##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data curatedOvarianData
###
##############################################################################
##############################################################################
* checking for file ‘curatedOvarianData/DESCRIPTION’ ... OK
* preparing ‘curatedOvarianData’:
* 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 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2016/02/01>
Babel <3.9q> and hyphenation patterns for 29 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.4-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.10, 2016/02/22 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 366.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 366.
) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [1{/var/lib/texmf/fonts
/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (42.89548pt too wide) in paragraph at lines 94--97
[]\T1/ptm/m/n/10 For "pri-mary_therapy_outcome_success": com-pletere-sponse|par
tialresponse|progressivedisease|stabledisease:
Overfull \hbox (14.36601pt too wide) in paragraph at lines 115--117
[]\T1/ptm/m/n/10 For "site_of_tumor_first_recurrence": (metas-ta-sis / lo-core-
gional / none / lo-core-gional_plus_metastatic).
[2] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [3]
Overfull \hbox (1142.78088pt too wide) in paragraph at lines 187--187
[] \T1/zi4/m/n/10 Experimenter name: Bentink S, Haibe-Kains B, Risch T, Fan J
-B, Hirsch MS, Holton K, Rubio R, April C, Chen J, Wickham-Garcia E, Liu J, Cul
hane A, Drapkin R, Quackenbush J, Matulonis UA: Angiogenic mRNA and microRNA ge
ne expression signature predicts a novel subtype of serous ovarian cancer. PLoS
ONE 2012, 7:e30269.[]
Overfull \hbox (157.78088pt too wide) in paragraph at lines 190--190
[] \T1/zi4/m/n/10 Title: Angiogenic mRNA and microRNA gene expression signatu
re predicts a novel subtype of serous ovarian cancer.[]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [4]
Underfull \vbox (badness 10000) has occurred while \output is active [5]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (610.78088pt too wide) in paragraph at lines 309--309
[] \T1/zi4/m/n/10 Experimenter name: Partheen K, Levan K, Osterberg L, Horvat
h G.Expression analysis of stage III serous ovarian adenocarcinoma distinguishe
s a sub-group of survivors. Eur J Cancer. 2006 Nov; 42(16):2846-54.[]
Overfull \hbox (144.78088pt too wide) in paragraph at lines 312--312
[] \T1/zi4/m/n/10 Title: Expression analysis of stage III serous ovarian aden
ocarcinoma distinguishes a sub-group of survivors.[]
[6]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 348--348
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[7] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [8]
Overfull \hbox (1335.78088pt too wide) in paragraph at lines 426--426
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tajima A, Komata D, Yamamot
o T, Kodama S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H,
Kudo Y, Inoue I, Tanaka K.Gene expression profiling of advanced-stage serous o
varian cancers distinguishes novel subclasses and implicates ZEB2 in tumor prog
ression and prognosis. Cancer Sci. 2009 Aug; 100(8):1421-8.[]
Overfull \hbox (393.78088pt too wide) in paragraph at lines 429--429
[] \T1/zi4/m/n/10 Title: Gene expression profiling of advanced-stage serous o
varian cancers distinguishes novel subclasses and implicates ZEB2 in tumor prog
ression and prognosis.[]
[9] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [10]
Overfull \hbox (890.78088pt too wide) in paragraph at lines 518--518
[] \T1/zi4/m/n/10 Experimenter name: Crijns AP, Fehrmann RS, de Jong S, Gerbe
ns F, Meersma GJ, Klip HG, Hollema H, Hofstra RM, te Meerman GJ, de Vries EG, v
an der Zee AG.Survival-related profile, pathways, and transcription factors in
ovarian cancer. PLoS Med. 2009 Feb 3; 6(2):e24.[]
Overfull \hbox (38.78088pt too wide) in paragraph at lines 521--521
[] \T1/zi4/m/n/10 Title: Survival-related profile, pathways, and transcriptio
n factors in ovarian cancer.[]
[11]
Underfull \vbox (badness 10000) has occurred while \output is active [12]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (657.78088pt too wide) in paragraph at lines 636--636
[] \T1/zi4/m/n/10 Experimenter name: Denkert C, Budczies J, Darb-Esfahani S,
Gy??rffy B et al. A prognostic gene expression index in ovarian cancer - valida
tion across different independent data sets. J Pathol 2009 Jun;218(2):273-80.[]
Overfull \hbox (157.78088pt too wide) in paragraph at lines 639--639
[] \T1/zi4/m/n/10 Title: A prognostic gene expression index in ovarian cancer
- validation across different independent data sets.[]
[13] [14] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (3.12666pt too wide) in paragraph at lines 749--750
[]\T1/ptm/m/n/10 Advanced-stage ovar-ian can-cer pa-tients are gen-er-ally trea
ted with platinum/taxane-based chemother-
[15]
Overfull \hbox (1327.78088pt too wide) in paragraph at lines 762--762
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tajima A, Yahata T, Kodama
S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H, Kudo Y, Kot
era K, Masuzaki H, Tashiro H, Katabuchi H, Inoue I, Tanaka K.Gene expression pr
ofile for predicting survival in advanced-stage serous ovarian cancer across tw
o independent datasets. PLoS One. 2010 Mar 12; 5(3):e9615.[]
Overfull \hbox (232.78088pt too wide) in paragraph at lines 765--765
[] \T1/zi4/m/n/10 Title: Gene expression profile for predicting survival in a
dvanced-stage serous ovarian cancer across two independent datasets.[]
[16] [17] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [18]
Overfull \hbox (1594.78088pt too wide) in paragraph at lines 900--900
[] \T1/zi4/m/n/10 Experimenter name: Mok SC, Bonome T, Vathipadiekal V, Bell
A, Johnson ME, Wong KK, Park DC, Hao K, Yip DK, Donninger H, Ozbun L, Samimi G,
Brady J, Randonovich M, Pise-Masison CA, Barrett JC, Wong WH, Welch WR, Berkow
itz RS, Birrer MJ.A gene signature predictive for outcome in advanced ovarian c
ancer identifies a survival factor: microfibril-associated glycoprotein 2. Canc
er Cell. 2009 Dec 8; 16(6):521-32.[]
Overfull \hbox (305.78088pt too wide) in paragraph at lines 903--903
[] \T1/zi4/m/n/10 Title: A gene signature predictive for outcome in advanced
ovarian cancer identifies a survival factor: microfibril-associated glycoprotei
n 2.[]
[19]
Underfull \vbox (badness 10000) has occurred while \output is active [20]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (930.78088pt too wide) in paragraph at lines 1035--1035
[] \T1/zi4/m/n/10 Experimenter name: Konstantinopoulos PA, Spentzos D, Karlan
BY, Taniguchi T et al. Gene expression profile of BRCAness that correlates wit
h responsiveness to chemotherapy and with outcome in patients with epithelial o
varian cancer. J Clin Oncol 2010 Aug 1;28(22):3555-61.[]
[21]
Overfull \hbox (367.78088pt too wide) in paragraph at lines 1038--1038
[] \T1/zi4/m/n/10 Title: Gene expression profile of BRCAness that correlates
with responsiveness to chemotherapy and with outcome in patients with epithelia
l ovarian cancer.[]
[22] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [23]
Overfull \hbox (930.78088pt too wide) in paragraph at lines 1133--1133
[] \T1/zi4/m/n/10 Experimenter name: Konstantinopoulos PA, Spentzos D, Karlan
BY, Taniguchi T et al. Gene expression profile of BRCAness that correlates wit
h responsiveness to chemotherapy and with outcome in patients with epithelial o
varian cancer. J Clin Oncol 2010 Aug 1;28(22):3555-61.[]
Overfull \hbox (367.78088pt too wide) in paragraph at lines 1136--1136
[] \T1/zi4/m/n/10 Title: Gene expression profile of BRCAness that correlates
with responsiveness to chemotherapy and with outcome in patients with epithelia
l ovarian cancer.[]
[24] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [25]
Overfull \hbox (1522.78088pt too wide) in paragraph at lines 1231--1231
[] \T1/zi4/m/n/10 Experimenter name: Meyniel JP, Cottu PH, Decraene C, Stern
MH, Couturier J, Lebigot I, Nicolas A, Weber N, Fourchotte V, Alran S, Rapinat
A, Gentien D, Roman-Roman S, Mignot L, Sastre-Garau X.A genomic and transcripto
mic approach for a differential diagnosis between primary and secondary ovarian
carcinomas in patients with a previous history of breast cancer. BMC Cancer. 2
010 May 21; 10:222.[]
Overfull \hbox (468.78088pt too wide) in paragraph at lines 1234--1234
[] \T1/zi4/m/n/10 Title: A genomic and transcriptomic approach for a differen
tial diagnosis between primary and secondary ovarian carcinomas in patients wit
h a previous history of breast cancer.[]
[26] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [27]
Overfull \hbox (108.78088pt too wide) in paragraph at lines 1339--1339
[] \T1/zi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[]
[28] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [29]
Overfull \hbox (137.78088pt too wide) in paragraph at lines 1451--1451
[] \T1/zi4/m/n/10 Experimenter name: Mateescu B, Batista L, Mariani O, Meynie
l J, Cottu PH, Sastre-Garau X, Mechta-Grigoriou F[]
Overfull \hbox (90.78088pt too wide) in paragraph at lines 1454--1454
[] \T1/zi4/m/n/10 Title: miR-141 and miR-200a act on ovarian tumorigenesis by
controlling oxidative stress response.[]
[30] [31] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [32]
Overfull \hbox (946.78088pt too wide) in paragraph at lines 1577--1577
[] \T1/zi4/m/n/10 Experimenter name: Bonome T, Levine DA, Shih J, Randonovich
M, Pise-Masison CA, Bogomolniy F, Ozbun L, Brady J, Barrett JC, Boyd J, Birrer
MJ: A Gene Signature Predicting for Survival in Suboptimally Debulked Patients
with Ovarian Cancer. Cancer Research 2008, 68:5478 -5486.[]
Overfull \hbox (109.78088pt too wide) in paragraph at lines 1580--1580
[] \T1/zi4/m/n/10 Title: A gene signature predicting for survival in suboptim
