##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data curatedCRCData
###
##############################################################################
##############################################################################
* checking for file ‘curatedCRCData/DESCRIPTION’ ... OK
* preparing ‘curatedCRCData’:
* 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-3.5-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}]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (929.78088pt too wide) in paragraph at lines 91--91
[] \T1/zi4/m/n/10 Experimenter name: Auman JT, Church R, Lee SY, Watson MA, F
leshman JW, Mcleod HL.??Celecoxib pre-treatment in human colorectal adenocarcin
oma patients is associated with gene expression alterations suggestive of dimin
ished cellular proliferation.??Eur J Cancer??2008 Aug[]
[2]
Overfull \hbox (444.78088pt too wide) in paragraph at lines 94--94
[] \T1/zi4/m/n/10 Title: Celecoxib pre-treatment in human colorectal adenocar
cinoma patients is associated with gene expression alterations suggestive of di
minished cellular proliferation.[]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [3]
Underfull \vbox (badness 10000) has occurred while \output is active [4]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (541.78088pt too wide) in paragraph at lines 221--221
[] \T1/zi4/m/n/10 Experimenter name: Lips EH, van Eijk R, de Graaf EJ, Oostin
g J et al.??Integrating chromosomal aberrations and gene expression profiles to
dissect rectal tumorigenesis.BMC Cancer??2008 Oct 29[]
Overfull \hbox (121.78088pt too wide) in paragraph at lines 224--224
[] \T1/zi4/m/n/10 Title: Integrating chromosomal aberrations and gene express
ion profiles to dissect rectal tumorigenesis.[]
[5] [6] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [7]
Overfull \hbox (633.78088pt too wide) in paragraph at lines 336--336
[] \T1/zi4/m/n/10 Experimenter name: Staub E, Groene J, Heinze M, Mennerich D
et al.??An expression module of WIPF1-coexpressed genes identifies patients wi
th favorable prognosis in three tumor types.??J Mol Med (Berl)??2009 Jun[]
Overfull \hbox (202.78088pt too wide) in paragraph at lines 339--339
[] \T1/zi4/m/n/10 Title: An expression module of WIPF1-coexpressed genes iden
tifies patients with favorable prognosis in three tumor types.[]
[8]
Underfull \vbox (badness 10000) has occurred while \output is active [9]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (5.87547pt too wide) in paragraph at lines 487--488
\T1/ptm/m/n/10 stream ef-fects of dif-fer-en-tial gene ex-pres-sion.DNA mi-croa
r-ray data on 89 MSI and 140 microsatellite-
[10]
Overfull \hbox (714.78088pt too wide) in paragraph at lines 500--500
[] \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Lipton L, Gibbs P, Chapman
M et al.??DNA copy-number alterations underlie gene expression differences betw
een microsatellite stable and unstable colorectal cancers.??Clin Cancer Res??20
08 Dec 15[]
Overfull \hbox (268.78088pt too wide) in paragraph at lines 503--503
[] \T1/zi4/m/n/10 Title: DNA copy-number alterations underlie gene expression
differences between microsatellite stable and unstable colorectal cancers.[]
[11] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (5.87547pt too wide) in paragraph at lines 573--574
\T1/ptm/m/n/10 stream ef-fects of dif-fer-en-tial gene ex-pres-sion.DNA mi-croa
r-ray data on 89 MSI and 140 microsatellite-
[12]
Overfull \hbox (696.78088pt too wide) in paragraph at lines 586--586
[] \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Lipton L, Gibbs P, Chapman
M et al. DNA copy-number alterations underlie gene expression differences betwe
en microsatellite stable and unstable colorectal cancers. Clin Cancer Res 2008
Dec 15[]
Overfull \hbox (268.78088pt too wide) in paragraph at lines 589--589
[] \T1/zi4/m/n/10 Title: DNA copy-number alterations underlie gene expression
differences between microsatellite stable and unstable colorectal cancers.[]
[13] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [14]
Overfull \hbox (707.78088pt too wide) in paragraph at lines 672--672
[] \T1/zi4/m/n/10 Experimenter name: Watanabe T, Kobunai T, Yamamoto Y, Matsu
da K et al.??Gene expression signature and response to the use of leucovorin, f
luorouracil and oxaliplatin in colorectal cancer patients.??Clin Transl Oncol??
2011 Jun[]
Overfull \hbox (250.78088pt too wide) in paragraph at lines 675--675
[] \T1/zi4/m/n/10 Title: Gene expression signature and response to the use of
leucovorin, fluorouracil and oxaliplatin in colorectal cancer patients.[]
Underfull \vbox (badness 1881) has occurred while \output is active [15]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [16]
Overfull \hbox (701.78088pt too wide) in paragraph at lines 754--754
[] \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Gibbs P, Christie M, Prakas
h S et al.??Metastasis-Associated Gene Expression Changes Predict Poor Outcomes
in Patients with Dukes Stage B and C Colorectal Cancer.??Clin Cancer Res??2009
Dec 15[]
Overfull \hbox (245.78088pt too wide) in paragraph at lines 757--757
[] \T1/zi4/m/n/10 Title: Metastasis-Associated Gene Expression Changes Predic
t Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer.[]
[17]
Underfull \vbox (badness 10000) has occurred while \output is active [18]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (519.78088pt too wide) in paragraph at lines 892--892
[] \T1/zi4/m/n/10 Experimenter name: Reid JF, Gariboldi M, Sokolova V, Capobi
anco P et al.??Integrative approach for prioritizing cancer genes in sporadic c
olon cancer.??Genes Chromosomes Cancer??2009 Nov[]
Overfull \hbox (17.78088pt too wide) in paragraph at lines 895--895
[] \T1/zi4/m/n/10 Title: Integrative approach for prioritizing cancer genes i
n sporadic colon cancer.[]
[19] [20]
Underfull \vbox (badness 10000) has occurred while \output is active [21]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (641.78088pt too wide) in paragraph at lines 1038--1038
[] \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[]
[22]
Overfull \hbox (222.78088pt too wide) in paragraph at lines 1041--1041
[] \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[]
[23]
Underfull \vbox (badness 10000) has occurred while \output is active [24]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [25]
Overfull \hbox (641.78088pt too wide) in paragraph at lines 1202--1202
[] \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[]
Overfull \hbox (222.78088pt too wide) in paragraph at lines 1205--1205
[] \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[]
[26] [27]
Underfull \vbox (badness 10000) has occurred while \output is active [28]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (641.78088pt too wide) in paragraph at lines 1362--1362
[] \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[]
Overfull \hbox (222.78088pt too wide) in paragraph at lines 1365--1365
[] \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[]
[29] [30]
Underfull \vbox (badness 10000) has occurred while \output is active [31]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (601.78088pt too wide) in paragraph at lines 1518--1518
[] \T1/zi4/m/n/10 Experimenter name: Matsuyama T, Ishikawa T, Mogushi K, Yosh
ida T et al.??MUC12 mRNA expression is an independent marker of prognosis in st
age II and stage III colorectal cancer.??Int J Cancer??2010 Nov 15[]
Overfull \hbox (150.78088pt too wide) in paragraph at lines 1521--1521
[] \T1/zi4/m/n/10 Title: MUC12 mRNA expression is an independent marker of pr
ognosis in stage II and stage III colorectal cancer.[]
[32] [33] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (108.78088pt too wide) in paragraph at lines 1624--1624
[] \T1/zi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[]
[34] [35] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (8.67705pt too wide) in paragraph at lines 1741--1742
[]\T1/ptm/m/n/10 This study aimed to iden-tify a novel biomarker or a tar-get o
f treat-ment for col-orec-tal can-cer (CRC).The
[36]
Overfull \hbox (479.78088pt too wide) in paragraph at lines 1754--1754
[] \T1/zi4/m/n/10 Experimenter name: Tsukamoto S, Ishikawa T, Iida S, Ishigur
