738 \T1/ptm/m/n/10 !!.abun-dance, method=method, ref-er-ence = ref-er-ence, ac-tion ="get", ... ) [..] mu-tate(.proportion_0_corrected [69] [70] [71] Underfull \vbox (badness 10000) has occurred while \output is active [72] Overfull \hbox (104.10625pt too wide) in paragraph at lines 3929--3930 []\T1/ptm/m/n/10 This wrap-per ex-e-cutes en-sem-ble gene en-rich-ment anal-y-s es of the dataset us-ing EGSEA (DOI:0.12688/f1000research.12544.1) Overfull \hbox (16.85628pt too wide) in paragraph at lines 3939--3943 []\T1/ptm/m/n/10 # Make sure tran-script names are ad-ja-cent [...] as_matrix(r ownames = !!.en-trez) edgeR::DGEList(counts Overfull \hbox (20.2169pt too wide) in paragraph at lines 3944--3946 []\T1/ptm/m/n/10 idx = buil-dIdx(entrezIDs = row-names(dge), species = species, msigdb.gsets = msigdb.gsets, kegg.exclude [73] Overfull \hbox (137.23795pt too wide) in paragraph at lines 3981--3981 []\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini %>% tidybulk() %>% as_tibble() % >% symbol_to_entrez( .transcript = feature, .sample = sample)[] Overfull \hbox (173.23795pt too wide) in paragraph at lines 3982--3982 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] Overfull \hbox (126.71648pt too wide) in paragraph at lines 3993--3993 [] \T1/zi4/m/n/9 gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6" , "c7", "kegg_disease", "kegg_metabolism", "kegg_signaling"),[] [74] [75] [76] Overfull \hbox (137.23795pt too wide) in paragraph at lines 4139--4139 []\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini %>% tidybulk() %>% as_tibble() % >% symbol_to_entrez( .transcript = feature, .sample = sample)[] Overfull \hbox (173.23795pt too wide) in paragraph at lines 4140--4140 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] Overfull \hbox (3.75021pt too wide) in paragraph at lines 4141--4141 []\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = feature %in% c("TNFRSF 4", "PLCH2", "PADI4", "PAX7"))[] [77] Underfull \vbox (badness 10000) has occurred while \output is active [78] Overfull \hbox (31.37613pt too wide) in paragraph at lines 4270--4280 []\T1/ptm/m/n/10 # Ex-e-cute cal-cu-la-tion nest(data = -gs_cat) mu-tate(fit = map( data, ~ clus-ter-Pro-filer::GSEA( my_entrez_rank, Overfull \hbox (137.23795pt too wide) in paragraph at lines 4301--4301 []\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini %>% tidybulk() %>% as_tibble() % >% symbol_to_entrez( .transcript = feature, .sample = sample)[] Overfull \hbox (173.23795pt too wide) in paragraph at lines 4302--4302 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] Overfull \hbox (3.75021pt too wide) in paragraph at lines 4303--4303 []\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = feature %in% c("TNFRSF 4", "PLCH2", "PADI4", "PAX7"))[] [79] [80] Overfull \hbox (22.20665pt too wide) in paragraph at lines 4409--4410 \T1/ptm/m/n/10 forms: mul-ti-vari-able (rec-om-mended) or uni-vari-able Re-spec -tively: \"fac-tor_of_interest [81] Overfull \hbox (1.61646pt too wide) in paragraph at lines 4417--4418 []\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther \"ciber-sort\", \"epic\" or \"ll sr\". The re-gres-sion method [82] Overfull \hbox (5.09679pt too wide) in paragraph at lines 4494--4495 []\T1/ptm/m/n/10 tidybulk() cre-ates a `tt` ob-ject from a `tbl` for-mat-ted as | | | [83] [84] [85] [86] No file Rd2.ind. [87] (/tmp/RtmpeYe5YI/Rbuild386827695bc1d9/tidybulk/.Rd2pdf3696679/Rd2.aux) ) (see the transcript file for additional information) {/usr/share/texlive/te xmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/ fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inco nsolata/i4-t1-0.enc} Output written on Rd2.pdf (87 pages, 208282 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (225 entries accepted, 0 rejected). Sorting entries.....done (1912 comparisons). Generating output file Rd2.ind....done (421 lines written, 0 warnings). Output written in Rd2.ind. 