ally debulked patients with ovarian cancer.[]
[33]
Underfull \vbox (badness 10000) has occurred while \output is active [34]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (746.78088pt too wide) in paragraph at lines 1720--1720
[] \T1/zi4/m/n/10 Experimenter name: Gillet JP, Calcagno AM, Varma S, Davidso
n B et al. Multidrug resistance-linked gene signature predicts overall survival
of patients with primary ovarian serous carcinoma. Clin Cancer Res 2012 Jun 1;
18(11):3197-206.[]
[35]
Overfull \hbox (228.78088pt too wide) in paragraph at lines 1723--1723
[] \T1/zi4/m/n/10 Title: Multidrug resistance-linked gene signature predicts
overall survival of patients with primary ovarian serous carcinoma.[]
[36] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [37]
Overfull \hbox (96.78088pt too wide) in paragraph at lines 1842--1842
[] \T1/zi4/m/n/10 Experimenter name: Ferriss JS, Kim Y, Duska L, Birrer M, Le
vine DA, Moskaluk C,Theodorescu D, Lee JK[]
Overfull \hbox (311.78088pt too wide) in paragraph at lines 1845--1845
[] \T1/zi4/m/n/10 Title: Multi-gene expression predictors of single drug resp
onses to adjuvant chemotherapy in ovarian carcinoma: predicting platinum resist
ance.[]
[38] [39] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [40]
Overfull \hbox (858.78088pt too wide) in paragraph at lines 1988--1988
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tsunoda T, Shigemizu D, Fuj
iwara H et al. High-risk ovarian cancer based on 126-gene expression signature
is uniquely characterized by downregulation of antigen presentation pathway. Cl
in Cancer Res 2012 Mar 1;18(5):1374-85.[]
Overfull \hbox (330.78088pt too wide) in paragraph at lines 1991--1991
[] \T1/zi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
[41] [42] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [43]
Overfull \hbox (858.78088pt too wide) in paragraph at lines 2115--2115
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tsunoda T, Shigemizu D, Fuj
iwara H et al. High-risk ovarian cancer based on 126-gene expression signature
is uniquely characterized by downregulation of antigen presentation pathway. Cl
in Cancer Res 2012 Mar 1;18(5):1374-85.[]
Overfull \hbox (330.78088pt too wide) in paragraph at lines 2118--2118
[] \T1/zi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
[44] [45] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [46]
Overfull \hbox (75.78088pt too wide) in paragraph at lines 2245--2245
[] \T1/zi4/m/n/10 Title: COL11A1 promotes tumor progression and predicts poor
clinical outcome in ovarian cancer.[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2281--2281
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[47] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [48]
Overfull \hbox (479.78088pt too wide) in paragraph at lines 2351--2351
[] \T1/zi4/m/n/10 Experimenter name: Pils D1, Hager G, Tong D, Aust S, Heinze
G, Kohl M, Schuster E, Wolf A, Sehouli J, Braicu I, Vergote I, Cadron I, Mahne
r S, Hofstetter G, Speiser P, Zeillinger R[]
Overfull \hbox (169.78088pt too wide) in paragraph at lines 2354--2354
[] \T1/zi4/m/n/10 Title: Validating the impact of a molecular subtype in ovar
ian cancer on outcomes: a study of the OVCAD Consortium.[]
[49] [50] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [51]
Overfull \hbox (153.78088pt too wide) in paragraph at lines 2478--2478
[] \T1/zi4/m/n/10 Experimenter name: Karlan BY, Dering J, Walsh C, Orsulic S,
Lester J, Anderson LA, Ginther CL, Fejzo M, Slamon D[]
Overfull \hbox (141.78088pt too wide) in paragraph at lines 2481--2481
[] \T1/zi4/m/n/10 Title: POSTN/TGFBI-associated stromal signature predicts po
or prognosis in serous epithelial ovarian cancer.[]
[52]
Underfull \vbox (badness 10000) has occurred while \output is active [53]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Underfull \hbox (badness 1337) in paragraph at lines 2599--2599
[] \T1/ptm/m/it/10 Lysophos-pha-tidic acid-induced tran-scrip-tional pro-file r
ep-re-sents
[54]
Overfull \hbox (1036.78088pt too wide) in paragraph at lines 2617--2617
[] \T1/zi4/m/n/10 Experimenter name: Murph MM, Liu W, Yu S, Lu Y, Hall H, Hen
nessy BT, Lahad J, Schaner M, Helland A, Kristensen G, Brresen-Dale AL, Mills G
B. Lysophosphatidic acid-induced transcriptional profile represents serous epit
helial ovarian carcinoma and worsened prognosis. PLoS One. 2009; 4(5):e5583.[]
Overfull \hbox (255.78088pt too wide) in paragraph at lines 2620--2620
[] \T1/zi4/m/n/10 Title: Lysophosphatidic acid-induced transcriptional profil
e represents serous epithelial ovarian carcinoma and worsened prognosis.[]
[55] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [56]
Overfull \hbox (1001.78088pt too wide) in paragraph at lines 2725--2725
[] \T1/zi4/m/n/10 Experimenter name: Ouellet V, Provencher DM, Maugard CM, Le
Page C, Ren F, Lussier C, Novak J, Ge B, Hudson TJ, Tonin PN, Mes-Masson A-M:
Discrimination between serous low malignant potential and invasive epithelial o
varian tumors using molecular profiling. Oncogene 2005, 24:4672-4687.[]
[57] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [58]
Overfull \hbox (959.78088pt too wide) in paragraph at lines 2821--2821
[] \T1/zi4/m/n/10 Experimenter name: Marchini S, Mariani P, Chiorino G, Marra
zzo E, Bonomi R, Fruscio R, Clivio L, Garbi A, Torri V, Cinquini M, Dell\TS1/zi
4/m/n/10 '\T1/zi4/m/n/10 Anna T, Apolone G, Broggini M, D\TS1/zi4/m/n/10 '\T1/z
i4/m/n/10 Incalci M.Analysis of gene expression in early-stage ovarian cancer.
Clin Cancer Res. 2008 Dec 1; 14(23):7850-60.[]
[59]
Underfull \vbox (badness 10000) has occurred while \output is active [60]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1341.78088pt too wide) in paragraph at lines 2947--2947
[] \T1/zi4/m/n/10 Experimenter name: Tothill RW, Tinker AV, George J, Brown R
, Fox SB, Lade S, Johnson DS, Trivett MK, Etemadmoghadam D, Locandro B, Trafica
nte N, Fereday S, Hung JA, Chiew YE, Haviv I, Gertig D, DeFazio A, Bowtell DD.N
ovel molecular subtypes of serous and endometrioid ovarian cancer linked to cli
nical outcome. Clin Cancer Res. 2008 Aug 15; 14(16):5198-208.[]
Overfull \hbox (104.78088pt too wide) in paragraph at lines 2950--2950
[] \T1/zi4/m/n/10 Title: Novel molecular subtypes of serous and endometrioid
ovarian cancer linked to clinical outcome.[]
[61] [62]
Underfull \vbox (badness 10000) has occurred while \output is active [63]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1042.78088pt too wide) in paragraph at lines 3102--3102
[] \T1/zi4/m/n/10 Experimenter name: Berchuck A, Iversen ES, Lancaster JM, Pi
ttman J, Luo J, Lee P, Murphy S, Dressman HK, Febbo PG, West M, Nevins JR, Mark
s JR.Patterns of gene expression that characterize long-term survival in advanc
ed stage serous ovarian cancers. Clin Cancer Res. 2005 May 15; 11(10):3686-96.[
]
Overfull \hbox (163.78088pt too wide) in paragraph at lines 3105--3105
[] \T1/zi4/m/n/10 Title: Patterns of gene expression that characterize long-t
erm survival in advanced stage serous ovarian cancers.[]
[64]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 3143--3143
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[65] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [66]
Overfull \hbox (1258.78088pt too wide) in paragraph at lines 3225--3225
[] \T1/zi4/m/n/10 Experimenter name: Dressman HK, Berchuck A, Chan G, Zhai J,
Bild A, Sayer R, Cragun J, Clarke J, Whitaker RS, Li L, Gray J, Marks J, Ginsb
urg GS, Potti A, West M, Nevins JR, Lancaster JM.An integrated genomic-based ap
proach to individualized treatment of patients with advanced-stage ovarian canc
er. J Clin Oncol. 2007 Feb 10; 25(5):517-25.[]
Overfull \hbox (194.78088pt too wide) in paragraph at lines 3228--3228
[] \T1/zi4/m/n/10 Title: An integrated genomic-based approach to individualiz
ed treatment of patients with advanced-stage ovarian cancer.[]
[67] [68] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [69]
Overfull \hbox (1274.78088pt too wide) in paragraph at lines 3353--3353
[] \T1/zi4/m/n/10 Experimenter name: Berchuck A, Iversen ES, Luo J, Clarke JP
, Horne H, Levine DA, Boyd J, Alonso MA, Secord AA, Bernardini MQ, Barnett JC,
Boren T, Murphy SK, Dressman HK, Marks JR, Lancaster JM.Microarray analysis of
early stage serous ovarian cancers shows profiles predictive of favorable outco
me. Clin Cancer Res. 2009 Apr 1; 15(7):2448-55.[]
Overfull \hbox (158.78088pt too wide) in paragraph at lines 3356--3356
[] \T1/zi4/m/n/10 Title: Microarray analysis of early stage serous ovarian ca
ncers shows profiles predictive of favorable outcome.[]
[70]
Underfull \vbox (badness 10000) has occurred while \output is active [71]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3485--3485
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[72] [73]
Underfull \vbox (badness 10000) has occurred while \output is active [74]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [75]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3661--3661
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[76]
Underfull \vbox (badness 10000) has occurred while \output is active [77]
Underfull \vbox (badness 10000) has occurred while \output is active [78]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3834--3834
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[79] [80]
Underfull \vbox (badness 10000) has occurred while \output is active [81]
No file Rd2.ind.
[82] (/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.aux
)
Package rerunfilecheck Warning: File `Rd2.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
)
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts
/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola
ta/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/inconsolata/In
consolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (82 pages, 221912 bytes).