o M et al.??Clinical significance of osteoprotegerin expression in human colore
ctal cancer.??Clin Cancer Res2011 Apr 15[]
Overfull \hbox (33.78088pt too wide) in paragraph at lines 1757--1757
[] \T1/zi4/m/n/10 Title: Clinical significance of osteoprotegerin expression
in human colorectal cancer.[]
[37] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [38]
Overfull \hbox (742.78088pt too wide) in paragraph at lines 1856--1856
[] \T1/zi4/m/n/10 Experimenter name: Kogo R, Shimamura T, Mimori K, Kawahara
K et al.??Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modi
fication and is associated with poor prognosis in colorectal cancers.??Cancer R
es??2011 Oct 15[]
Overfull \hbox (320.78088pt too wide) in paragraph at lines 1859--1859
[] \T1/zi4/m/n/10 Title: Long noncoding RNA HOTAIR regulates polycomb-depende
nt chromatin modification and is associated with poor prognosis in colorectal c
ancers.[]
[39] [40] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [41]
Overfull \hbox (881.78088pt too wide) in paragraph at lines 1983--1983
[] \T1/zi4/m/n/10 Experimenter name: Sveen A,????esen TH,??Rognum TO,??Lothe
RA,??Skotheim RI. Transcriptome instability in colorectal cancer identified by
exon microarray analyses: Associations with splicing factor expression levels a
nd patient survival. Genome Med 2011 May 27[]
Overfull \hbox (428.78088pt too wide) in paragraph at lines 1986--1986
[] \T1/zi4/m/n/10 Title: Transcriptome instability in colorectal cancer ident
ified by exon microarray analyses: Associations with splicing factor expression
levels and patient survival.[]
[42] [43] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (845.78088pt too wide) in paragraph at lines 2106--2106
[] \T1/zi4/m/n/10 Experimenter name: Sveen A, Agesen TH, Nesbakken A, Rognum
TO et al.??Transcriptome instability in colorectal cancer identified by exon mi
croarray analyses: Associations with splicing factor expression levels and pati
ent survival.Genome Med??2011 May 27[]
[44]
Overfull \hbox (428.78088pt too wide) in paragraph at lines 2109--2109
[] \T1/zi4/m/n/10 Title: Transcriptome instability in colorectal cancer ident
ified by exon microarray analyses: Associations with splicing factor expression
levels and patient survival.[]
[45] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [46]
Overfull \hbox (731.78088pt too wide) in paragraph at lines 2229--2229
[] \T1/zi4/m/n/10 Experimenter name: Bandr??E,??Malumbres R,??Cubedo E,??Sola
J,??Garc??Foncillas J,??Labarga A. A gene signature of 8 genes could identify
the risk of recurrence and progression in Dukes\TS1/zi4/m/n/10 ' \T1/zi4/m/n/10
B colon cancer patients. Oncol Rep 2007 May[]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2230--2230
[] \T1/zi4/m/n/10 Laboratory: Bandr??E,??Malumbres R,??Cubedo E,??Sola J,??Ga
rc??Foncillas J,??Labarga A 2005[]
Overfull \hbox (207.78088pt too wide) in paragraph at lines 2232--2232
[] \T1/zi4/m/n/10 Title: A gene signature of 8 genes could identify the risk
of recurrence and progression in Dukes\TS1/zi4/m/n/10 ' \T1/zi4/m/n/10 B colon
cancer patients.[]
[47] [48] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [49]
Overfull \hbox (1051.78088pt too wide) in paragraph at lines 2371--2371
[] \T1/zi4/m/n/10 Experimenter name: Vilar E,??Gruber SB,??Rennert G,??Bartni
k CM,??Stenzel SL,??Iniesta MD,??Raskin L,Mukherjee B,??Ahn J,??Moreno V,??Morg
an MA. MRE11 deficiency increases sensitivity to poly(ADP-ribose) polymerase in
hibition in microsatellite unstable colorectal cancers. Cancer Res 2011 Apr 1[]
Overfull \hbox (269.78088pt too wide) in paragraph at lines 2374--2374
[] \T1/zi4/m/n/10 Title: MRE11 deficiency increases sensitivity to poly(ADP-r
ibose) polymerase inhibition in microsatellite unstable colorectal cancers.[]
[50] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [51]
Overfull \hbox (1051.78088pt too wide) in paragraph at lines 2465--2465
[] \T1/zi4/m/n/10 Experimenter name: Vilar E,??Gruber SB,??Rennert G,??Bartni
k CM,??Stenzel SL,??Iniesta MD,??Raskin L,Mukherjee B,??Ahn J,??Moreno V,??Morg
an MA. MRE11 deficiency increases sensitivity to poly(ADP-ribose) polymerase in
hibition in microsatellite unstable colorectal cancers. Cancer Res 2011 Apr 1[]
Overfull \hbox (269.78088pt too wide) in paragraph at lines 2468--2468
[] \T1/zi4/m/n/10 Title: MRE11 deficiency increases sensitivity to poly(ADP-r
ibose) polymerase inhibition in microsatellite unstable colorectal cancers.[]
[52] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [53]
Overfull \hbox (428.78088pt too wide) in paragraph at lines 2559--2559
[] \T1/zi4/m/n/10 Experimenter name: Birnbaum DJ, Laibe S, Ferrari A, Lagarde
A et al.??Expression Profiles in Stage II Colon Cancer According to APC Gene S
tatus.??Transl Oncol??2012 Apr[]
Overfull \hbox (5.78088pt too wide) in paragraph at lines 2562--2562
[] \T1/zi4/m/n/10 Title: Expression Profiles in Stage II Colon Cancer Accordi
ng to APC Gene Status.[]
[54]
Underfull \vbox (badness 10000) has occurred while \output is active [55]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (84.78088pt too wide) in paragraph at lines 2697--2697
[] \T1/zi4/m/n/10 Experimenter name: Bernal M,??Garc??Alcalde F,??Concha ????
Blanco A,??Garrido F,??Ruiz-Cabello F[]
Overfull \hbox (74.78088pt too wide) in paragraph at lines 2698--2698
[] \T1/zi4/m/n/10 Laboratory: Bernal M,??Garc??Alcalde F,??Concha ????Blanco
A,??Garrido F,??Ruiz-Cabello F 2011[]
Overfull \hbox (240.78088pt too wide) in paragraph at lines 2700--2700
[] \T1/zi4/m/n/10 Title: Genome-wide profiling characterizes CRCs with geneti
c instability and specific routes to HLA class I loss and immunoescape[]
[56] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [57]
Overfull \hbox (501.78088pt too wide) in paragraph at lines 2783--2783
[] \T1/zi4/m/n/10 Experimenter name: Tsuji S, Midorikawa Y, Takahashi T, Yagi
K et al.??Potential responders to FOLFOX therapy for colorectal cancer by Rand
om Forests analysis.??Br J Cancer??2012 Jan 3[]
Overfull \hbox (75.78088pt too wide) in paragraph at lines 2786--2786
[] \T1/zi4/m/n/10 Title: Potential responders to FOLFOX therapy for colorecta
l cancer by Random Forests analysis.[]
[58] [59] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [60]
Overfull \hbox (588.78088pt too wide) in paragraph at lines 2921--2921
[] \T1/zi4/m/n/10 Experimenter name: Bianchini M, Levy E, Zucchini C, Pinski
V et al.??Comparative study of gene expression by cDNA microarray in human colo
rectal cancer tissues and normal mucosa.??Int J Oncol??2006 Jul[]
Overfull \hbox (176.78088pt too wide) in paragraph at lines 2924--2924
[] \T1/zi4/m/n/10 Title: Comparative study of gene expression by cDNA microar
ray in human colorectal cancer tissues and normal mucosa.[]
[61] [62] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [63]
Overfull \hbox (682.78088pt too wide) in paragraph at lines 3047--3047
[] \T1/zi4/m/n/10 Experimenter name: de Sousa E Melo F, Colak S, Buikhuisen J
, Koster J et al.??Methylation of cancer-stem-cell-associated Wnt target genes
predicts poor prognosis in colorectal cancer patients.??Cell Stem Cell??2011 No
v 4[]
Overfull \hbox (83.78088pt too wide) in paragraph at lines 3050--3050
[] \T1/zi4/m/n/10 Title: Mutations in the Ras-Raf Axis underlie the prognosti
c value of CD133 in colorectal cancer.[]
[64] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [65]
Overfull \hbox (622.78088pt too wide) in paragraph at lines 3157--3157
[] \T1/zi4/m/n/10 Experimenter name: Marisa L, de Reyni??A, Duval A, Selves J
et al.??Gene expression classification of colon cancer into molecular subtypes
: characterization, validation, and prognostic value.??PLoS Med??2013[]
Overfull \hbox (248.78088pt too wide) in paragraph at lines 3160--3160
[] \T1/zi4/m/n/10 Title: Gene expression classification of colon cancer into
molecular subtypes: characterization, validation, and prognostic value.[]
[66] [67]
Underfull \vbox (badness 10000) has occurred while \output is active [68]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (383.78088pt too wide) in paragraph at lines 3311--3311