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This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode LaTeX2e <2020-02-02> patch level 2 L3 programming layer <2020-02-14> (./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2019/12/20 v1.4l Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (/home/biocbuild/bbs-3.13-bioc/R/share/texmf/tex/latex/Rd.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/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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Use [desc()] [9] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) Overfull \hbox (41.25328pt too wide) in paragraph at lines 479--479 []\T1/zi4/m/n/9 tidybulk::se_mini %>% tidybulk() %>% select(feature, count) %> % head %>% as_matrix(rownames=feature)[] [10] [11] [12] [13] [14] [15] [16] [17] Underfull \vbox (badness 10000) has occurred while \output is active [18] [19] Overfull \hbox (159.74715pt too wide) in paragraph at lines 967--967 []\T1/zi4/m/n/9 tidybulk::se_mini %>% tidybulk() %>% filter(sample=="SRR174003 4") %>% deconvolve_cellularity(sample, feature, count, cores = 1)[] [20] [21] Overfull \hbox (10.85692pt too wide) in paragraph at lines 1104--1105 []\T1/ptm/m/n/10 ensembl_to_symbol() takes as in-put a `tbl` for-mat-ted as | < SAM-PLE> | | [22] [23] [24] [25] [26] [27] Overfull \hbox (7.27914pt too wide) in paragraph at lines 1451--1453 []\T1/ptm/m/n/10 When `.drop = TRUE`, empty groups are dropped. See [group_by_d rop_default()] [28] Overfull \hbox (1.76709pt too wide) in paragraph at lines 1487--1488 []\T1/ptm/m/n/10 identify_abundant() takes as in-put a `tbl` for-mat-ted as | < SAM-PLE> | | [29] Overfull \hbox (53.61636pt too wide) in paragraph at lines 1582--1589 []\T1/ptm/m/n/10 Underlying method: edgeR::filterByExpr( data, min.count = min- i-mum_counts, group = string_factor_of_interest, [30] [31] [32] [33] Overfull \hbox (81.74408pt too wide) in paragraph at lines 1761--1761 []\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble( ) %>% distinct(sample) %>% mutate(source = "AU")[] Overfull \hbox (81.74408pt too wide) in paragraph at lines 1765--1765 []\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble( ) %>% distinct(sample) %>% mutate(source = "AU")[] Overfull \hbox (81.74408pt too wide) in paragraph at lines 1769--1769 []\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble( ) %>% distinct(sample) %>% mutate(source = "AU")[] [34] Underfull \vbox (badness 10000) has occurred while \output is active [35] Overfull \hbox (53.61636pt too wide) in paragraph at lines 1878--1885 []\T1/ptm/m/n/10 Underlying method: edgeR::filterByExpr( data, min.count = min- i-mum_counts, group = string_factor_of_interest, [36] [37] [38] Overfull \hbox (81.74408pt too wide) in paragraph at lines 2059--2059 []\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble( ) %>% distinct(sample) %>% mutate(source = "AU")[] [39] [40] [41] [42] [43] [44] Overfull \hbox (6.40688pt too wide) in paragraph at lines 2412--2413 []\T1/ptm/m/n/10 reduce_dimensions() takes as in-put a `tbl` for-mat-ted as | < SAM-PLE> | | [45] Underfull \vbox (badness 10000) has occurred while \output is active [46] [47] Overfull \hbox (10.3875pt too wide) in paragraph at lines 2602--2603 []\T1/ptm/m/n/10 remove_redundancy() takes as in-put a `tbl` for-mat-ted as | < SAM-PLE> | | Overfull \hbox (18.57648pt too wide) in paragraph at lines 2602--2603 \T1/ptm/m/n/10 | <...