Transcript written on Rd2.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2016/02/01>
Babel <3.9q> and hyphenation patterns for 29 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.4-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.10, 2016/02/22 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 366.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 366.
) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.out)
(/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.toc
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (42.89548pt too wide) in paragraph at lines 94--97
[]\T1/ptm/m/n/10 For "pri-mary_therapy_outcome_success": com-pletere-sponse|par
tialresponse|progressivedisease|stabledisease:
Overfull \hbox (14.36601pt too wide) in paragraph at lines 115--117
[]\T1/ptm/m/n/10 For "site_of_tumor_first_recurrence": (metas-ta-sis / lo-core-
gional / none / lo-core-gional_plus_metastatic).
[3] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1142.78088pt too wide) in paragraph at lines 187--187
[] \T1/zi4/m/n/10 Experimenter name: Bentink S, Haibe-Kains B, Risch T, Fan J
-B, Hirsch MS, Holton K, Rubio R, April C, Chen J, Wickham-Garcia E, Liu J, Cul
hane A, Drapkin R, Quackenbush J, Matulonis UA: Angiogenic mRNA and microRNA ge
ne expression signature predicts a novel subtype of serous ovarian cancer. PLoS
ONE 2012, 7:e30269.[]
Overfull \hbox (157.78088pt too wide) in paragraph at lines 190--190
[] \T1/zi4/m/n/10 Title: Angiogenic mRNA and microRNA gene expression signatu
re predicts a novel subtype of serous ovarian cancer.[]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [4] [5]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [6]
Overfull \hbox (610.78088pt too wide) in paragraph at lines 309--309
[] \T1/zi4/m/n/10 Experimenter name: Partheen K, Levan K, Osterberg L, Horvat
h G.Expression analysis of stage III serous ovarian adenocarcinoma distinguishe
s a sub-group of survivors. Eur J Cancer. 2006 Nov; 42(16):2846-54.[]
Overfull \hbox (144.78088pt too wide) in paragraph at lines 312--312
[] \T1/zi4/m/n/10 Title: Expression analysis of stage III serous ovarian aden
ocarcinoma distinguishes a sub-group of survivors.[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 348--348
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[7]
Underfull \vbox (badness 10000) has occurred while \output is active [8]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1335.78088pt too wide) in paragraph at lines 426--426
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tajima A, Komata D, Yamamot
o T, Kodama S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H,
Kudo Y, Inoue I, Tanaka K.Gene expression profiling of advanced-stage serous o
varian cancers distinguishes novel subclasses and implicates ZEB2 in tumor prog
ression and prognosis. Cancer Sci. 2009 Aug; 100(8):1421-8.[]
Overfull \hbox (393.78088pt too wide) in paragraph at lines 429--429
[] \T1/zi4/m/n/10 Title: Gene expression profiling of advanced-stage serous o
varian cancers distinguishes novel subclasses and implicates ZEB2 in tumor prog
ression and prognosis.[]
[9] [10] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (890.78088pt too wide) in paragraph at lines 518--518
[] \T1/zi4/m/n/10 Experimenter name: Crijns AP, Fehrmann RS, de Jong S, Gerbe
ns F, Meersma GJ, Klip HG, Hollema H, Hofstra RM, te Meerman GJ, de Vries EG, v
an der Zee AG.Survival-related profile, pathways, and transcription factors in
ovarian cancer. PLoS Med. 2009 Feb 3; 6(2):e24.[]
Overfull \hbox (38.78088pt too wide) in paragraph at lines 521--521
[] \T1/zi4/m/n/10 Title: Survival-related profile, pathways, and transcriptio
n factors in ovarian cancer.[]
[11] [12] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [13]
Overfull \hbox (657.78088pt too wide) in paragraph at lines 636--636
[] \T1/zi4/m/n/10 Experimenter name: Denkert C, Budczies J, Darb-Esfahani S,
Gy??rffy B et al. A prognostic gene expression index in ovarian cancer - valida
tion across different independent data sets. J Pathol 2009 Jun;218(2):273-80.[]
Overfull \hbox (157.78088pt too wide) in paragraph at lines 639--639
[] \T1/zi4/m/n/10 Title: A prognostic gene expression index in ovarian cancer
- validation across different independent data sets.[]
[14] [15] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (3.12666pt too wide) in paragraph at lines 749--750
[]\T1/ptm/m/n/10 Advanced-stage ovar-ian can-cer pa-tients are gen-er-ally trea
ted with platinum/taxane-based chemother-
[16]
Overfull \hbox (1327.78088pt too wide) in paragraph at lines 762--762
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tajima A, Yahata T, Kodama
S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H, Kudo Y, Kot
era K, Masuzaki H, Tashiro H, Katabuchi H, Inoue I, Tanaka K.Gene expression pr
ofile for predicting survival in advanced-stage serous ovarian cancer across tw
o independent datasets. PLoS One. 2010 Mar 12; 5(3):e9615.[]
Overfull \hbox (232.78088pt too wide) in paragraph at lines 765--765
[] \T1/zi4/m/n/10 Title: Gene expression profile for predicting survival in a
dvanced-stage serous ovarian cancer across two independent datasets.[]
[17]
Underfull \vbox (badness 10000) has occurred while \output is active [18]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1594.78088pt too wide) in paragraph at lines 900--900
[] \T1/zi4/m/n/10 Experimenter name: Mok SC, Bonome T, Vathipadiekal V, Bell
A, Johnson ME, Wong KK, Park DC, Hao K, Yip DK, Donninger H, Ozbun L, Samimi G,
Brady J, Randonovich M, Pise-Masison CA, Barrett JC, Wong WH, Welch WR, Berkow
itz RS, Birrer MJ.A gene signature predictive for outcome in advanced ovarian c
ancer identifies a survival factor: microfibril-associated glycoprotein 2. Canc
er Cell. 2009 Dec 8; 16(6):521-32.[]
Overfull \hbox (305.78088pt too wide) in paragraph at lines 903--903
[] \T1/zi4/m/n/10 Title: A gene signature predictive for outcome in advanced
ovarian cancer identifies a survival factor: microfibril-associated glycoprotei
n 2.[]
[19] [20] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [21]
Overfull \hbox (930.78088pt too wide) in paragraph at lines 1035--1035
[] \T1/zi4/m/n/10 Experimenter name: Konstantinopoulos PA, Spentzos D, Karlan
BY, Taniguchi T et al. Gene expression profile of BRCAness that correlates wit
h responsiveness to chemotherapy and with outcome in patients with epithelial o
varian cancer. J Clin Oncol 2010 Aug 1;28(22):3555-61.[]
Overfull \hbox (367.78088pt too wide) in paragraph at lines 1038--1038
[] \T1/zi4/m/n/10 Title: Gene expression profile of BRCAness that correlates
with responsiveness to chemotherapy and with outcome in patients with epithelia
l ovarian cancer.[]
[22] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [23]
Overfull \hbox (930.78088pt too wide) in paragraph at lines 1133--1133
[] \T1/zi4/m/n/10 Experimenter name: Konstantinopoulos PA, Spentzos D, Karlan
BY, Taniguchi T et al. Gene expression profile of BRCAness that correlates wit
h responsiveness to chemotherapy and with outcome in patients with epithelial o
varian cancer. J Clin Oncol 2010 Aug 1;28(22):3555-61.[]
Overfull \hbox (367.78088pt too wide) in paragraph at lines 1136--1136
[] \T1/zi4/m/n/10 Title: Gene expression profile of BRCAness that correlates
with responsiveness to chemotherapy and with outcome in patients with epithelia
l ovarian cancer.[]
[24] [25] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1522.78088pt too wide) in paragraph at lines 1231--1231
[] \T1/zi4/m/n/10 Experimenter name: Meyniel JP, Cottu PH, Decraene C, Stern
MH, Couturier J, Lebigot I, Nicolas A, Weber N, Fourchotte V, Alran S, Rapinat
A, Gentien D, Roman-Roman S, Mignot L, Sastre-Garau X.A genomic and transcripto
mic approach for a differential diagnosis between primary and secondary ovarian
carcinomas in patients with a previous history of breast cancer. BMC Cancer. 2
010 May 21; 10:222.[]
Overfull \hbox (468.78088pt too wide) in paragraph at lines 1234--1234
[] \T1/zi4/m/n/10 Title: A genomic and transcriptomic approach for a differen
tial diagnosis between primary and secondary ovarian carcinomas in patients wit
h a previous history of breast cancer.[]
[26] [27] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (108.78088pt too wide) in paragraph at lines 1339--1339
[] \T1/zi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[]
[28] [29] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [30]
Overfull \hbox (137.78088pt too wide) in paragraph at lines 1451--1451
[] \T1/zi4/m/n/10 Experimenter name: Mateescu B, Batista L, Mariani O, Meynie
l J, Cottu PH, Sastre-Garau X, Mechta-Grigoriou F[]
Overfull \hbox (90.78088pt too wide) in paragraph at lines 1454--1454
[] \T1/zi4/m/n/10 Title: miR-141 and miR-200a act on ovarian tumorigenesis by
controlling oxidative stress response.[]
[31]
Underfull \vbox (badness 10000) has occurred while \output is active [32]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (946.78088pt too wide) in paragraph at lines 1577--1577
[] \T1/zi4/m/n/10 Experimenter name: Bonome T, Levine DA, Shih J, Randonovich
M, Pise-Masison CA, Bogomolniy F, Ozbun L, Brady J, Barrett JC, Boyd J, Birrer
MJ: A Gene Signature Predicting for Survival in Suboptimally Debulked Patients
with Ovarian Cancer. Cancer Research 2008, 68:5478 -5486.[]
Overfull \hbox (109.78088pt too wide) in paragraph at lines 1580--1580
[] \T1/zi4/m/n/10 Title: A gene signature predicting for survival in suboptim
ally debulked patients with ovarian cancer.[]
[33] [34] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [35]
Overfull \hbox (746.78088pt too wide) in paragraph at lines 1720--1720
[] \T1/zi4/m/n/10 Experimenter name: Gillet JP, Calcagno AM, Varma S, Davidso
n B et al. Multidrug resistance-linked gene signature predicts overall survival
of patients with primary ovarian serous carcinoma. Clin Cancer Res 2012 Jun 1;