[] \T1/zi4/m/n/10 Experimenter name: Graudens E, Boulanger V, Mollard C, Mari
age-Samson R et al.??Deciphering cellular states of innate tumor drug responses
.??Genome Biol??2006[]
[69] [70]
Underfull \vbox (badness 10000) has occurred while \output is active [71]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (483.78088pt too wide) in paragraph at lines 3457--3457
[] \T1/zi4/m/n/10 Experimenter name: Laiho P, Kokko A, Vanharanta S, Salovaar
a R et al.??Serrated carcinomas form a subclass of colorectal cancer with disti
nct molecular basis.??Oncogene2007 Jan 11[]
Overfull \hbox (70.78088pt too wide) in paragraph at lines 3460--3460
[] \T1/zi4/m/n/10 Title: Serrated carcinomas form a subclass of colorectal ca
ncer with distinct molecular basis.[]
[72] [73] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [74]
Overfull \hbox (425.78088pt too wide) in paragraph at lines 3583--3583
[] \T1/zi4/m/n/10 Experimenter name: Watanabe T, Kobunai T, Sakamoto E, Yamam
oto Y et al.??Gene expression signature for recurrence in stage III colorectal
cancers.??Cancer??2009 Jan 15[]
Overfull \hbox (2.78088pt too wide) in paragraph at lines 3586--3586
[] \T1/zi4/m/n/10 Title: Gene expression signature for recurrence in stage II
I colorectal cancers.[]
[75] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [76]
Overfull \hbox (317.78088pt too wide) in paragraph at lines 3689--3689
[] \T1/zi4/m/n/10 Experimenter name: Profiling project of a panel of tubular
adenoma and serrated adenoma patient material collected in the Academic Medical
Center[]
Overfull \hbox (144.78088pt too wide) in paragraph at lines 3690--3690
[] \T1/zi4/m/n/10 Laboratory: Medema JP,??de Sousa E Melo F,??Vermeulen L,??J
ansen M,??Dekker E,??Van Noesel C,??Fessler E 2013[]
[77] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (189.78088pt too wide) in paragraph at lines 3767--3767
[] \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
of human colon and rectal cancer. Nature 2012, 487:330-337[]
Overfull \hbox (8.78088pt too wide) in paragraph at lines 3770--3770
[] \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[]
[78] [79]
Underfull \vbox (badness 10000) has occurred while \output is active [80]
Underfull \vbox (badness 10000) has occurred while \output is active [81]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [82]
Overfull \hbox (189.78088pt too wide) in paragraph at lines 4000--4000
[] \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
of human colon and rectal cancer. Nature 2012, 487:330-337[]
Overfull \hbox (8.78088pt too wide) in paragraph at lines 4003--4003
[] \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[]
[83] [84]
Underfull \vbox (badness 10000) has occurred while \output is active [85]
Underfull \vbox (badness 10000) has occurred while \output is active [86]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [87]
Overfull \hbox (189.78088pt too wide) in paragraph at lines 4249--4249
[] \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
of human colon and rectal cancer. Nature 2012, 487:330-337[]
Overfull \hbox (8.78088pt too wide) in paragraph at lines 4252--4252
[] \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[]
[88] [89]
Underfull \vbox (badness 10000) has occurred while \output is active [90]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (189.78088pt too wide) in paragraph at lines 4418--4418
[] \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
of human colon and rectal cancer. Nature 2012, 487:330-337[]
Overfull \hbox (8.78088pt too wide) in paragraph at lines 4421--4421
[] \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[]
[91] [92]
Underfull \vbox (badness 10000) has occurred while \output is active [93]
Underfull \vbox (badness 10000) has occurred while \output is active [94]
Underfull \vbox (badness 10000) has occurred while \output is active [95]
No file Rd2.ind.
[96] (/tmp/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/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 (96 pages, 228399 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-3.5-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/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/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/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/Rd2.out)
(/tmp/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/Rd2.toc [1{/var/l
ib/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (929.78088pt too wide) in paragraph at lines 91--91
[] \T1/zi4/m/n/10 Experimenter name: Auman JT, Church R, Lee SY, Watson MA, F
leshman JW, Mcleod HL.??Celecoxib pre-treatment in human colorectal adenocarcin
oma patients is associated with gene expression alterations suggestive of dimin
ished cellular proliferation.??Eur J Cancer??2008 Aug[]
Overfull \hbox (444.78088pt too wide) in paragraph at lines 94--94
[] \T1/zi4/m/n/10 Title: Celecoxib pre-treatment in human colorectal adenocar
cinoma patients is associated with gene expression alterations suggestive of di
minished cellular proliferation.[]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [3] [4]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [5]
Overfull \hbox (541.78088pt too wide) in paragraph at lines 221--221
[] \T1/zi4/m/n/10 Experimenter name: Lips EH, van Eijk R, de Graaf EJ, Oostin
g J et al.??Integrating chromosomal aberrations and gene expression profiles to
dissect rectal tumorigenesis.BMC Cancer??2008 Oct 29[]
Overfull \hbox (121.78088pt too wide) in paragraph at lines 224--224
[] \T1/zi4/m/n/10 Title: Integrating chromosomal aberrations and gene express
ion profiles to dissect rectal tumorigenesis.[]
[6] [7] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (633.78088pt too wide) in paragraph at lines 336--336
[] \T1/zi4/m/n/10 Experimenter name: Staub E, Groene J, Heinze M, Mennerich D
et al.??An expression module of WIPF1-coexpressed genes identifies patients wi
th favorable prognosis in three tumor types.??J Mol Med (Berl)??2009 Jun[]
Overfull \hbox (202.78088pt too wide) in paragraph at lines 339--339
[] \T1/zi4/m/n/10 Title: An expression module of WIPF1-coexpressed genes iden
tifies patients with favorable prognosis in three tumor types.[]
[8] [9]
Underfull \vbox (badness 10000) has occurred while \output is active [10]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (5.87547pt too wide) in paragraph at lines 487--488
\T1/ptm/m/n/10 stream ef-fects of dif-fer-en-tial gene ex-pres-sion.DNA mi-croa
r-ray data on 89 MSI and 140 microsatellite-
[11]
Overfull \hbox (714.78088pt too wide) in paragraph at lines 500--500
[] \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Lipton L, Gibbs P, Chapman
M et al.??DNA copy-number alterations underlie gene expression differences betw
een microsatellite stable and unstable colorectal cancers.??Clin Cancer Res??20
08 Dec 15[]
Overfull \hbox (268.78088pt too wide) in paragraph at lines 503--503
[] \T1/zi4/m/n/10 Title: DNA copy-number alterations underlie gene expression
differences between microsatellite stable and unstable colorectal cancers.[]
[12] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (5.87547pt too wide) in paragraph at lines 573--574
\T1/ptm/m/n/10 stream ef-fects of dif-fer-en-tial gene ex-pres-sion.DNA mi-croa
r-ray data on 89 MSI and 140 microsatellite-
Overfull \hbox (696.78088pt too wide) in paragraph at lines 586--586
[] \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Lipton L, Gibbs P, Chapman
M et al. DNA copy-number alterations underlie gene expression differences betwe
en microsatellite stable and unstable colorectal cancers. Clin Cancer Res 2008
Dec 15[]
[13]
Overfull \hbox (268.78088pt too wide) in paragraph at lines 589--589
[] \T1/zi4/m/n/10 Title: DNA copy-number alterations underlie gene expression
differences between microsatellite stable and unstable colorectal cancers.[]
[14] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (707.78088pt too wide) in paragraph at lines 672--672
[] \T1/zi4/m/n/10 Experimenter name: Watanabe T, Kobunai T, Yamamoto Y, Matsu
da K et al.??Gene expression signature and response to the use of leucovorin, f
luorouracil and oxaliplatin in colorectal cancer patients.??Clin Transl Oncol??