> | for cor-re-la-tion method or | | | <...> | for re-duced_dimensions [48] [49] Underfull \vbox (badness 10000) has occurred while \output is active [50] [51] [52] [53] Underfull \vbox (badness 10000) has occurred while \output is active [54] [55] Overfull \hbox (79.64253pt too wide) in paragraph at lines 2977--2977 []\T1/zi4/m/n/9 counts.MDS.rotated = rotate_dimensions(counts.MDS, \TS1/cmtt/ m/n/9 `\T1/zi4/m/n/9 Dim1\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , \TS1/cmtt/m/n/9 `\T1/ zi4/m/n/9 Dim2\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , rotation_degrees = 45, .element = sample)[] [56] [57] Overfull \hbox (41.07668pt too wide) in paragraph at lines 3122--3124 []\T1/ptm/m/n/10 Underlying method edgeR::calcNormFactors(.data, method = c("TM M","TMMwsp","RLE","upperquartile")) [58] [59] [60] Overfull \hbox (83.24715pt too wide) in paragraph at lines 3312--3312 []\T1/zi4/m/n/9 tidybulk::se_mini %>% tidybulk() %>% as_tibble() %>% symbol_to _entrez(.transcript = feature, .sample = sample)[] [61] [62] Underfull \vbox (badness 10000) has occurred while \output is active [63] Underfull \vbox (badness 10000) has occurred while \output is active [64] Overfull \hbox (40.04678pt too wide) in paragraph at lines 3476--3477 []\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther "edgeR_quasi_likelihood" (i.e., QLF), "edgeR_likelihood_ratio" Overfull \hbox (104.18698pt too wide) in paragraph at lines 3476--3477 \T1/ptm/m/n/10 (i.e., LRT), "edger_robust_likelihood_ratio", "DE-Seq2", "limma_ voom", "limma_voom_sample_weights" Overfull \hbox (58.60709pt too wide) in paragraph at lines 3480--3481 \T1/ptm/m/n/10 and limma-voom (i.e., edgeR::calcNormFactors; "TMM","TMMwsp","RL E","upperquartile"). Overfull \hbox (21.76895pt too wide) in paragraph at lines 3499--3501 \T1/zi4/m/n/10 btp616$[][]\T1/ptm/m/n/10 , limma-voom [][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1186 / gb-[]2014-[]15-[]2-[]r29$[][]\T1/ptm/m/n/10 , li mma_voom_sample_weights Overfull \hbox (28.64075pt too wide) in paragraph at lines 3499--3501 [][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1093 / nar / gkv412$[][] \T1/p tm/m/n/10 or DE-Seq2 [][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1186 / s1 3059-[]014-[]0550-[]8$[][] [65] Overfull \hbox (26.17642pt too wide) in paragraph at lines 3505--3511 []\T1/ptm/m/n/10 # Fil-ter keep_abundant( fac-tor_of_interest = !!(as.symbol(pa rse_formula(.formula)[1])), min-i-mum_counts Overfull \hbox (24.77638pt too wide) in paragraph at lines 3512--3516 []\T1/ptm/m/n/10 # For-mat se-lect(!!.transcript,!!.sample,!!.abundance) spread (!!.sample,!!.abundance) as_matrix(rownames Overfull \hbox (81.21483pt too wide) in paragraph at lines 3517--3521 []\T1/ptm/m/n/10 # edgeR edgeR::DGEList(counts = .) edgeR::calcNormFactors(meth od = scal-ing_method) edgeR::estimateDisp(design) Overfull \hbox (3.26636pt too wide) in paragraph at lines 3522--3525 []\T1/ptm/m/n/10 # Fit edgeR::glmQLFit(design) edgeR::glmQLFTest(coef = 2, con- trast = my_contrasts) // or glmLRT Overfull \hbox (100.91638pt too wide) in paragraph at lines 3526--3532 []\T1/ptm/m/n/10 Underlying method for DE-Seq2 frame-work: keep_abundant( fac-t or_of_interest = !!as.symbol(parse_formula(.formula)[[1]]), [66] [67] Underfull \vbox (badness 10000) has occurred while \output is active [68] Overfull \hbox (22.20665pt too wide) in paragraph at lines 3689--3690 \T1/ptm/m/n/10 forms: mul-ti-vari-able (rec-om-mended) or uni-vari-able Re-spec -tively: \"fac-tor_of_interest Overfull \hbox (1.61646pt too wide) in paragraph at lines 