18(11):3197-206.[]
Overfull \hbox (228.78088pt too wide) in paragraph at lines 1723--1723
[] \T1/zi4/m/n/10 Title: Multidrug resistance-linked gene signature predicts
overall survival of patients with primary ovarian serous carcinoma.[]
[36] [37] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [38]
Overfull \hbox (96.78088pt too wide) in paragraph at lines 1842--1842
[] \T1/zi4/m/n/10 Experimenter name: Ferriss JS, Kim Y, Duska L, Birrer M, Le
vine DA, Moskaluk C,Theodorescu D, Lee JK[]
Overfull \hbox (311.78088pt too wide) in paragraph at lines 1845--1845
[] \T1/zi4/m/n/10 Title: Multi-gene expression predictors of single drug resp
onses to adjuvant chemotherapy in ovarian carcinoma: predicting platinum resist
ance.[]
[39]
Underfull \vbox (badness 10000) has occurred while \output is active [40]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [41]
Overfull \hbox (858.78088pt too wide) in paragraph at lines 1988--1988
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tsunoda T, Shigemizu D, Fuj
iwara H et al. High-risk ovarian cancer based on 126-gene expression signature
is uniquely characterized by downregulation of antigen presentation pathway. Cl
in Cancer Res 2012 Mar 1;18(5):1374-85.[]
Overfull \hbox (330.78088pt too wide) in paragraph at lines 1991--1991
[] \T1/zi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
[42]
Underfull \vbox (badness 10000) has occurred while \output is active [43]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (858.78088pt too wide) in paragraph at lines 2115--2115
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tsunoda T, Shigemizu D, Fuj
iwara H et al. High-risk ovarian cancer based on 126-gene expression signature
is uniquely characterized by downregulation of antigen presentation pathway. Cl
in Cancer Res 2012 Mar 1;18(5):1374-85.[]
Overfull \hbox (330.78088pt too wide) in paragraph at lines 2118--2118
[] \T1/zi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
[44] [45] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [46]
Overfull \hbox (75.78088pt too wide) in paragraph at lines 2245--2245
[] \T1/zi4/m/n/10 Title: COL11A1 promotes tumor progression and predicts poor
clinical outcome in ovarian cancer.[]
[47]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2281--2281
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[48] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (479.78088pt too wide) in paragraph at lines 2351--2351
[] \T1/zi4/m/n/10 Experimenter name: Pils D1, Hager G, Tong D, Aust S, Heinze
G, Kohl M, Schuster E, Wolf A, Sehouli J, Braicu I, Vergote I, Cadron I, Mahne
r S, Hofstetter G, Speiser P, Zeillinger R[]
Overfull \hbox (169.78088pt too wide) in paragraph at lines 2354--2354
[] \T1/zi4/m/n/10 Title: Validating the impact of a molecular subtype in ovar
ian cancer on outcomes: a study of the OVCAD Consortium.[]
[49] [50] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [51]
Overfull \hbox (153.78088pt too wide) in paragraph at lines 2478--2478
[] \T1/zi4/m/n/10 Experimenter name: Karlan BY, Dering J, Walsh C, Orsulic S,
Lester J, Anderson LA, Ginther CL, Fejzo M, Slamon D[]
Overfull \hbox (141.78088pt too wide) in paragraph at lines 2481--2481
[] \T1/zi4/m/n/10 Title: POSTN/TGFBI-associated stromal signature predicts po
or prognosis in serous epithelial ovarian cancer.[]
[52] [53] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Underfull \hbox (badness 1337) in paragraph at lines 2599--2599
[] \T1/ptm/m/it/10 Lysophos-pha-tidic acid-induced tran-scrip-tional pro-file r
ep-re-sents
[54]
Overfull \hbox (1036.78088pt too wide) in paragraph at lines 2617--2617
[] \T1/zi4/m/n/10 Experimenter name: Murph MM, Liu W, Yu S, Lu Y, Hall H, Hen
nessy BT, Lahad J, Schaner M, Helland A, Kristensen G, Brresen-Dale AL, Mills G
B. Lysophosphatidic acid-induced transcriptional profile represents serous epit
helial ovarian carcinoma and worsened prognosis. PLoS One. 2009; 4(5):e5583.[]
Overfull \hbox (255.78088pt too wide) in paragraph at lines 2620--2620
[] \T1/zi4/m/n/10 Title: Lysophosphatidic acid-induced transcriptional profil
e represents serous epithelial ovarian carcinoma and worsened prognosis.[]
[55] [56] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1001.78088pt too wide) in paragraph at lines 2725--2725
[] \T1/zi4/m/n/10 Experimenter name: Ouellet V, Provencher DM, Maugard CM, Le
Page C, Ren F, Lussier C, Novak J, Ge B, Hudson TJ, Tonin PN, Mes-Masson A-M:
Discrimination between serous low malignant potential and invasive epithelial o
varian tumors using molecular profiling. Oncogene 2005, 24:4672-4687.[]
[57] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [58]
Overfull \hbox (959.78088pt too wide) in paragraph at lines 2821--2821
[] \T1/zi4/m/n/10 Experimenter name: Marchini S, Mariani P, Chiorino G, Marra
zzo E, Bonomi R, Fruscio R, Clivio L, Garbi A, Torri V, Cinquini M, Dell\TS1/zi
4/m/n/10 '\T1/zi4/m/n/10 Anna T, Apolone G, Broggini M, D\TS1/zi4/m/n/10 '\T1/z
i4/m/n/10 Incalci M.Analysis of gene expression in early-stage ovarian cancer.
Clin Cancer Res. 2008 Dec 1; 14(23):7850-60.[]
[59] [60] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [61]
Overfull \hbox (1341.78088pt too wide) in paragraph at lines 2947--2947
[] \T1/zi4/m/n/10 Experimenter name: Tothill RW, Tinker AV, George J, Brown R
, Fox SB, Lade S, Johnson DS, Trivett MK, Etemadmoghadam D, Locandro B, Trafica
nte N, Fereday S, Hung JA, Chiew YE, Haviv I, Gertig D, DeFazio A, Bowtell DD.N
ovel molecular subtypes of serous and endometrioid ovarian cancer linked to cli
nical outcome. Clin Cancer Res. 2008 Aug 15; 14(16):5198-208.[]
Overfull \hbox (104.78088pt too wide) in paragraph at lines 2950--2950
[] \T1/zi4/m/n/10 Title: Novel molecular subtypes of serous and endometrioid
ovarian cancer linked to clinical outcome.[]
[62]
Underfull \vbox (badness 10000) has occurred while \output is active [63]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [64]
Overfull \hbox (1042.78088pt too wide) in paragraph at lines 3102--3102
[] \T1/zi4/m/n/10 Experimenter name: Berchuck A, Iversen ES, Lancaster JM, Pi
ttman J, Luo J, Lee P, Murphy S, Dressman HK, Febbo PG, West M, Nevins JR, Mark
s JR.Patterns of gene expression that characterize long-term survival in advanc
ed stage serous ovarian cancers. Clin Cancer Res. 2005 May 15; 11(10):3686-96.[
]
Overfull \hbox (163.78088pt too wide) in paragraph at lines 3105--3105
[] \T1/zi4/m/n/10 Title: Patterns of gene expression that characterize long-t
erm survival in advanced stage serous ovarian cancers.[]
[65]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 3143--3143
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[66] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1258.78088pt too wide) in paragraph at lines 3225--3225
[] \T1/zi4/m/n/10 Experimenter name: Dressman HK, Berchuck A, Chan G, Zhai J,
Bild A, Sayer R, Cragun J, Clarke J, Whitaker RS, Li L, Gray J, Marks J, Ginsb
urg GS, Potti A, West M, Nevins JR, Lancaster JM.An integrated genomic-based ap
proach to individualized treatment of patients with advanced-stage ovarian canc
er. J Clin Oncol. 2007 Feb 10; 25(5):517-25.[]
Overfull \hbox (194.78088pt too wide) in paragraph at lines 3228--3228
[] \T1/zi4/m/n/10 Title: An integrated genomic-based approach to individualiz
ed treatment of patients with advanced-stage ovarian cancer.[]
[67] [68] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [69]
Overfull \hbox (1274.78088pt too wide) in paragraph at lines 3353--3353
[] \T1/zi4/m/n/10 Experimenter name: Berchuck A, Iversen ES, Luo J, Clarke JP
, Horne H, Levine DA, Boyd J, Alonso MA, Secord AA, Bernardini MQ, Barnett JC,
Boren T, Murphy SK, Dressman HK, Marks JR, Lancaster JM.Microarray analysis of
early stage serous ovarian cancers shows profiles predictive of favorable outco
me. Clin Cancer Res. 2009 Apr 1; 15(7):2448-55.[]
Overfull \hbox (158.78088pt too wide) in paragraph at lines 3356--3356
[] \T1/zi4/m/n/10 Title: Microarray analysis of early stage serous ovarian ca
ncers shows profiles predictive of favorable outcome.[]
[70] [71] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [72]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3485--3485
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[73]
Underfull \vbox (badness 10000) has occurred while \output is active [74]
Underfull \vbox (badness 10000) has occurred while \output is active [75]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3661--3661
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[76] [77]
Underfull \vbox (badness 10000) has occurred while \output is active [78]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [79]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3834--3834
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[80]
Underfull \vbox (badness 10000) has occurred while \output is active [81]
Underfull \vbox (badness 10000) has occurred while \output is active [82]
No file Rd2.ind.
[83] (/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.aux
) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts
/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola
ta/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/inconsolata/In
consolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (83 pages, 225729 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2015] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (92 entries accepted, 0 rejected).
Sorting entries....done (616 comparisons).
Generating output file Rd2.ind....done (146 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2016/02/01>
Babel <3.9q> and hyphenation patterns for 29 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.4-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.10, 2016/02/22 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 366.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 366.
) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.out)
(/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.toc
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (42.89548pt too wide) in paragraph at lines 94--97
[]\T1/ptm/m/n/10 For "pri-mary_therapy_outcome_success": com-pletere-sponse|par
tialresponse|progressivedisease|stabledisease:
Overfull \hbox (14.36601pt too wide) in paragraph at lines 115--117
[]\T1/ptm/m/n/10 For "site_of_tumor_first_recurrence": (metas-ta-sis / lo-core-
gional / none / lo-core-gional_plus_metastatic).
[3] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1142.78088pt too wide) in paragraph at lines 187--187
[] \T1/zi4/m/n/10 Experimenter name: Bentink S, Haibe-Kains B, Risch T, Fan J
-B, Hirsch MS, Holton K, Rubio R, April C, Chen J, Wickham-Garcia E, Liu J, Cul
hane A, Drapkin R, Quackenbush J, Matulonis UA: Angiogenic mRNA and microRNA ge
ne expression signature predicts a novel subtype of serous ovarian cancer. PLoS
ONE 2012, 7:e30269.[]
Overfull \hbox (157.78088pt too wide) in paragraph at lines 190--190
[] \T1/zi4/m/n/10 Title: Angiogenic mRNA and microRNA gene expression signatu
re predicts a novel subtype of serous ovarian cancer.[]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [4] [5]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [6]
Overfull \hbox (610.78088pt too wide) in paragraph at lines 309--309
[] \T1/zi4/m/n/10 Experimenter name: Partheen K, Levan K, Osterberg L, Horvat
h G.Expression analysis of stage III serous ovarian adenocarcinoma distinguishe
s a sub-group of survivors. Eur J Cancer. 2006 Nov; 42(16):2846-54.[]
Overfull \hbox (144.78088pt too wide) in paragraph at lines 312--312
[] \T1/zi4/m/n/10 Title: Expression analysis of stage III serous ovarian aden
ocarcinoma distinguishes a sub-group of survivors.[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 348--348
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[7]
Underfull \vbox (badness 10000) has occurred while \output is active [8]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1335.78088pt too wide) in paragraph at lines 426--426
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tajima A, Komata D, Yamamot
o T, Kodama S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H,
Kudo Y, Inoue I, Tanaka K.Gene expression profiling of advanced-stage serous o
varian cancers distinguishes novel subclasses and implicates ZEB2 in tumor prog
ression and prognosis. Cancer Sci. 2009 Aug; 100(8):1421-8.[]
Overfull \hbox (393.78088pt too wide) in paragraph at lines 429--429
[] \T1/zi4/m/n/10 Title: Gene expression profiling of advanced-stage serous o
varian cancers distinguishes novel subclasses and implicates ZEB2 in tumor prog
ression and prognosis.[]
[9] [10] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (890.78088pt too wide) in paragraph at lines 518--518
[] \T1/zi4/m/n/10 Experimenter name: Crijns AP, Fehrmann RS, de Jong S, Gerbe
ns F, Meersma GJ, Klip HG, Hollema H, Hofstra RM, te Meerman GJ, de Vries EG, v
an der Zee AG.Survival-related profile, pathways, and transcription factors in
ovarian cancer. PLoS Med. 2009 Feb 3; 6(2):e24.[]
Overfull \hbox (38.78088pt too wide) in paragraph at lines 521--521
[] \T1/zi4/m/n/10 Title: Survival-related profile, pathways, and transcriptio
n factors in ovarian cancer.[]
[11] [12] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [13]
Overfull \hbox (657.78088pt too wide) in paragraph at lines 636--636
[] \T1/zi4/m/n/10 Experimenter name: Denkert C, Budczies J, Darb-Esfahani S,
Gy??rffy B et al. A prognostic gene expression index in ovarian cancer - valida
tion across different independent data sets. J Pathol 2009 Jun;218(2):273-80.[]
Overfull \hbox (157.78088pt too wide) in paragraph at lines 639--639
[] \T1/zi4/m/n/10 Title: A prognostic gene expression index in ovarian cancer
- validation across different independent data sets.[]
[14] [15] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (3.12666pt too wide) in paragraph at lines 749--750
[]\T1/ptm/m/n/10 Advanced-stage ovar-ian can-cer pa-tients are gen-er-ally trea
ted with platinum/taxane-based chemother-
[16]
Overfull \hbox (1327.78088pt too wide) in paragraph at lines 762--762
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tajima A, Yahata T, Kodama
S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H, Kudo Y, Kot
era K, Masuzaki H, Tashiro H, Katabuchi H, Inoue I, Tanaka K.Gene expression pr
ofile for predicting survival in advanced-stage serous ovarian cancer across tw
o independent datasets. PLoS One. 2010 Mar 12; 5(3):e9615.[]
Overfull \hbox (232.78088pt too wide) in paragraph at lines 765--765
[] \T1/zi4/m/n/10 Title: Gene expression profile for predicting survival in a
dvanced-stage serous ovarian cancer across two independent datasets.[]
[17]
Underfull \vbox (badness 10000) has occurred while \output is active [18]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1594.78088pt too wide) in paragraph at lines 900--900
[] \T1/zi4/m/n/10 Experimenter name: Mok SC, Bonome T, Vathipadiekal V, Bell
A, Johnson ME, Wong KK, Park DC, Hao K, Yip DK, Donninger H, Ozbun L, Samimi G,
Brady J, Randonovich M, Pise-Masison CA, Barrett JC, Wong WH, Welch WR, Berkow
itz RS, Birrer MJ.A gene signature predictive for outcome in advanced ovarian c
ancer identifies a survival factor: microfibril-associated glycoprotein 2. Canc
er Cell. 2009 Dec 8; 16(6):521-32.[]
Overfull \hbox (305.78088pt too wide) in paragraph at lines 903--903
[] \T1/zi4/m/n/10 Title: A gene signature predictive for outcome in advanced
ovarian cancer identifies a survival factor: microfibril-associated glycoprotei
n 2.[]
[19] [20] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [21]
Overfull \hbox (930.78088pt too wide) in paragraph at lines 1035--1035
[] \T1/zi4/m/n/10 Experimenter name: Konstantinopoulos PA, Spentzos D, Karlan
BY, Taniguchi T et al. Gene expression profile of BRCAness that correlates wit
h responsiveness to chemotherapy and with outcome in patients with epithelial o
varian cancer. J Clin Oncol 2010 Aug 1;28(22):3555-61.[]
Overfull \hbox (367.78088pt too wide) in paragraph at lines 1038--1038
[] \T1/zi4/m/n/10 Title: Gene expression profile of BRCAness that correlates
with responsiveness to chemotherapy and with outcome in patients with epithelia
l ovarian cancer.[]
[22] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [23]
Overfull \hbox (930.78088pt too wide) in paragraph at lines 1133--1133
[] \T1/zi4/m/n/10 Experimenter name: Konstantinopoulos PA, Spentzos D, Karlan
BY, Taniguchi T et al. Gene expression profile of BRCAness that correlates wit
h responsiveness to chemotherapy and with outcome in patients with epithelial o
varian cancer. J Clin Oncol 2010 Aug 1;28(22):3555-61.[]
Overfull \hbox (367.78088pt too wide) in paragraph at lines 1136--1136
[] \T1/zi4/m/n/10 Title: Gene expression profile of BRCAness that correlates
with responsiveness to chemotherapy and with outcome in patients with epithelia
l ovarian cancer.[]
[24] [25] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1522.78088pt too wide) in paragraph at lines 1231--1231
[] \T1/zi4/m/n/10 Experimenter name: Meyniel JP, Cottu PH, Decraene C, Stern
MH, Couturier J, Lebigot I, Nicolas A, Weber N, Fourchotte V, Alran S, Rapinat
A, Gentien D, Roman-Roman S, Mignot L, Sastre-Garau X.A genomic and transcripto
mic approach for a differential diagnosis between primary and secondary ovarian
carcinomas in patients with a previous history of breast cancer. BMC Cancer. 2
010 May 21; 10:222.[]
Overfull \hbox (468.78088pt too wide) in paragraph at lines 1234--1234
[] \T1/zi4/m/n/10 Title: A genomic and transcriptomic approach for a differen
tial diagnosis between primary and secondary ovarian carcinomas in patients wit
h a previous history of breast cancer.[]
[26] [27] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (108.78088pt too wide) in paragraph at lines 1339--1339
[] \T1/zi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[]
[28] [29] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [30]
Overfull \hbox (137.78088pt too wide) in paragraph at lines 1451--1451
[] \T1/zi4/m/n/10 Experimenter name: Mateescu B, Batista L, Mariani O, Meynie
l J, Cottu PH, Sastre-Garau X, Mechta-Grigoriou F[]
Overfull \hbox (90.78088pt too wide) in paragraph at lines 1454--1454
[] \T1/zi4/m/n/10 Title: miR-141 and miR-200a act on ovarian tumorigenesis by
controlling oxidative stress response.[]
[31]
Underfull \vbox (badness 10000) has occurred while \output is active [32]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (946.78088pt too wide) in paragraph at lines 1577--1577
[] \T1/zi4/m/n/10 Experimenter name: Bonome T, Levine DA, Shih J, Randonovich
M, Pise-Masison CA, Bogomolniy F, Ozbun L, Brady J, Barrett JC, Boyd J, Birrer
MJ: A Gene Signature Predicting for Survival in Suboptimally Debulked Patients
with Ovarian Cancer. Cancer Research 2008, 68:5478 -5486.[]
Overfull \hbox (109.78088pt too wide) in paragraph at lines 1580--1580
[] \T1/zi4/m/n/10 Title: A gene signature predicting for survival in suboptim
ally debulked patients with ovarian cancer.[]
[33] [34] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [35]
Overfull \hbox (746.78088pt too wide) in paragraph at lines 1720--1720
[] \T1/zi4/m/n/10 Experimenter name: Gillet JP, Calcagno AM, Varma S, Davidso
n B et al. Multidrug resistance-linked gene signature predicts overall survival
of patients with primary ovarian serous carcinoma. Clin Cancer Res 2012 Jun 1;
18(11):3197-206.[]
Overfull \hbox (228.78088pt too wide) in paragraph at lines 1723--1723
[] \T1/zi4/m/n/10 Title: Multidrug resistance-linked gene signature predicts
overall survival of patients with primary ovarian serous carcinoma.[]
[36] [37] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [38]
Overfull \hbox (96.78088pt too wide) in paragraph at lines 1842--1842
[] \T1/zi4/m/n/10 Experimenter name: Ferriss JS, Kim Y, Duska L, Birrer M, Le
vine DA, Moskaluk C,Theodorescu D, Lee JK[]
Overfull \hbox (311.78088pt too wide) in paragraph at lines 1845--1845
[] \T1/zi4/m/n/10 Title: Multi-gene expression predictors of single drug resp