2011 Jun[]
Overfull \hbox (250.78088pt too wide) in paragraph at lines 675--675
[] \T1/zi4/m/n/10 Title: Gene expression signature and response to the use of
leucovorin, fluorouracil and oxaliplatin in colorectal cancer patients.[]
[15] [16] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (701.78088pt too wide) in paragraph at lines 754--754
[] \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Gibbs P, Christie M, Prakas
h S et al.??Metastasis-Associated Gene Expression Changes Predict Poor Outcomes
in Patients with Dukes Stage B and C Colorectal Cancer.??Clin Cancer Res??2009
Dec 15[]
Overfull \hbox (245.78088pt too wide) in paragraph at lines 757--757
[] \T1/zi4/m/n/10 Title: Metastasis-Associated Gene Expression Changes Predic
t Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer.[]
[17] [18] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [19]
Overfull \hbox (519.78088pt too wide) in paragraph at lines 892--892
[] \T1/zi4/m/n/10 Experimenter name: Reid JF, Gariboldi M, Sokolova V, Capobi
anco P et al.??Integrative approach for prioritizing cancer genes in sporadic c
olon cancer.??Genes Chromosomes Cancer??2009 Nov[]
Overfull \hbox (17.78088pt too wide) in paragraph at lines 895--895
[] \T1/zi4/m/n/10 Title: Integrative approach for prioritizing cancer genes i
n sporadic colon cancer.[]
[20] [21] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [22]
Overfull \hbox (641.78088pt too wide) in paragraph at lines 1038--1038
[] \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[]
Overfull \hbox (222.78088pt too wide) in paragraph at lines 1041--1041
[] \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[]
[23] [24]
Underfull \vbox (badness 10000) has occurred while \output is active [25]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [26]
Overfull \hbox (641.78088pt too wide) in paragraph at lines 1202--1202
[] \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[]
Overfull \hbox (222.78088pt too wide) in paragraph at lines 1205--1205
[] \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[]
[27]
Underfull \vbox (badness 10000) has occurred while \output is active [28]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [29]
Overfull \hbox (641.78088pt too wide) in paragraph at lines 1362--1362
[] \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[]
Overfull \hbox (222.78088pt too wide) in paragraph at lines 1365--1365
[] \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[]
[30] [31] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [32]
Overfull \hbox (601.78088pt too wide) in paragraph at lines 1518--1518
[] \T1/zi4/m/n/10 Experimenter name: Matsuyama T, Ishikawa T, Mogushi K, Yosh
ida T et al.??MUC12 mRNA expression is an independent marker of prognosis in st
age II and stage III colorectal cancer.??Int J Cancer??2010 Nov 15[]
Overfull \hbox (150.78088pt too wide) in paragraph at lines 1521--1521
[] \T1/zi4/m/n/10 Title: MUC12 mRNA expression is an independent marker of pr
ognosis in stage II and stage III colorectal cancer.[]
[33] [34] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (108.78088pt too wide) in paragraph at lines 1624--1624
[] \T1/zi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[]
[35] [36] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (8.67705pt too wide) in paragraph at lines 1741--1742
[]\T1/ptm/m/n/10 This study aimed to iden-tify a novel biomarker or a tar-get o
f treat-ment for col-orec-tal can-cer (CRC).The
Overfull \hbox (479.78088pt too wide) in paragraph at lines 1754--1754
[] \T1/zi4/m/n/10 Experimenter name: Tsukamoto S, Ishikawa T, Iida S, Ishigur
o M et al.??Clinical significance of osteoprotegerin expression in human colore
ctal cancer.??Clin Cancer Res2011 Apr 15[]
[37]
Overfull \hbox (33.78088pt too wide) in paragraph at lines 1757--1757
[] \T1/zi4/m/n/10 Title: Clinical significance of osteoprotegerin expression
in human colorectal cancer.[]
[38] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [39]
Overfull \hbox (742.78088pt too wide) in paragraph at lines 1856--1856
[] \T1/zi4/m/n/10 Experimenter name: Kogo R, Shimamura T, Mimori K, Kawahara
K et al.??Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modi
fication and is associated with poor prognosis in colorectal cancers.??Cancer R
es??2011 Oct 15[]
Overfull \hbox (320.78088pt too wide) in paragraph at lines 1859--1859
[] \T1/zi4/m/n/10 Title: Long noncoding RNA HOTAIR regulates polycomb-depende
nt chromatin modification and is associated with poor prognosis in colorectal c
ancers.[]
[40]
Underfull \vbox (badness 10000) has occurred while \output is active [41]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (881.78088pt too wide) in paragraph at lines 1983--1983
[] \T1/zi4/m/n/10 Experimenter name: Sveen A,????esen TH,??Rognum TO,??Lothe
RA,??Skotheim RI. Transcriptome instability in colorectal cancer identified by
exon microarray analyses: Associations with splicing factor expression levels a
nd patient survival. Genome Med 2011 May 27[]
Overfull \hbox (428.78088pt too wide) in paragraph at lines 1986--1986
[] \T1/zi4/m/n/10 Title: Transcriptome instability in colorectal cancer ident
ified by exon microarray analyses: Associations with splicing factor expression
levels and patient survival.[]
[42] [43] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [44]
Overfull \hbox (845.78088pt too wide) in paragraph at lines 2106--2106
[] \T1/zi4/m/n/10 Experimenter name: Sveen A, Agesen TH, Nesbakken A, Rognum
TO et al.??Transcriptome instability in colorectal cancer identified by exon mi
croarray analyses: Associations with splicing factor expression levels and pati
ent survival.Genome Med??2011 May 27[]
Overfull \hbox (428.78088pt too wide) in paragraph at lines 2109--2109
[] \T1/zi4/m/n/10 Title: Transcriptome instability in colorectal cancer ident
ified by exon microarray analyses: Associations with splicing factor expression
levels and patient survival.[]
[45] [46] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (731.78088pt too wide) in paragraph at lines 2229--2229
[] \T1/zi4/m/n/10 Experimenter name: Bandr??E,??Malumbres R,??Cubedo E,??Sola
J,??Garc??Foncillas J,??Labarga A. A gene signature of 8 genes could identify
the risk of recurrence and progression in Dukes\TS1/zi4/m/n/10 ' \T1/zi4/m/n/10
B colon cancer patients. Oncol Rep 2007 May[]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2230--2230
[] \T1/zi4/m/n/10 Laboratory: Bandr??E,??Malumbres R,??Cubedo E,??Sola J,??Ga
rc??Foncillas J,??Labarga A 2005[]
Overfull \hbox (207.78088pt too wide) in paragraph at lines 2232--2232
[] \T1/zi4/m/n/10 Title: A gene signature of 8 genes could identify the risk
of recurrence and progression in Dukes\TS1/zi4/m/n/10 ' \T1/zi4/m/n/10 B colon
cancer patients.[]
[47] [48]
Underfull \vbox (badness 10000) has occurred while \output is active [49]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1051.78088pt too wide) in paragraph at lines 2371--2371
[] \T1/zi4/m/n/10 Experimenter name: Vilar E,??Gruber SB,??Rennert G,??Bartni
k CM,??Stenzel SL,??Iniesta MD,??Raskin L,Mukherjee B,??Ahn J,??Moreno V,??Morg
an MA. MRE11 deficiency increases sensitivity to poly(ADP-ribose) polymerase in
hibition in microsatellite unstable colorectal cancers. Cancer Res 2011 Apr 1[]
Overfull \hbox (269.78088pt too wide) in paragraph at lines 2374--2374
[] \T1/zi4/m/n/10 Title: MRE11 deficiency increases sensitivity to poly(ADP-r
ibose) polymerase inhibition in microsatellite unstable colorectal cancers.[]
[50] [51] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1051.78088pt too wide) in paragraph at lines 2465--2465
[] \T1/zi4/m/n/10 Experimenter name: Vilar E,??Gruber SB,??Rennert G,??Bartni
k CM,??Stenzel SL,??Iniesta MD,??Raskin L,Mukherjee B,??Ahn J,??Moreno V,??Morg
an MA. MRE11 deficiency increases sensitivity to poly(ADP-ribose) polymerase in
hibition in microsatellite unstable colorectal cancers. Cancer Res 2011 Apr 1[]
Overfull \hbox (269.78088pt too wide) in paragraph at lines 2468--2468
[] \T1/zi4/m/n/10 Title: MRE11 deficiency increases sensitivity to poly(ADP-r
ibose) polymerase inhibition in microsatellite unstable colorectal cancers.[]
[52] [53] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (428.78088pt too wide) in paragraph at lines 2559--2559
[] \T1/zi4/m/n/10 Experimenter name: Birnbaum DJ, Laibe S, Ferrari A, Lagarde
A et al.??Expression Profiles in Stage II Colon Cancer According to APC Gene S
tatus.??Transl Oncol??2012 Apr[]
Overfull \hbox (5.78088pt too wide) in paragraph at lines 2562--2562
[] \T1/zi4/m/n/10 Title: Expression Profiles in Stage II Colon Cancer Accordi
ng to APC Gene Status.[]
[54] [55]
Underfull \vbox (badness 10000) has occurred while \output is active [56]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (84.78088pt too wide) in paragraph at lines 2697--2697
[] \T1/zi4/m/n/10 Experimenter name: Bernal M,??Garc??Alcalde F,??Concha ????