3697--3698 []\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther \"ciber-sort\", \"epic\" or \"ll sr\". The re-gres-sion method Overfull \hbox (54.31668pt too wide) in paragraph at lines 3714--3725 \T1/ptm/m/n/10 script, !!.abun-dance, method=method, ref-er-ence = ref-er-ence, ac-tion="get", ... ) [..] betareg::betareg(.my_formula, Overfull \hbox (33.15706pt too wide) in paragraph at lines 3726--3738 \T1/ptm/m/n/10 !!.abun-dance, method=method, ref-er-ence = ref-er-ence, ac-tion ="get", ... ) [..] mu-tate(.proportion_0_corrected [69] [70] [71] Underfull \vbox (badness 10000) has occurred while \output is active [72] Overfull \hbox (104.10625pt too wide) in paragraph at lines 3929--3930 []\T1/ptm/m/n/10 This wrap-per ex-e-cutes en-sem-ble gene en-rich-ment anal-y-s es of the dataset us-ing EGSEA (DOI:0.12688/f1000research.12544.1) Overfull \hbox (16.85628pt too wide) in paragraph at lines 3939--3943 []\T1/ptm/m/n/10 # Make sure tran-script names are ad-ja-cent [...] as_matrix(r ownames = !!.en-trez) edgeR::DGEList(counts Overfull \hbox (20.2169pt too wide) in paragraph at lines 3944--3946 []\T1/ptm/m/n/10 idx = buil-dIdx(entrezIDs = row-names(dge), species = species, msigdb.gsets = msigdb.gsets, kegg.exclude [73] Overfull \hbox (137.23795pt too wide) in paragraph at lines 3981--3981 []\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini %>% tidybulk() %>% as_tibble() % >% symbol_to_entrez( .transcript = feature, .sample = sample)[] Overfull \hbox (173.23795pt too wide) in paragraph at lines 3982--3982 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] Overfull \hbox (126.71648pt too wide) in paragraph at lines 3993--3993 [] \T1/zi4/m/n/9 gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6" , "c7", "kegg_disease", "kegg_metabolism", "kegg_signaling"),[] [74] [75] [76] Overfull \hbox (137.23795pt too wide) in paragraph at lines 4139--4139 []\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini %>% tidybulk() %>% as_tibble() % >% symbol_to_entrez( .transcript = feature, .sample = sample)[] Overfull \hbox (173.23795pt too wide) in paragraph at lines 4140--4140 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] Overfull \hbox (3.75021pt too wide) in paragraph at lines 4141--4141 []\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = feature %in% c("TNFRSF 4", "PLCH2", "PADI4", "PAX7"))[] [77] Underfull \vbox (badness 10000) has occurred while \output is active [78] Overfull \hbox (31.37613pt too wide) in paragraph at lines 4270--4280 []\T1/ptm/m/n/10 # Ex-e-cute cal-cu-la-tion nest(data = -gs_cat) mu-tate(fit = map( data, ~ clus-ter-Pro-filer::GSEA( my_entrez_rank, Overfull \hbox (137.23795pt too wide) in paragraph at lines 4301--4301 []\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini %>% tidybulk() %>% as_tibble() % >% symbol_to_entrez( .transcript = feature, .sample = sample)[] Overfull \hbox (173.23795pt too wide) in paragraph at lines 4302--4302 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] Overfull \hbox (3.75021pt too wide) in paragraph at lines 4303--4303 []\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = feature %in% c("TNFRSF 4", "PLCH2", "PADI4", "PAX7"))[] [79] [80] Overfull \hbox (22.20665pt too wide) in paragraph at lines 4409--4410 \T1/ptm/m/n/10 forms: mul-ti-vari-able (rec-om-mended) or uni-vari-able Re-spec -tively: \"fac-tor_of_interest [81] Overfull \hbox (1.61646pt too wide) in paragraph at lines 4417--4418 []\T1/ptm/m/n/10 A string char-ac-ter. 