onses to adjuvant chemotherapy in ovarian carcinoma: predicting platinum resist
ance.[]
[39]
Underfull \vbox (badness 10000) has occurred while \output is active [40]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [41]
Overfull \hbox (858.78088pt too wide) in paragraph at lines 1988--1988
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tsunoda T, Shigemizu D, Fuj
iwara H et al. High-risk ovarian cancer based on 126-gene expression signature
is uniquely characterized by downregulation of antigen presentation pathway. Cl
in Cancer Res 2012 Mar 1;18(5):1374-85.[]
Overfull \hbox (330.78088pt too wide) in paragraph at lines 1991--1991
[] \T1/zi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
[42]
Underfull \vbox (badness 10000) has occurred while \output is active [43]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (858.78088pt too wide) in paragraph at lines 2115--2115
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tsunoda T, Shigemizu D, Fuj
iwara H et al. High-risk ovarian cancer based on 126-gene expression signature
is uniquely characterized by downregulation of antigen presentation pathway. Cl
in Cancer Res 2012 Mar 1;18(5):1374-85.[]
Overfull \hbox (330.78088pt too wide) in paragraph at lines 2118--2118
[] \T1/zi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
[44] [45] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [46]
Overfull \hbox (75.78088pt too wide) in paragraph at lines 2245--2245
[] \T1/zi4/m/n/10 Title: COL11A1 promotes tumor progression and predicts poor
clinical outcome in ovarian cancer.[]
[47]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2281--2281
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[48] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (479.78088pt too wide) in paragraph at lines 2351--2351
[] \T1/zi4/m/n/10 Experimenter name: Pils D1, Hager G, Tong D, Aust S, Heinze
G, Kohl M, Schuster E, Wolf A, Sehouli J, Braicu I, Vergote I, Cadron I, Mahne
r S, Hofstetter G, Speiser P, Zeillinger R[]
Overfull \hbox (169.78088pt too wide) in paragraph at lines 2354--2354
[] \T1/zi4/m/n/10 Title: Validating the impact of a molecular subtype in ovar
ian cancer on outcomes: a study of the OVCAD Consortium.[]
[49] [50] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [51]
Overfull \hbox (153.78088pt too wide) in paragraph at lines 2478--2478
[] \T1/zi4/m/n/10 Experimenter name: Karlan BY, Dering J, Walsh C, Orsulic S,
Lester J, Anderson LA, Ginther CL, Fejzo M, Slamon D[]
Overfull \hbox (141.78088pt too wide) in paragraph at lines 2481--2481
[] \T1/zi4/m/n/10 Title: POSTN/TGFBI-associated stromal signature predicts po
or prognosis in serous epithelial ovarian cancer.[]
[52] [53] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Underfull \hbox (badness 1337) in paragraph at lines 2599--2599
[] \T1/ptm/m/it/10 Lysophos-pha-tidic acid-induced tran-scrip-tional pro-file r
ep-re-sents
[54]
Overfull \hbox (1036.78088pt too wide) in paragraph at lines 2617--2617
[] \T1/zi4/m/n/10 Experimenter name: Murph MM, Liu W, Yu S, Lu Y, Hall H, Hen
nessy BT, Lahad J, Schaner M, Helland A, Kristensen G, Brresen-Dale AL, Mills G
B. Lysophosphatidic acid-induced transcriptional profile represents serous epit
helial ovarian carcinoma and worsened prognosis. PLoS One. 2009; 4(5):e5583.[]
Overfull \hbox (255.78088pt too wide) in paragraph at lines 2620--2620
[] \T1/zi4/m/n/10 Title: Lysophosphatidic acid-induced transcriptional profil
e represents serous epithelial ovarian carcinoma and worsened prognosis.[]
[55] [56] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1001.78088pt too wide) in paragraph at lines 2725--2725
[] \T1/zi4/m/n/10 Experimenter name: Ouellet V, Provencher DM, Maugard CM, Le
Page C, Ren F, Lussier C, Novak J, Ge B, Hudson TJ, Tonin PN, Mes-Masson A-M:
Discrimination between serous low malignant potential and invasive epithelial o
varian tumors using molecular profiling. Oncogene 2005, 24:4672-4687.[]
[57] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [58]
Overfull \hbox (959.78088pt too wide) in paragraph at lines 2821--2821
[] \T1/zi4/m/n/10 Experimenter name: Marchini S, Mariani P, Chiorino G, Marra
zzo E, Bonomi R, Fruscio R, Clivio L, Garbi A, Torri V, Cinquini M, Dell\TS1/zi
4/m/n/10 '\T1/zi4/m/n/10 Anna T, Apolone G, Broggini M, D\TS1/zi4/m/n/10 '\T1/z
i4/m/n/10 Incalci M.Analysis of gene expression in early-stage ovarian cancer.
Clin Cancer Res. 2008 Dec 1; 14(23):7850-60.[]
[59] [60] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [61]
Overfull \hbox (1341.78088pt too wide) in paragraph at lines 2947--2947
[] \T1/zi4/m/n/10 Experimenter name: Tothill RW, Tinker AV, George J, Brown R
, Fox SB, Lade S, Johnson DS, Trivett MK, Etemadmoghadam D, Locandro B, Trafica
nte N, Fereday S, Hung JA, Chiew YE, Haviv I, Gertig D, DeFazio A, Bowtell DD.N
ovel molecular subtypes of serous and endometrioid ovarian cancer linked to cli
nical outcome. Clin Cancer Res. 2008 Aug 15; 14(16):5198-208.[]
Overfull \hbox (104.78088pt too wide) in paragraph at lines 2950--2950
[] \T1/zi4/m/n/10 Title: Novel molecular subtypes of serous and endometrioid
ovarian cancer linked to clinical outcome.[]
[62]
Underfull \vbox (badness 10000) has occurred while \output is active [63]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [64]
Overfull \hbox (1042.78088pt too wide) in paragraph at lines 3102--3102
[] \T1/zi4/m/n/10 Experimenter name: Berchuck A, Iversen ES, Lancaster JM, Pi
ttman J, Luo J, Lee P, Murphy S, Dressman HK, Febbo PG, West M, Nevins JR, Mark
s JR.Patterns of gene expression that characterize long-term survival in advanc
ed stage serous ovarian cancers. Clin Cancer Res. 2005 May 15; 11(10):3686-96.[
]
Overfull \hbox (163.78088pt too wide) in paragraph at lines 3105--3105
[] \T1/zi4/m/n/10 Title: Patterns of gene expression that characterize long-t
erm survival in advanced stage serous ovarian cancers.[]
[65]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 3143--3143
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[66] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1258.78088pt too wide) in paragraph at lines 3225--3225
[] \T1/zi4/m/n/10 Experimenter name: Dressman HK, Berchuck A, Chan G, Zhai J,
Bild A, Sayer R, Cragun J, Clarke J, Whitaker RS, Li L, Gray J, Marks J, Ginsb
urg GS, Potti A, West M, Nevins JR, Lancaster JM.An integrated genomic-based ap
proach to individualized treatment of patients with advanced-stage ovarian canc
er. J Clin Oncol. 2007 Feb 10; 25(5):517-25.[]
Overfull \hbox (194.78088pt too wide) in paragraph at lines 3228--3228
[] \T1/zi4/m/n/10 Title: An integrated genomic-based approach to individualiz
ed treatment of patients with advanced-stage ovarian cancer.[]
[67] [68] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [69]
Overfull \hbox (1274.78088pt too wide) in paragraph at lines 3353--3353
[] \T1/zi4/m/n/10 Experimenter name: Berchuck A, Iversen ES, Luo J, Clarke JP
, Horne H, Levine DA, Boyd J, Alonso MA, Secord AA, Bernardini MQ, Barnett JC,
Boren T, Murphy SK, Dressman HK, Marks JR, Lancaster JM.Microarray analysis of
early stage serous ovarian cancers shows profiles predictive of favorable outco
me. Clin Cancer Res. 2009 Apr 1; 15(7):2448-55.[]
Overfull \hbox (158.78088pt too wide) in paragraph at lines 3356--3356
[] \T1/zi4/m/n/10 Title: Microarray analysis of early stage serous ovarian ca
ncers shows profiles predictive of favorable outcome.[]
[70] [71] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [72]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3485--3485
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[73]
Underfull \vbox (badness 10000) has occurred while \output is active [74]
Underfull \vbox (badness 10000) has occurred while \output is active [75]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3661--3661
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[76] [77]
Underfull \vbox (badness 10000) has occurred while \output is active [78]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [79]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3834--3834
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[80]
Underfull \vbox (badness 10000) has occurred while \output is active [81]
Underfull \vbox (badness 10000) has occurred while \output is active [82]
(/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.ind
[83]
LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font) using `T1/zi4/m/n' instead on input line 37.
[84] [85])
(/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.aux)
Package rerunfilecheck Warning: File `Rd2.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
LaTeX Font Warning: Some font shapes were not available, defaults substituted.
)
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts
/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola
ta/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/inconsolata/In
consolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb
></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on Rd2.pdf (85 pages, 238323 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2015] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (92 entries accepted, 0 rejected).
Sorting entries....done (616 comparisons).
Generating output file Rd2.ind....done (146 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2016/02/01>
Babel <3.9q> and hyphenation patterns for 29 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.4-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.10, 2016/02/22 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 366.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 366.
) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.out)
(/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.toc
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (42.89548pt too wide) in paragraph at lines 94--97
[]\T1/ptm/m/n/10 For "pri-mary_therapy_outcome_success": com-pletere-sponse|par
tialresponse|progressivedisease|stabledisease:
Overfull \hbox (14.36601pt too wide) in paragraph at lines 115--117
[]\T1/ptm/m/n/10 For "site_of_tumor_first_recurrence": (metas-ta-sis / lo-core-
gional / none / lo-core-gional_plus_metastatic).