Blanco A,??Garrido F,??Ruiz-Cabello F[]
Overfull \hbox (74.78088pt too wide) in paragraph at lines 2698--2698
[] \T1/zi4/m/n/10 Laboratory: Bernal M,??Garc??Alcalde F,??Concha ????Blanco
A,??Garrido F,??Ruiz-Cabello F 2011[]
Overfull \hbox (240.78088pt too wide) in paragraph at lines 2700--2700
[] \T1/zi4/m/n/10 Title: Genome-wide profiling characterizes CRCs with geneti
c instability and specific routes to HLA class I loss and immunoescape[]
[57] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [58]
Overfull \hbox (501.78088pt too wide) in paragraph at lines 2783--2783
[] \T1/zi4/m/n/10 Experimenter name: Tsuji S, Midorikawa Y, Takahashi T, Yagi
K et al.??Potential responders to FOLFOX therapy for colorectal cancer by Rand
om Forests analysis.??Br J Cancer??2012 Jan 3[]
Overfull \hbox (75.78088pt too wide) in paragraph at lines 2786--2786
[] \T1/zi4/m/n/10 Title: Potential responders to FOLFOX therapy for colorecta
l cancer by Random Forests analysis.[]
[59]
Underfull \vbox (badness 10000) has occurred while \output is active [60]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (588.78088pt too wide) in paragraph at lines 2921--2921
[] \T1/zi4/m/n/10 Experimenter name: Bianchini M, Levy E, Zucchini C, Pinski
V et al.??Comparative study of gene expression by cDNA microarray in human colo
rectal cancer tissues and normal mucosa.??Int J Oncol??2006 Jul[]
[61]
Overfull \hbox (176.78088pt too wide) in paragraph at lines 2924--2924
[] \T1/zi4/m/n/10 Title: Comparative study of gene expression by cDNA microar
ray in human colorectal cancer tissues and normal mucosa.[]
[62] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [63]
Overfull \hbox (682.78088pt too wide) in paragraph at lines 3047--3047
[] \T1/zi4/m/n/10 Experimenter name: de Sousa E Melo F, Colak S, Buikhuisen J
, Koster J et al.??Methylation of cancer-stem-cell-associated Wnt target genes
predicts poor prognosis in colorectal cancer patients.??Cell Stem Cell??2011 No
v 4[]
Overfull \hbox (83.78088pt too wide) in paragraph at lines 3050--3050
[] \T1/zi4/m/n/10 Title: Mutations in the Ras-Raf Axis underlie the prognosti
c value of CD133 in colorectal cancer.[]
[64] [65] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [66]
Overfull \hbox (622.78088pt too wide) in paragraph at lines 3157--3157
[] \T1/zi4/m/n/10 Experimenter name: Marisa L, de Reyni??A, Duval A, Selves J
et al.??Gene expression classification of colon cancer into molecular subtypes
: characterization, validation, and prognostic value.??PLoS Med??2013[]
Overfull \hbox (248.78088pt too wide) in paragraph at lines 3160--3160
[] \T1/zi4/m/n/10 Title: Gene expression classification of colon cancer into
molecular subtypes: characterization, validation, and prognostic value.[]
[67]
Underfull \vbox (badness 10000) has occurred while \output is active [68]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [69]
Overfull \hbox (383.78088pt too wide) in paragraph at lines 3311--3311
[] \T1/zi4/m/n/10 Experimenter name: Graudens E, Boulanger V, Mollard C, Mari
age-Samson R et al.??Deciphering cellular states of innate tumor drug responses
.??Genome Biol??2006[]
[70] [71] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [72]
Overfull \hbox (483.78088pt too wide) in paragraph at lines 3457--3457
[] \T1/zi4/m/n/10 Experimenter name: Laiho P, Kokko A, Vanharanta S, Salovaar
a R et al.??Serrated carcinomas form a subclass of colorectal cancer with disti
nct molecular basis.??Oncogene2007 Jan 11[]
Overfull \hbox (70.78088pt too wide) in paragraph at lines 3460--3460
[] \T1/zi4/m/n/10 Title: Serrated carcinomas form a subclass of colorectal ca
ncer with distinct molecular basis.[]
[73]
Underfull \vbox (badness 10000) has occurred while \output is active [74]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (425.78088pt too wide) in paragraph at lines 3583--3583
[] \T1/zi4/m/n/10 Experimenter name: Watanabe T, Kobunai T, Sakamoto E, Yamam
oto Y et al.??Gene expression signature for recurrence in stage III colorectal
cancers.??Cancer??2009 Jan 15[]
Overfull \hbox (2.78088pt too wide) in paragraph at lines 3586--3586
[] \T1/zi4/m/n/10 Title: Gene expression signature for recurrence in stage II
I colorectal cancers.[]
[75] [76] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (317.78088pt too wide) in paragraph at lines 3689--3689
[] \T1/zi4/m/n/10 Experimenter name: Profiling project of a panel of tubular
adenoma and serrated adenoma patient material collected in the Academic Medical
Center[]
Overfull \hbox (144.78088pt too wide) in paragraph at lines 3690--3690
[] \T1/zi4/m/n/10 Laboratory: Medema JP,??de Sousa E Melo F,??Vermeulen L,??J
ansen M,??Dekker E,??Van Noesel C,??Fessler E 2013[]
[77] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [78]
Overfull \hbox (189.78088pt too wide) in paragraph at lines 3767--3767
[] \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
of human colon and rectal cancer. Nature 2012, 487:330-337[]
Overfull \hbox (8.78088pt too wide) in paragraph at lines 3770--3770
[] \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[]
[79] [80]
Underfull \vbox (badness 10000) has occurred while \output is active [81]
Underfull \vbox (badness 10000) has occurred while \output is active [82]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [83]
Overfull \hbox (189.78088pt too wide) in paragraph at lines 4000--4000
[] \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
of human colon and rectal cancer. Nature 2012, 487:330-337[]
Overfull \hbox (8.78088pt too wide) in paragraph at lines 4003--4003
[] \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[]
[84]
Underfull \vbox (badness 10000) has occurred while \output is active [85]
Underfull \vbox (badness 10000) has occurred while \output is active [86]
Underfull \vbox (badness 10000) has occurred while \output is active [87]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (189.78088pt too wide) in paragraph at lines 4249--4249
[] \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
of human colon and rectal cancer. Nature 2012, 487:330-337[]
[88]
Overfull \hbox (8.78088pt too wide) in paragraph at lines 4252--4252
[] \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[]
[89]
Underfull \vbox (badness 10000) has occurred while \output is active [90]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [91]
Overfull \hbox (189.78088pt too wide) in paragraph at lines 4418--4418
[] \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
of human colon and rectal cancer. Nature 2012, 487:330-337[]
Overfull \hbox (8.78088pt too wide) in paragraph at lines 4421--4421
[] \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[]
[92] [93]
Underfull \vbox (badness 10000) has occurred while \output is active [94]
Underfull \vbox (badness 10000) has occurred while \output is active [95]
No file Rd2.ind.
[96] (/tmp/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/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 (96 pages, 233842 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2015] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (104 entries accepted, 0 rejected).
Sorting entries....done (712 comparisons).