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information) {/usr/share/texlive/te xmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/ fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inco nsolata/i4-t1-0.enc} Output written on Rd2.pdf (92 pages, 228771 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (225 entries accepted, 0 rejected). Sorting entries.....done (1912 comparisons). Generating output file Rd2.ind....done (421 lines written, 0 warnings). Output written in Rd2.ind. Transcript written in Rd2.ilg. 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See [group_by_d rop_default()] [28] Overfull \hbox (1.76709pt too wide) in paragraph at lines 1487--1488 []\T1/ptm/m/n/10 identify_abundant() takes as in-put a `tbl` for-mat-ted as | < SAM-PLE> | | [29] Overfull \hbox (53.61636pt too wide) in paragraph at lines 1582--1589 []\T1/ptm/m/n/10 Underlying method: edgeR::filterByExpr( data, min.count = min- i-mum_counts, group = string_factor_of_interest, [30] [31] [32] [33] Overfull \hbox (81.74408pt too wide) in paragraph at lines 1761--1761 []\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble( ) %>% distinct(sample) %>% mutate(source = "AU")[] Overfull \hbox (81.74408pt too wide) in paragraph at lines 1765--1765 []\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble( ) %>% distinct(sample) %>% mutate(source = "AU")[] Overfull \hbox (81.74408pt too wide) in paragraph at lines 1769--1769 []\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble( ) %>% distinct(sample) %>% mutate(source = "AU")[] [34] Underfull \vbox (badness 10000) has occurred while \output is active [35] Overfull \hbox (53.61636pt too wide) in paragraph at lines 1878--1885 []\T1/ptm/m/n/10 Underlying method: edgeR::filterByExpr( data, min.count = min- i-mum_counts, group = string_factor_of_interest, [36] [37] [38] Overfull \hbox (81.74408pt too wide) in paragraph at lines 2059--2059 []\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble( ) %>% distinct(sample) %>% mutate(source = "AU")[] [39] [40] [41] [42] [43] [44] Overfull \hbox (6.40688pt too wide) in paragraph at lines 2412--2413 []\T1/ptm/m/n/10 reduce_dimensions() takes as in-put a `tbl` for-mat-ted as | < SAM-PLE> | | [45] Underfull \vbox (badness 10000) has occurred while \output is active [46] [47] Overfull \hbox (10.3875pt too wide) in paragraph at lines 2602--2603 []\T1/ptm/m/n/10 remove_redundancy() takes as in-put a `tbl` for-mat-ted as | < SAM-PLE> | | Overfull \hbox (18.57648pt too wide) in paragraph at lines 2602--2603 \T1/ptm/m/n/10 | <...> | for cor-re-la-tion method or | | | <...> | for re-duced_dimensions [48] [49] Underfull \vbox (badness 10000) has occurred while \output is active [50] [51] [52] [53] Underfull \vbox (badness 10000) has occurred while \output is active [54] [55] Overfull \hbox (79.64253pt too wide) in paragraph at lines 2977--2977 []\T1/zi4/m/n/9 counts.MDS.rotated = rotate_dimensions(counts.MDS, \TS1/cmtt/ m/n/9 `\T1/zi4/m/n/9 Dim1\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , \TS1/cmtt/m/n/9 `\T1/ zi4/m/n/9 Dim2\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , rotation_degrees = 45, .element = sample)[] [56] [57] Overfull \hbox (41.07668pt too wide) in paragraph at lines 3122--3124 []\T1/ptm/m/n/10 Underlying method edgeR::calcNormFactors(.data, method = c("TM M","TMMwsp","RLE","upperquartile")) [58] [59] [60] Overfull \hbox (83.24715pt too wide) in paragraph at lines 3312--3312 []\T1/zi4/m/n/9 tidybulk::se_mini %>% tidybulk() %>% as_tibble() %>% symbol_to _entrez(.transcript = feature, .sample = sample)[] [61] [62] Underfull \vbox (badness 10000) has occurred while \output is active [63] Underfull \vbox (badness 10000) has occurred while \output is active [64] Overfull \hbox (40.04678pt too wide) in paragraph at lines 3476--3477 []\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther "edgeR_quasi_likelihood" (i.e., QLF), "edgeR_likelihood_ratio" Overfull \hbox (104.18698pt too wide) in paragraph at lines 3476--3477 \T1/ptm/m/n/10 (i.e., LRT), "edger_robust_likelihood_ratio", "DE-Seq2", "limma_ voom", "limma_voom_sample_weights" Overfull \hbox (58.60709pt too wide) in paragraph at lines 3480--3481 \T1/ptm/m/n/10 and limma-voom (i.e., edgeR::calcNormFactors; "TMM","TMMwsp","RL E","upperquartile"). Overfull \hbox (21.76895pt too wide) in paragraph at lines 3499--3501 \T1/zi4/m/n/10 btp616$[][]\T1/ptm/m/n/10 , limma-voom [][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1186 / gb-[]2014-[]15-[]2-[]r29$[][]\T1/ptm/m/n/10 , li mma_voom_sample_weights Overfull \hbox (28.64075pt too wide) in paragraph at lines 3499--3501 [][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1093 / nar / gkv412$[][] \T1/p tm/m/n/10 or DE-Seq2 [][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1186 / s1 3059-[]014-[]0550-[]8$[][] [65] Overfull \hbox (26.17642pt too wide) in paragraph at lines 3505--3511 []\T1/ptm/m/n/10 # Fil-ter keep_abundant( fac-tor_of_interest = !!(as.symbol(pa rse_formula(.formula)[1])), min-i-mum_counts Overfull \hbox (24.77638pt too wide) in paragraph at lines 3512--3516 []\T1/ptm/m/n/10 # For-mat se-lect(!!.transcript,!!.sample,!!.abundance) spread (!!.sample,!!.abundance) as_matrix(rownames Overfull \hbox (81.21483pt too wide) in paragraph at lines 3517--3521 []\T1/ptm/m/n/10 # edgeR edgeR::DGEList(counts = .) edgeR::calcNormFactors(meth od = scal-ing_method) edgeR::estimateDisp(design) Overfull \hbox (3.26636pt too wide) in paragraph at lines 3522--3525 []\T1/ptm/m/n/10 # Fit edgeR::glmQLFit(design) edgeR::glmQLFTest(coef = 2, con- trast = my_contrasts) // or glmLRT Overfull \hbox (100.91638pt too wide) in paragraph at lines 3526--3532 []\T1/ptm/m/n/10 Underlying method for DE-Seq2 frame-work: keep_abundant( fac-t or_of_interest = !!as.symbol(parse_formula(.formula)[[1]]), [66] [67] Underfull \vbox (badness 10000) has occurred while \output is active [68] Overfull \hbox (22.20665pt too wide) in paragraph at lines 3689--3690 \T1/ptm/m/n/10 forms: mul-ti-vari-able (rec-om-mended) or uni-vari-able Re-spec -tively: \"fac-tor_of_interest Overfull \hbox (1.61646pt too wide) in paragraph at lines 3697--3698 []\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther \"ciber-sort\", \"epic\" or \"ll sr\". The re-gres-sion method Overfull \hbox (54.31668pt too wide) in paragraph at lines 3714--3725 \T1/ptm/m/n/10 script, !!.abun-dance, method=method, ref-er-ence = ref-er-ence, ac-tion="get", ... ) [..] betareg::betareg(.my_formula, Overfull \hbox (33.15706pt too wide) in paragraph at lines 3726--3738 \T1/ptm/m/n/10 !!.abun-dance, method=method, ref-er-ence = ref-er-ence, ac-tion ="get", ... ) [..] mu-tate(.proportion_0_corrected [69] [70] [71] Underfull \vbox (badness 10000) has occurred while \output is active [72] Overfull \hbox (104.10625pt too wide) in paragraph at lines 3929--3930 []\T1/ptm/m/n/10 This wrap-per ex-e-cutes en-sem-ble gene en-rich-ment anal-y-s es of the dataset us-ing EGSEA (DOI:0.12688/f1000research.12544.1) Overfull \hbox (16.85628pt too wide) in paragraph at lines 3939--3943 []\T1/ptm/m/n/10 # Make sure tran-script names are ad-ja-cent [...] as_matrix(r ownames = !!.en-trez) edgeR::DGEList(counts Overfull \hbox (20.2169pt too wide) in paragraph at lines 3944--3946 []\T1/ptm/m/n/10 idx = buil-dIdx(entrezIDs = row-names(dge), species = species, msigdb.gsets = msigdb.gsets, kegg.exclude [73] Overfull \hbox (137.23795pt too wide) in paragraph at lines 3981--3981 []\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini %>% tidybulk() %>% as_tibble() % >% symbol_to_entrez( .transcript = feature, .sample = sample)[] Overfull \hbox (173.23795pt too wide) in paragraph at lines 3982--3982 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] Overfull \hbox (126.71648pt too wide) in paragraph at lines 3993--3993 [] \T1/zi4/m/n/9 gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6" , "c7", "kegg_disease", "kegg_metabolism", "kegg_signaling"),[] [74] [75] [76] Overfull \hbox (137.23795pt too wide) in paragraph at lines 4139--4139 []\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini %>% tidybulk() %>% as_tibble() % >% symbol_to_entrez( .transcript = feature, .sample = sample)[] Overfull \hbox (173.23795pt too wide) in paragraph at lines 4140--4140 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] Overfull \hbox (3.75021pt too wide) in paragraph at lines 4141--4141 []\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = feature %in% c("TNFRSF 4", "PLCH2", "PADI4", "PAX7"))[] [77] Underfull \vbox (badness 10000) has occurred while \output is active [78] Overfull \hbox (31.37613pt too wide) in paragraph at lines 4270--4280 []\T1/ptm/m/n/10 # Ex-e-cute cal-cu-la-tion nest(data = -gs_cat) mu-tate(fit = map( data, ~ clus-ter-Pro-filer::GSEA( my_entrez_rank, Overfull \hbox (137.23795pt too wide) in paragraph at lines 4301--4301 []\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini %>% tidybulk() %>% as_tibble() % >% symbol_to_entrez( .transcript = feature, .sample = sample)[] Overfull \hbox (173.23795pt too wide) in paragraph at lines 4302--4302 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] Overfull \hbox (3.75021pt too wide) in paragraph at lines 4303--4303 []\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = feature %in% c("TNFRSF 4", "PLCH2", "PADI4", "PAX7"))[] [79] [80] Overfull \hbox (22.20665pt too wide) in paragraph at lines 4409--4410 \T1/ptm/m/n/10 forms: mul-ti-vari-able (rec-om-mended) or uni-vari-able Re-spec -tively: \"fac-tor_of_interest [81] Overfull \hbox (1.61646pt too wide) in paragraph at lines 4417--4418 []\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther \"ciber-sort\", \"epic\" or \"ll sr\". The re-gres-sion method [82] Overfull \hbox (5.09679pt too wide) in paragraph at lines 4494--4495 []\T1/ptm/m/n/10 tidybulk() cre-ates a `tt` ob-ject from a `tbl` for-mat-ted as | | | [83] [84] [85] [86] (/tmp/RtmpeYe5YI/Rbuild386827695bc1d9/tidybulk/.Rd2pdf3696679/Rd2.ind [87] Overfull \hbox (18.3567pt too wide) in paragraph at lines 12--14 []| \T1/zi4/m/n/10 vignette_manuscript_signature_boxplot\T1/ptm/m/n/10 , Overfull \hbox (3.3567pt too wide) in paragraph at lines 14--16 []| \T1/zi4/m/n/10 vignette_manuscript_signature_tsne\T1/ptm/m/n/10 , Overfull \hbox (8.3567pt too wide) in paragraph at lines 16--18 []| \T1/zi4/m/n/10 vignette_manuscript_signature_tsne2\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 27. 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at lines 401--403 []\T1/zi4/m/it/10 tidybulk_SAM_BAM,character,character-method [91] [92]) (/tmp/RtmpeYe5YI/Rbuild386827695bc1d9/tidybulk/.Rd2pdf3696679/Rd2.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information) {/usr/share/texlive/te xmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/ fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inco nsolata/i4-t1-0.enc} Output written on Rd2.pdf (92 pages, 229180 bytes). Transcript written on Rd2.log. Saving output to ‘/tmp/RtmpeYe5YI/Rbuild386827695bc1d9/tidybulk/build/tidybulk.pdf’ ... Done * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘tidybulk_1.4.0.tar.gz’