[3] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1142.78088pt too wide) in paragraph at lines 187--187
[] \T1/zi4/m/n/10 Experimenter name: Bentink S, Haibe-Kains B, Risch T, Fan J
-B, Hirsch MS, Holton K, Rubio R, April C, Chen J, Wickham-Garcia E, Liu J, Cul
hane A, Drapkin R, Quackenbush J, Matulonis UA: Angiogenic mRNA and microRNA ge
ne expression signature predicts a novel subtype of serous ovarian cancer. PLoS
ONE 2012, 7:e30269.[]
Overfull \hbox (157.78088pt too wide) in paragraph at lines 190--190
[] \T1/zi4/m/n/10 Title: Angiogenic mRNA and microRNA gene expression signatu
re predicts a novel subtype of serous ovarian cancer.[]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [4] [5]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [6]
Overfull \hbox (610.78088pt too wide) in paragraph at lines 309--309
[] \T1/zi4/m/n/10 Experimenter name: Partheen K, Levan K, Osterberg L, Horvat
h G.Expression analysis of stage III serous ovarian adenocarcinoma distinguishe
s a sub-group of survivors. Eur J Cancer. 2006 Nov; 42(16):2846-54.[]
Overfull \hbox (144.78088pt too wide) in paragraph at lines 312--312
[] \T1/zi4/m/n/10 Title: Expression analysis of stage III serous ovarian aden
ocarcinoma distinguishes a sub-group of survivors.[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 348--348
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[7]
Underfull \vbox (badness 10000) has occurred while \output is active [8]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1335.78088pt too wide) in paragraph at lines 426--426
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tajima A, Komata D, Yamamot
o T, Kodama S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H,
Kudo Y, Inoue I, Tanaka K.Gene expression profiling of advanced-stage serous o
varian cancers distinguishes novel subclasses and implicates ZEB2 in tumor prog
ression and prognosis. Cancer Sci. 2009 Aug; 100(8):1421-8.[]
Overfull \hbox (393.78088pt too wide) in paragraph at lines 429--429
[] \T1/zi4/m/n/10 Title: Gene expression profiling of advanced-stage serous o
varian cancers distinguishes novel subclasses and implicates ZEB2 in tumor prog
ression and prognosis.[]
[9] [10] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (890.78088pt too wide) in paragraph at lines 518--518
[] \T1/zi4/m/n/10 Experimenter name: Crijns AP, Fehrmann RS, de Jong S, Gerbe
ns F, Meersma GJ, Klip HG, Hollema H, Hofstra RM, te Meerman GJ, de Vries EG, v
an der Zee AG.Survival-related profile, pathways, and transcription factors in
ovarian cancer. PLoS Med. 2009 Feb 3; 6(2):e24.[]
Overfull \hbox (38.78088pt too wide) in paragraph at lines 521--521
[] \T1/zi4/m/n/10 Title: Survival-related profile, pathways, and transcriptio
n factors in ovarian cancer.[]
[11] [12] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [13]
Overfull \hbox (657.78088pt too wide) in paragraph at lines 636--636
[] \T1/zi4/m/n/10 Experimenter name: Denkert C, Budczies J, Darb-Esfahani S,
Gy??rffy B et al. A prognostic gene expression index in ovarian cancer - valida
tion across different independent data sets. J Pathol 2009 Jun;218(2):273-80.[]
Overfull \hbox (157.78088pt too wide) in paragraph at lines 639--639
[] \T1/zi4/m/n/10 Title: A prognostic gene expression index in ovarian cancer
- validation across different independent data sets.[]
[14] [15] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (3.12666pt too wide) in paragraph at lines 749--750
[]\T1/ptm/m/n/10 Advanced-stage ovar-ian can-cer pa-tients are gen-er-ally trea
ted with platinum/taxane-based chemother-
[16]
Overfull \hbox (1327.78088pt too wide) in paragraph at lines 762--762
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tajima A, Yahata T, Kodama
S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H, Kudo Y, Kot
era K, Masuzaki H, Tashiro H, Katabuchi H, Inoue I, Tanaka K.Gene expression pr
ofile for predicting survival in advanced-stage serous ovarian cancer across tw
o independent datasets. PLoS One. 2010 Mar 12; 5(3):e9615.[]
Overfull \hbox (232.78088pt too wide) in paragraph at lines 765--765
[] \T1/zi4/m/n/10 Title: Gene expression profile for predicting survival in a
dvanced-stage serous ovarian cancer across two independent datasets.[]
[17]
Underfull \vbox (badness 10000) has occurred while \output is active [18]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1594.78088pt too wide) in paragraph at lines 900--900
[] \T1/zi4/m/n/10 Experimenter name: Mok SC, Bonome T, Vathipadiekal V, Bell
A, Johnson ME, Wong KK, Park DC, Hao K, Yip DK, Donninger H, Ozbun L, Samimi G,
Brady J, Randonovich M, Pise-Masison CA, Barrett JC, Wong WH, Welch WR, Berkow
itz RS, Birrer MJ.A gene signature predictive for outcome in advanced ovarian c
ancer identifies a survival factor: microfibril-associated glycoprotein 2. Canc
er Cell. 2009 Dec 8; 16(6):521-32.[]
Overfull \hbox (305.78088pt too wide) in paragraph at lines 903--903
[] \T1/zi4/m/n/10 Title: A gene signature predictive for outcome in advanced
ovarian cancer identifies a survival factor: microfibril-associated glycoprotei
n 2.[]
[19] [20] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [21]
Overfull \hbox (930.78088pt too wide) in paragraph at lines 1035--1035
[] \T1/zi4/m/n/10 Experimenter name: Konstantinopoulos PA, Spentzos D, Karlan
BY, Taniguchi T et al. Gene expression profile of BRCAness that correlates wit
h responsiveness to chemotherapy and with outcome in patients with epithelial o
varian cancer. J Clin Oncol 2010 Aug 1;28(22):3555-61.[]
Overfull \hbox (367.78088pt too wide) in paragraph at lines 1038--1038
[] \T1/zi4/m/n/10 Title: Gene expression profile of BRCAness that correlates
with responsiveness to chemotherapy and with outcome in patients with epithelia
l ovarian cancer.[]
[22] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [23]
Overfull \hbox (930.78088pt too wide) in paragraph at lines 1133--1133
[] \T1/zi4/m/n/10 Experimenter name: Konstantinopoulos PA, Spentzos D, Karlan
BY, Taniguchi T et al. Gene expression profile of BRCAness that correlates wit
h responsiveness to chemotherapy and with outcome in patients with epithelial o
varian cancer. J Clin Oncol 2010 Aug 1;28(22):3555-61.[]
Overfull \hbox (367.78088pt too wide) in paragraph at lines 1136--1136
[] \T1/zi4/m/n/10 Title: Gene expression profile of BRCAness that correlates
with responsiveness to chemotherapy and with outcome in patients with epithelia
l ovarian cancer.[]
[24] [25] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1522.78088pt too wide) in paragraph at lines 1231--1231
[] \T1/zi4/m/n/10 Experimenter name: Meyniel JP, Cottu PH, Decraene C, Stern
MH, Couturier J, Lebigot I, Nicolas A, Weber N, Fourchotte V, Alran S, Rapinat
A, Gentien D, Roman-Roman S, Mignot L, Sastre-Garau X.A genomic and transcripto
mic approach for a differential diagnosis between primary and secondary ovarian
carcinomas in patients with a previous history of breast cancer. BMC Cancer. 2
010 May 21; 10:222.[]
Overfull \hbox (468.78088pt too wide) in paragraph at lines 1234--1234
[] \T1/zi4/m/n/10 Title: A genomic and transcriptomic approach for a differen
tial diagnosis between primary and secondary ovarian carcinomas in patients wit
h a previous history of breast cancer.[]
[26] [27] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (108.78088pt too wide) in paragraph at lines 1339--1339
[] \T1/zi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[]
[28] [29] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [30]
Overfull \hbox (137.78088pt too wide) in paragraph at lines 1451--1451
[] \T1/zi4/m/n/10 Experimenter name: Mateescu B, Batista L, Mariani O, Meynie
l J, Cottu PH, Sastre-Garau X, Mechta-Grigoriou F[]
Overfull \hbox (90.78088pt too wide) in paragraph at lines 1454--1454
[] \T1/zi4/m/n/10 Title: miR-141 and miR-200a act on ovarian tumorigenesis by
controlling oxidative stress response.[]
[31]
Underfull \vbox (badness 10000) has occurred while \output is active [32]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (946.78088pt too wide) in paragraph at lines 1577--1577
[] \T1/zi4/m/n/10 Experimenter name: Bonome T, Levine DA, Shih J, Randonovich
M, Pise-Masison CA, Bogomolniy F, Ozbun L, Brady J, Barrett JC, Boyd J, Birrer
MJ: A Gene Signature Predicting for Survival in Suboptimally Debulked Patients
with Ovarian Cancer. Cancer Research 2008, 68:5478 -5486.[]
Overfull \hbox (109.78088pt too wide) in paragraph at lines 1580--1580
[] \T1/zi4/m/n/10 Title: A gene signature predicting for survival in suboptim
ally debulked patients with ovarian cancer.[]
[33] [34] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [35]
Overfull \hbox (746.78088pt too wide) in paragraph at lines 1720--1720
[] \T1/zi4/m/n/10 Experimenter name: Gillet JP, Calcagno AM, Varma S, Davidso
n B et al. Multidrug resistance-linked gene signature predicts overall survival
of patients with primary ovarian serous carcinoma. Clin Cancer Res 2012 Jun 1;
18(11):3197-206.[]
Overfull \hbox (228.78088pt too wide) in paragraph at lines 1723--1723
[] \T1/zi4/m/n/10 Title: Multidrug resistance-linked gene signature predicts
overall survival of patients with primary ovarian serous carcinoma.[]
[36] [37] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [38]
Overfull \hbox (96.78088pt too wide) in paragraph at lines 1842--1842
[] \T1/zi4/m/n/10 Experimenter name: Ferriss JS, Kim Y, Duska L, Birrer M, Le
vine DA, Moskaluk C,Theodorescu D, Lee JK[]
Overfull \hbox (311.78088pt too wide) in paragraph at lines 1845--1845