Generating output file Rd2.ind....done (156 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-3.5-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/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/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/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/Rd2.out)
(/tmp/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/Rd2.toc [1{/var/l
ib/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (929.78088pt too wide) in paragraph at lines 91--91
[] \T1/zi4/m/n/10 Experimenter name: Auman JT, Church R, Lee SY, Watson MA, F
leshman JW, Mcleod HL.??Celecoxib pre-treatment in human colorectal adenocarcin
oma patients is associated with gene expression alterations suggestive of dimin
ished cellular proliferation.??Eur J Cancer??2008 Aug[]
Overfull \hbox (444.78088pt too wide) in paragraph at lines 94--94
[] \T1/zi4/m/n/10 Title: Celecoxib pre-treatment in human colorectal adenocar
cinoma patients is associated with gene expression alterations suggestive of di
minished cellular proliferation.[]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [3] [4]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [5]
Overfull \hbox (541.78088pt too wide) in paragraph at lines 221--221
[] \T1/zi4/m/n/10 Experimenter name: Lips EH, van Eijk R, de Graaf EJ, Oostin
g J et al.??Integrating chromosomal aberrations and gene expression profiles to
dissect rectal tumorigenesis.BMC Cancer??2008 Oct 29[]
Overfull \hbox (121.78088pt too wide) in paragraph at lines 224--224
[] \T1/zi4/m/n/10 Title: Integrating chromosomal aberrations and gene express
ion profiles to dissect rectal tumorigenesis.[]
[6] [7] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (633.78088pt too wide) in paragraph at lines 336--336
[] \T1/zi4/m/n/10 Experimenter name: Staub E, Groene J, Heinze M, Mennerich D
et al.??An expression module of WIPF1-coexpressed genes identifies patients wi
th favorable prognosis in three tumor types.??J Mol Med (Berl)??2009 Jun[]
Overfull \hbox (202.78088pt too wide) in paragraph at lines 339--339
[] \T1/zi4/m/n/10 Title: An expression module of WIPF1-coexpressed genes iden
tifies patients with favorable prognosis in three tumor types.[]
[8] [9]
Underfull \vbox (badness 10000) has occurred while \output is active [10]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (5.87547pt too wide) in paragraph at lines 487--488
\T1/ptm/m/n/10 stream ef-fects of dif-fer-en-tial gene ex-pres-sion.DNA mi-croa
r-ray data on 89 MSI and 140 microsatellite-
[11]
Overfull \hbox (714.78088pt too wide) in paragraph at lines 500--500
[] \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Lipton L, Gibbs P, Chapman
M et al.??DNA copy-number alterations underlie gene expression differences betw
een microsatellite stable and unstable colorectal cancers.??Clin Cancer Res??20
08 Dec 15[]
Overfull \hbox (268.78088pt too wide) in paragraph at lines 503--503
[] \T1/zi4/m/n/10 Title: DNA copy-number alterations underlie gene expression
differences between microsatellite stable and unstable colorectal cancers.[]
[12] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (5.87547pt too wide) in paragraph at lines 573--574
\T1/ptm/m/n/10 stream ef-fects of dif-fer-en-tial gene ex-pres-sion.DNA mi-croa
r-ray data on 89 MSI and 140 microsatellite-
Overfull \hbox (696.78088pt too wide) in paragraph at lines 586--586
[] \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Lipton L, Gibbs P, Chapman
M et al. DNA copy-number alterations underlie gene expression differences betwe
en microsatellite stable and unstable colorectal cancers. Clin Cancer Res 2008
Dec 15[]
[13]
Overfull \hbox (268.78088pt too wide) in paragraph at lines 589--589
[] \T1/zi4/m/n/10 Title: DNA copy-number alterations underlie gene expression
differences between microsatellite stable and unstable colorectal cancers.[]
[14] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (707.78088pt too wide) in paragraph at lines 672--672
[] \T1/zi4/m/n/10 Experimenter name: Watanabe T, Kobunai T, Yamamoto Y, Matsu
da K et al.??Gene expression signature and response to the use of leucovorin, f
luorouracil and oxaliplatin in colorectal cancer patients.??Clin Transl Oncol??
2011 Jun[]
Overfull \hbox (250.78088pt too wide) in paragraph at lines 675--675
[] \T1/zi4/m/n/10 Title: Gene expression signature and response to the use of
leucovorin, fluorouracil and oxaliplatin in colorectal cancer patients.[]
[15] [16] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (701.78088pt too wide) in paragraph at lines 754--754
[] \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Gibbs P, Christie M, Prakas
h S et al.??Metastasis-Associated Gene Expression Changes Predict Poor Outcomes
in Patients with Dukes Stage B and C Colorectal Cancer.??Clin Cancer Res??2009
Dec 15[]
Overfull \hbox (245.78088pt too wide) in paragraph at lines 757--757
[] \T1/zi4/m/n/10 Title: Metastasis-Associated Gene Expression Changes Predic
t Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer.[]
[17] [18] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [19]
Overfull \hbox (519.78088pt too wide) in paragraph at lines 892--892
[] \T1/zi4/m/n/10 Experimenter name: Reid JF, Gariboldi M, Sokolova V, Capobi
anco P et al.??Integrative approach for prioritizing cancer genes in sporadic c
olon cancer.??Genes Chromosomes Cancer??2009 Nov[]
Overfull \hbox (17.78088pt too wide) in paragraph at lines 895--895
[] \T1/zi4/m/n/10 Title: Integrative approach for prioritizing cancer genes i
n sporadic colon cancer.[]
[20] [21] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [22]
Overfull \hbox (641.78088pt too wide) in paragraph at lines 1038--1038
[] \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[]
Overfull \hbox (222.78088pt too wide) in paragraph at lines 1041--1041
[] \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[]
[23] [24]
Underfull \vbox (badness 10000) has occurred while \output is active [25]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [26]
Overfull \hbox (641.78088pt too wide) in paragraph at lines 1202--1202
[] \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[]
Overfull \hbox (222.78088pt too wide) in paragraph at lines 1205--1205
[] \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[]
[27]
Underfull \vbox (badness 10000) has occurred while \output is active [28]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [29]
Overfull \hbox (641.78088pt too wide) in paragraph at lines 1362--1362
[] \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[]
Overfull \hbox (222.78088pt too wide) in paragraph at lines 1365--1365
[] \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[]
[30] [31] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [32]
Overfull \hbox (601.78088pt too wide) in paragraph at lines 1518--1518
[] \T1/zi4/m/n/10 Experimenter name: Matsuyama T, Ishikawa T, Mogushi K, Yosh
ida T et al.??MUC12 mRNA expression is an independent marker of prognosis in st
age II and stage III colorectal cancer.??Int J Cancer??2010 Nov 15[]
Overfull \hbox (150.78088pt too wide) in paragraph at lines 1521--1521
[] \T1/zi4/m/n/10 Title: MUC12 mRNA expression is an independent marker of pr
ognosis in stage II and stage III colorectal cancer.[]
[33] [34] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (108.78088pt too wide) in paragraph at lines 1624--1624
[] \T1/zi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[]
[35] [36] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (8.67705pt too wide) in paragraph at lines 1741--1742
[]\T1/ptm/m/n/10 This study aimed to iden-tify a novel biomarker or a tar-get o
f treat-ment for col-orec-tal can-cer (CRC).The
Overfull \hbox (479.78088pt too wide) in paragraph at lines 1754--1754
[] \T1/zi4/m/n/10 Experimenter name: Tsukamoto S, Ishikawa T, Iida S, Ishigur
o M et al.??Clinical significance of osteoprotegerin expression in human colore
ctal cancer.??Clin Cancer Res2011 Apr 15[]
[37]
Overfull \hbox (33.78088pt too wide) in paragraph at lines 1757--1757
[] \T1/zi4/m/n/10 Title: Clinical significance of osteoprotegerin expression
in human colorectal cancer.[]
[38] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [39]
Overfull \hbox (742.78088pt too wide) in paragraph at lines 1856--1856
[] \T1/zi4/m/n/10 Experimenter name: Kogo R, Shimamura T, Mimori K, Kawahara
K et al.??Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modi
fication and is associated with poor prognosis in colorectal cancers.??Cancer R
es??2011 Oct 15[]
Overfull \hbox (320.78088pt too wide) in paragraph at lines 1859--1859
[] \T1/zi4/m/n/10 Title: Long noncoding RNA HOTAIR regulates polycomb-depende
nt chromatin modification and is associated with poor prognosis in colorectal c
ancers.[]
[40]
Underfull \vbox (badness 10000) has occurred while \output is active [41]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (881.78088pt too wide) in paragraph at lines 1983--1983
[] \T1/zi4/m/n/10 Experimenter name: Sveen A,????esen TH,??Rognum TO,??Lothe
RA,??Skotheim RI. Transcriptome instability in colorectal cancer identified by
exon microarray analyses: Associations with splicing factor expression levels a
nd patient survival. Genome Med 2011 May 27[]
Overfull \hbox (428.78088pt too wide) in paragraph at lines 1986--1986
[] \T1/zi4/m/n/10 Title: Transcriptome instability in colorectal cancer ident
ified by exon microarray analyses: Associations with splicing factor expression
levels and patient survival.[]
[42] [43] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [44]
Overfull \hbox (845.78088pt too wide) in paragraph at lines 2106--2106
[] \T1/zi4/m/n/10 Experimenter name: Sveen A, Agesen TH, Nesbakken A, Rognum
TO et al.??Transcriptome instability in colorectal cancer identified by exon mi
croarray analyses: Associations with splicing factor expression levels and pati
ent survival.Genome Med??2011 May 27[]
Overfull \hbox (428.78088pt too wide) in paragraph at lines 2109--2109
[] \T1/zi4/m/n/10 Title: Transcriptome instability in colorectal cancer ident
ified by exon microarray analyses: Associations with splicing factor expression
levels and patient survival.[]
[45] [46] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (731.78088pt too wide) in paragraph at lines 2229--2229
[] \T1/zi4/m/n/10 Experimenter name: Bandr??E,??Malumbres R,??Cubedo E,??Sola
J,??Garc??Foncillas J,??Labarga A. A gene signature of 8 genes could identify
the risk of recurrence and progression in Dukes\TS1/zi4/m/n/10 ' \T1/zi4/m/n/10
B colon cancer patients. Oncol Rep 2007 May[]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2230--2230
[] \T1/zi4/m/n/10 Laboratory: Bandr??E,??Malumbres R,??Cubedo E,??Sola J,??Ga
rc??Foncillas J,??Labarga A 2005[]
Overfull \hbox (207.78088pt too wide) in paragraph at lines 2232--2232
[] \T1/zi4/m/n/10 Title: A gene signature of 8 genes could identify the risk
of recurrence and progression in Dukes\TS1/zi4/m/n/10 ' \T1/zi4/m/n/10 B colon
cancer patients.[]
[47] [48]
Underfull \vbox (badness 10000) has occurred while \output is active [49]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1051.78088pt too wide) in paragraph at lines 2371--2371
[] \T1/zi4/m/n/10 Experimenter name: Vilar E,??Gruber SB,??Rennert G,??Bartni
k CM,??Stenzel SL,??Iniesta MD,??Raskin L,Mukherjee B,??Ahn J,??Moreno V,??Morg
an MA. MRE11 deficiency increases sensitivity to poly(ADP-ribose) polymerase in
hibition in microsatellite unstable colorectal cancers. Cancer Res 2011 Apr 1[]
Overfull \hbox (269.78088pt too wide) in paragraph at lines 2374--2374
[] \T1/zi4/m/n/10 Title: MRE11 deficiency increases sensitivity to poly(ADP-r
ibose) polymerase inhibition in microsatellite unstable colorectal cancers.[]
[50] [51] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1051.78088pt too wide) in paragraph at lines 2465--2465
[] \T1/zi4/m/n/10 Experimenter name: Vilar E,??Gruber SB,??Rennert G,??Bartni
k CM,??Stenzel SL,??Iniesta MD,??Raskin L,Mukherjee B,??Ahn J,??Moreno V,??Morg
an MA. MRE11 deficiency increases sensitivity to poly(ADP-ribose) polymerase in
hibition in microsatellite unstable colorectal cancers. Cancer Res 2011 Apr 1[]
Overfull \hbox (269.78088pt too wide) in paragraph at lines 2468--2468
[] \T1/zi4/m/n/10 Title: MRE11 deficiency increases sensitivity to poly(ADP-r
ibose) polymerase inhibition in microsatellite unstable colorectal cancers.[]
[52] [53] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (428.78088pt too wide) in paragraph at lines 2559--2559
[] \T1/zi4/m/n/10 Experimenter name: Birnbaum DJ, Laibe S, Ferrari A, Lagarde
A et al.??Expression Profiles in Stage II Colon Cancer According to APC Gene S
tatus.??Transl Oncol??2012 Apr[]
Overfull \hbox (5.78088pt too wide) in paragraph at lines 2562--2562
[] \T1/zi4/m/n/10 Title: Expression Profiles in Stage II Colon Cancer Accordi
ng to APC Gene Status.[]
[54] [55]
Underfull \vbox (badness 10000) has occurred while \output is active [56]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (84.78088pt too wide) in paragraph at lines 2697--2697
[] \T1/zi4/m/n/10 Experimenter name: Bernal M,??Garc??Alcalde F,??Concha ????
Blanco A,??Garrido F,??Ruiz-Cabello F[]
Overfull \hbox (74.78088pt too wide) in paragraph at lines 2698--2698
[] \T1/zi4/m/n/10 Laboratory: Bernal M,??Garc??Alcalde F,??Concha ????Blanco
A,??Garrido F,??Ruiz-Cabello F 2011[]
Overfull \hbox (240.78088pt too wide) in paragraph at lines 2700--2700
[] \T1/zi4/m/n/10 Title: Genome-wide profiling characterizes CRCs with geneti
c instability and specific routes to HLA class I loss and immunoescape[]
[57] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [58]
Overfull \hbox (501.78088pt too wide) in paragraph at lines 2783--2783
[] \T1/zi4/m/n/10 Experimenter name: Tsuji S, Midorikawa Y, Takahashi T, Yagi
K et al.??Potential responders to FOLFOX therapy for colorectal cancer by Rand
om Forests analysis.??Br J Cancer??2012 Jan 3[]
Overfull \hbox (75.78088pt too wide) in paragraph at lines 2786--2786
[] \T1/zi4/m/n/10 Title: Potential responders to FOLFOX therapy for colorecta
l cancer by Random Forests analysis.[]
[59]
Underfull \vbox (badness 10000) has occurred while \output is active [60]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (588.78088pt too wide) in paragraph at lines 2921--2921
[] \T1/zi4/m/n/10 Experimenter name: Bianchini M, Levy E, Zucchini C, Pinski
V et al.??Comparative study of gene expression by cDNA microarray in human colo
rectal cancer tissues and normal mucosa.??Int J Oncol??2006 Jul[]
[61]
Overfull \hbox (176.78088pt too wide) in paragraph at lines 2924--2924
[] \T1/zi4/m/n/10 Title: Comparative study of gene expression by cDNA microar
ray in human colorectal cancer tissues and normal mucosa.[]
[62] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [63]
Overfull \hbox (682.78088pt too wide) in paragraph at lines 3047--3047
[] \T1/zi4/m/n/10 Experimenter name: de Sousa E Melo F, Colak S, Buikhuisen J
, Koster J et al.??Methylation of cancer-stem-cell-associated Wnt target genes
predicts poor prognosis in colorectal cancer patients.??Cell Stem Cell??2011 No
v 4[]
Overfull \hbox (83.78088pt too wide) in paragraph at lines 3050--3050
[] \T1/zi4/m/n/10 Title: Mutations in the Ras-Raf Axis underlie the prognosti
c value of CD133 in colorectal cancer.[]
[64] [65] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [66]
Overfull \hbox (622.78088pt too wide) in paragraph at lines 3157--3157
[] \T1/zi4/m/n/10 Experimenter name: Marisa L, de Reyni??A, Duval A, Selves J
et al.??Gene expression classification of colon cancer into molecular subtypes
: characterization, validation, and prognostic value.??PLoS Med??2013[]
Overfull \hbox (248.78088pt too wide) in paragraph at lines 3160--3160
[] \T1/zi4/m/n/10 Title: Gene expression classification of colon cancer into
molecular subtypes: characterization, validation, and prognostic value.[]
[67]
Underfull \vbox (badness 10000) has occurred while \output is active [68]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [69]
Overfull \hbox (383.78088pt too wide) in paragraph at lines 3311--3311
[] \T1/zi4/m/n/10 Experimenter name: Graudens E, Boulanger V, Mollard C, Mari
age-Samson R et al.??Deciphering cellular states of innate tumor drug responses
.??Genome Biol??2006[]
[70] [71] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [72]
Overfull \hbox (483.78088pt too wide) in paragraph at lines 3457--3457
[] \T1/zi4/m/n/10 Experimenter name: Laiho P, Kokko A, Vanharanta S, Salovaar
a R et al.??Serrated carcinomas form a subclass of colorectal cancer with disti
nct molecular basis.??Oncogene2007 Jan 11[]
Overfull \hbox (70.78088pt too wide) in paragraph at lines 3460--3460
[] \T1/zi4/m/n/10 Title: Serrated carcinomas form a subclass of colorectal ca
ncer with distinct molecular basis.[]
[73]
Underfull \vbox (badness 10000) has occurred while \output is active [74]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (425.78088pt too wide) in paragraph at lines 3583--3583
[] \T1/zi4/m/n/10 Experimenter name: Watanabe T, Kobunai T, Sakamoto E, Yamam
oto Y et al.??Gene expression signature for recurrence in stage III colorectal
cancers.??Cancer??2009 Jan 15[]
Overfull \hbox (2.78088pt too wide) in paragraph at lines 3586--3586
[] \T1/zi4/m/n/10 Title: Gene expression signature for recurrence in stage II
I colorectal cancers.[]
[75] [76] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (317.78088pt too wide) in paragraph at lines 3689--3689
[] \T1/zi4/m/n/10 Experimenter name: Profiling project of a panel of tubular
adenoma and serrated adenoma patient material collected in the Academic Medical
Center[]
Overfull \hbox (144.78088pt too wide) in paragraph at lines 3690--3690
[] \T1/zi4/m/n/10 Laboratory: Medema JP,??de Sousa E Melo F,??Vermeulen L,??J
ansen M,??Dekker E,??Van Noesel C,??Fessler E 2013[]
[77] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [78]
Overfull \hbox (189.78088pt too wide) in paragraph at lines 3767--3767
[] \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
of human colon and rectal cancer. Nature 2012, 487:330-337[]
Overfull \hbox (8.78088pt too wide) in paragraph at lines 3770--3770
[] \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[]
[79] [80]
Underfull \vbox (badness 10000) has occurred while \output is active [81]
Underfull \vbox (badness 10000) has occurred while \output is active [82]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [83]
Overfull \hbox (189.78088pt too wide) in paragraph at lines 4000--4000
[] \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
of human colon and rectal cancer. Nature 2012, 487:330-337[]
Overfull \hbox (8.78088pt too wide) in paragraph at lines 4003--4003
[] \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[]
[84]
Underfull \vbox (badness 10000) has occurred while \output is active [85]
Underfull \vbox (badness 10000) has occurred while \output is active [86]
Underfull \vbox (badness 10000) has occurred while \output is active [87]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (189.78088pt too wide) in paragraph at lines 4249--4249
[] \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
of human colon and rectal cancer. Nature 2012, 487:330-337[]
[88]
Overfull \hbox (8.78088pt too wide) in paragraph at lines 4252--4252
[] \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[]
[89]
Underfull \vbox (badness 10000) has occurred while \output is active [90]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [91]
Overfull \hbox (189.78088pt too wide) in paragraph at lines 4418--4418
[] \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
of human colon and rectal cancer. Nature 2012, 487:330-337[]
Overfull \hbox (8.78088pt too wide) in paragraph at lines 4421--4421
[] \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[]
[92] [93]
Underfull \vbox (badness 10000) has occurred while \output is active [94]
Underfull \vbox (badness 10000) has occurred while \output is active [95]
(/tmp/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/Rd2.ind [96]
LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font) using `T1/zi4/m/n' instead on input line 41.