[] \T1/zi4/m/n/10 Title: Multi-gene expression predictors of single drug resp
onses to adjuvant chemotherapy in ovarian carcinoma: predicting platinum resist
ance.[]
[39]
Underfull \vbox (badness 10000) has occurred while \output is active [40]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [41]
Overfull \hbox (858.78088pt too wide) in paragraph at lines 1988--1988
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tsunoda T, Shigemizu D, Fuj
iwara H et al. High-risk ovarian cancer based on 126-gene expression signature
is uniquely characterized by downregulation of antigen presentation pathway. Cl
in Cancer Res 2012 Mar 1;18(5):1374-85.[]
Overfull \hbox (330.78088pt too wide) in paragraph at lines 1991--1991
[] \T1/zi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
[42]
Underfull \vbox (badness 10000) has occurred while \output is active [43]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (858.78088pt too wide) in paragraph at lines 2115--2115
[] \T1/zi4/m/n/10 Experimenter name: Yoshihara K, Tsunoda T, Shigemizu D, Fuj
iwara H et al. High-risk ovarian cancer based on 126-gene expression signature
is uniquely characterized by downregulation of antigen presentation pathway. Cl
in Cancer Res 2012 Mar 1;18(5):1374-85.[]
Overfull \hbox (330.78088pt too wide) in paragraph at lines 2118--2118
[] \T1/zi4/m/n/10 Title: High-risk ovarian cancer based on 126-gene expressio
n signature is uniquely characterized by downregulation of antigen presentation
pathway.[]
[44] [45] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [46]
Overfull \hbox (75.78088pt too wide) in paragraph at lines 2245--2245
[] \T1/zi4/m/n/10 Title: COL11A1 promotes tumor progression and predicts poor
clinical outcome in ovarian cancer.[]
[47]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2281--2281
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[48] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (479.78088pt too wide) in paragraph at lines 2351--2351
[] \T1/zi4/m/n/10 Experimenter name: Pils D1, Hager G, Tong D, Aust S, Heinze
G, Kohl M, Schuster E, Wolf A, Sehouli J, Braicu I, Vergote I, Cadron I, Mahne
r S, Hofstetter G, Speiser P, Zeillinger R[]
Overfull \hbox (169.78088pt too wide) in paragraph at lines 2354--2354
[] \T1/zi4/m/n/10 Title: Validating the impact of a molecular subtype in ovar
ian cancer on outcomes: a study of the OVCAD Consortium.[]
[49] [50] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [51]
Overfull \hbox (153.78088pt too wide) in paragraph at lines 2478--2478
[] \T1/zi4/m/n/10 Experimenter name: Karlan BY, Dering J, Walsh C, Orsulic S,
Lester J, Anderson LA, Ginther CL, Fejzo M, Slamon D[]
Overfull \hbox (141.78088pt too wide) in paragraph at lines 2481--2481
[] \T1/zi4/m/n/10 Title: POSTN/TGFBI-associated stromal signature predicts po
or prognosis in serous epithelial ovarian cancer.[]
[52] [53] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Underfull \hbox (badness 1337) in paragraph at lines 2599--2599
[] \T1/ptm/m/it/10 Lysophos-pha-tidic acid-induced tran-scrip-tional pro-file r
ep-re-sents
[54]
Overfull \hbox (1036.78088pt too wide) in paragraph at lines 2617--2617
[] \T1/zi4/m/n/10 Experimenter name: Murph MM, Liu W, Yu S, Lu Y, Hall H, Hen
nessy BT, Lahad J, Schaner M, Helland A, Kristensen G, Brresen-Dale AL, Mills G
B. Lysophosphatidic acid-induced transcriptional profile represents serous epit
helial ovarian carcinoma and worsened prognosis. PLoS One. 2009; 4(5):e5583.[]
Overfull \hbox (255.78088pt too wide) in paragraph at lines 2620--2620
[] \T1/zi4/m/n/10 Title: Lysophosphatidic acid-induced transcriptional profil
e represents serous epithelial ovarian carcinoma and worsened prognosis.[]
[55] [56] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1001.78088pt too wide) in paragraph at lines 2725--2725
[] \T1/zi4/m/n/10 Experimenter name: Ouellet V, Provencher DM, Maugard CM, Le
Page C, Ren F, Lussier C, Novak J, Ge B, Hudson TJ, Tonin PN, Mes-Masson A-M:
Discrimination between serous low malignant potential and invasive epithelial o
varian tumors using molecular profiling. Oncogene 2005, 24:4672-4687.[]
[57] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [58]
Overfull \hbox (959.78088pt too wide) in paragraph at lines 2821--2821
[] \T1/zi4/m/n/10 Experimenter name: Marchini S, Mariani P, Chiorino G, Marra
zzo E, Bonomi R, Fruscio R, Clivio L, Garbi A, Torri V, Cinquini M, Dell\TS1/zi
4/m/n/10 '\T1/zi4/m/n/10 Anna T, Apolone G, Broggini M, D\TS1/zi4/m/n/10 '\T1/z
i4/m/n/10 Incalci M.Analysis of gene expression in early-stage ovarian cancer.
Clin Cancer Res. 2008 Dec 1; 14(23):7850-60.[]
[59] [60] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [61]
Overfull \hbox (1341.78088pt too wide) in paragraph at lines 2947--2947
[] \T1/zi4/m/n/10 Experimenter name: Tothill RW, Tinker AV, George J, Brown R
, Fox SB, Lade S, Johnson DS, Trivett MK, Etemadmoghadam D, Locandro B, Trafica
nte N, Fereday S, Hung JA, Chiew YE, Haviv I, Gertig D, DeFazio A, Bowtell DD.N
ovel molecular subtypes of serous and endometrioid ovarian cancer linked to cli
nical outcome. Clin Cancer Res. 2008 Aug 15; 14(16):5198-208.[]
Overfull \hbox (104.78088pt too wide) in paragraph at lines 2950--2950
[] \T1/zi4/m/n/10 Title: Novel molecular subtypes of serous and endometrioid
ovarian cancer linked to clinical outcome.[]
[62]
Underfull \vbox (badness 10000) has occurred while \output is active [63]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [64]
Overfull \hbox (1042.78088pt too wide) in paragraph at lines 3102--3102
[] \T1/zi4/m/n/10 Experimenter name: Berchuck A, Iversen ES, Lancaster JM, Pi
ttman J, Luo J, Lee P, Murphy S, Dressman HK, Febbo PG, West M, Nevins JR, Mark
s JR.Patterns of gene expression that characterize long-term survival in advanc
ed stage serous ovarian cancers. Clin Cancer Res. 2005 May 15; 11(10):3686-96.[
]
Overfull \hbox (163.78088pt too wide) in paragraph at lines 3105--3105
[] \T1/zi4/m/n/10 Title: Patterns of gene expression that characterize long-t
erm survival in advanced stage serous ovarian cancers.[]
[65]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 3143--3143
[]\T1/zi4/m/n/10 Binary overall survival summary (definitions of long and shor
t provided by study authors):[]
[66] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1258.78088pt too wide) in paragraph at lines 3225--3225
[] \T1/zi4/m/n/10 Experimenter name: Dressman HK, Berchuck A, Chan G, Zhai J,
Bild A, Sayer R, Cragun J, Clarke J, Whitaker RS, Li L, Gray J, Marks J, Ginsb
urg GS, Potti A, West M, Nevins JR, Lancaster JM.An integrated genomic-based ap
proach to individualized treatment of patients with advanced-stage ovarian canc
er. J Clin Oncol. 2007 Feb 10; 25(5):517-25.[]
Overfull \hbox (194.78088pt too wide) in paragraph at lines 3228--3228
[] \T1/zi4/m/n/10 Title: An integrated genomic-based approach to individualiz
ed treatment of patients with advanced-stage ovarian cancer.[]
[67] [68] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [69]
Overfull \hbox (1274.78088pt too wide) in paragraph at lines 3353--3353
[] \T1/zi4/m/n/10 Experimenter name: Berchuck A, Iversen ES, Luo J, Clarke JP
, Horne H, Levine DA, Boyd J, Alonso MA, Secord AA, Bernardini MQ, Barnett JC,
Boren T, Murphy SK, Dressman HK, Marks JR, Lancaster JM.Microarray analysis of
early stage serous ovarian cancers shows profiles predictive of favorable outco
me. Clin Cancer Res. 2009 Apr 1; 15(7):2448-55.[]
Overfull \hbox (158.78088pt too wide) in paragraph at lines 3356--3356
[] \T1/zi4/m/n/10 Title: Microarray analysis of early stage serous ovarian ca
ncers shows profiles predictive of favorable outcome.[]
[70] [71] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [72]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3485--3485
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[73]
Underfull \vbox (badness 10000) has occurred while \output is active [74]
Underfull \vbox (badness 10000) has occurred while \output is active [75]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3661--3661
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[76] [77]
Underfull \vbox (badness 10000) has occurred while \output is active [78]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [79]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3834--3834
[] \T1/zi4/m/n/10 Experimenter name: Integrated genomic analyses of ovarian c
arcinoma. Nature 2011, 474:609-615.[]
[80]
Underfull \vbox (badness 10000) has occurred while \output is active [81]
Underfull \vbox (badness 10000) has occurred while \output is active [82]
(/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.ind
[83]
LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font) using `T1/zi4/m/n' instead on input line 37.
[84] [85])
(/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/.Rd2pdf6142/Rd2.aux)
LaTeX Font Warning: Some font shapes were not available, defaults substituted.
)
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts
/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola
ta/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/inconsolata/In
consolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb
></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on Rd2.pdf (85 pages, 239225 bytes).
Transcript written on Rd2.log.
Saving output to ‘/tmp/RtmpxNq0Ik/Rbuild17fe43f25189/curatedOvarianData/build/curatedOvarianData.pdf’ ...
Done
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘curatedOvarianData_1.12.0.tar.gz’