[97] [98])
(/tmp/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/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 (98 pages, 247010 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2015] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (104 entries accepted, 0 rejected).
Sorting entries....done (712 comparisons).
Generating output file Rd2.ind....done (156 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-3.5-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/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/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/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/Rd2.out)
(/tmp/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/Rd2.toc [1{/var/l
ib/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (929.78088pt too wide) in paragraph at lines 91--91
[] \T1/zi4/m/n/10 Experimenter name: Auman JT, Church R, Lee SY, Watson MA, F
leshman JW, Mcleod HL.??Celecoxib pre-treatment in human colorectal adenocarcin
oma patients is associated with gene expression alterations suggestive of dimin
ished cellular proliferation.??Eur J Cancer??2008 Aug[]
Overfull \hbox (444.78088pt too wide) in paragraph at lines 94--94
[] \T1/zi4/m/n/10 Title: Celecoxib pre-treatment in human colorectal adenocar
cinoma patients is associated with gene expression alterations suggestive of di
minished cellular proliferation.[]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [3] [4]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [5]
Overfull \hbox (541.78088pt too wide) in paragraph at lines 221--221
[] \T1/zi4/m/n/10 Experimenter name: Lips EH, van Eijk R, de Graaf EJ, Oostin
g J et al.??Integrating chromosomal aberrations and gene expression profiles to
dissect rectal tumorigenesis.BMC Cancer??2008 Oct 29[]
Overfull \hbox (121.78088pt too wide) in paragraph at lines 224--224
[] \T1/zi4/m/n/10 Title: Integrating chromosomal aberrations and gene express
ion profiles to dissect rectal tumorigenesis.[]
[6] [7] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (633.78088pt too wide) in paragraph at lines 336--336
[] \T1/zi4/m/n/10 Experimenter name: Staub E, Groene J, Heinze M, Mennerich D
et al.??An expression module of WIPF1-coexpressed genes identifies patients wi
th favorable prognosis in three tumor types.??J Mol Med (Berl)??2009 Jun[]
Overfull \hbox (202.78088pt too wide) in paragraph at lines 339--339
[] \T1/zi4/m/n/10 Title: An expression module of WIPF1-coexpressed genes iden
tifies patients with favorable prognosis in three tumor types.[]
[8] [9]
Underfull \vbox (badness 10000) has occurred while \output is active [10]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (5.87547pt too wide) in paragraph at lines 487--488
\T1/ptm/m/n/10 stream ef-fects of dif-fer-en-tial gene ex-pres-sion.DNA mi-croa
r-ray data on 89 MSI and 140 microsatellite-
[11]
Overfull \hbox (714.78088pt too wide) in paragraph at lines 500--500
[] \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Lipton L, Gibbs P, Chapman
M et al.??DNA copy-number alterations underlie gene expression differences betw
een microsatellite stable and unstable colorectal cancers.??Clin Cancer Res??20
08 Dec 15[]
Overfull \hbox (268.78088pt too wide) in paragraph at lines 503--503
[] \T1/zi4/m/n/10 Title: DNA copy-number alterations underlie gene expression
differences between microsatellite stable and unstable colorectal cancers.[]
[12] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (5.87547pt too wide) in paragraph at lines 573--574
\T1/ptm/m/n/10 stream ef-fects of dif-fer-en-tial gene ex-pres-sion.DNA mi-croa
r-ray data on 89 MSI and 140 microsatellite-
[13]
Overfull \hbox (696.78088pt too wide) in paragraph at lines 586--586
[] \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Lipton L, Gibbs P, Chapman
M et al. DNA copy-number alterations underlie gene expression differences betwe
en microsatellite stable and unstable colorectal cancers. Clin Cancer Res 2008
Dec 15[]
Overfull \hbox (268.78088pt too wide) in paragraph at lines 589--589
[] \T1/zi4/m/n/10 Title: DNA copy-number alterations underlie gene expression
differences between microsatellite stable and unstable colorectal cancers.[]
[14] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (707.78088pt too wide) in paragraph at lines 672--672
[] \T1/zi4/m/n/10 Experimenter name: Watanabe T, Kobunai T, Yamamoto Y, Matsu
da K et al.??Gene expression signature and response to the use of leucovorin, f
luorouracil and oxaliplatin in colorectal cancer patients.??Clin Transl Oncol??
2011 Jun[]
Overfull \hbox (250.78088pt too wide) in paragraph at lines 675--675
[] \T1/zi4/m/n/10 Title: Gene expression signature and response to the use of
leucovorin, fluorouracil and oxaliplatin in colorectal cancer patients.[]
[15] [16] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (701.78088pt too wide) in paragraph at lines 754--754
[] \T1/zi4/m/n/10 Experimenter name: Jorissen RN, Gibbs P, Christie M, Prakas
h S et al.??Metastasis-Associated Gene Expression Changes Predict Poor Outcomes
in Patients with Dukes Stage B and C Colorectal Cancer.??Clin Cancer Res??2009
Dec 15[]
Overfull \hbox (245.78088pt too wide) in paragraph at lines 757--757
[] \T1/zi4/m/n/10 Title: Metastasis-Associated Gene Expression Changes Predic
t Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer.[]
[17] [18] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [19]
Overfull \hbox (519.78088pt too wide) in paragraph at lines 892--892
[] \T1/zi4/m/n/10 Experimenter name: Reid JF, Gariboldi M, Sokolova V, Capobi
anco P et al.??Integrative approach for prioritizing cancer genes in sporadic c
olon cancer.??Genes Chromosomes Cancer??2009 Nov[]
Overfull \hbox (17.78088pt too wide) in paragraph at lines 895--895
[] \T1/zi4/m/n/10 Title: Integrative approach for prioritizing cancer genes i
n sporadic colon cancer.[]
[20] [21] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [22]
Overfull \hbox (641.78088pt too wide) in paragraph at lines 1038--1038
[] \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[]
Overfull \hbox (222.78088pt too wide) in paragraph at lines 1041--1041
[] \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[]
[23] [24]
Underfull \vbox (badness 10000) has occurred while \output is active [25]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [26]
Overfull \hbox (641.78088pt too wide) in paragraph at lines 1202--1202
[] \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[]
Overfull \hbox (222.78088pt too wide) in paragraph at lines 1205--1205
[] \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[]
[27]
Underfull \vbox (badness 10000) has occurred while \output is active [28]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [29]
Overfull \hbox (641.78088pt too wide) in paragraph at lines 1362--1362
[] \T1/zi4/m/n/10 Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et
al.??Experimentally derived metastasis gene expression profile predicts recurr
ence and death in patients with colon cancer.??Gastroenterology??2010 Mar[]
Overfull \hbox (222.78088pt too wide) in paragraph at lines 1365--1365
[] \T1/zi4/m/n/10 Title: Experimentally derived metastasis gene expression pr
ofile predicts recurrence and death in patients with colon cancer.[]
[30] [31] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [32]
Overfull \hbox (601.78088pt too wide) in paragraph at lines 1518--1518
[] \T1/zi4/m/n/10 Experimenter name: Matsuyama T, Ishikawa T, Mogushi K, Yosh
ida T et al.??MUC12 mRNA expression is an independent marker of prognosis in st
age II and stage III colorectal cancer.??Int J Cancer??2010 Nov 15[]
Overfull \hbox (150.78088pt too wide) in paragraph at lines 1521--1521
[] \T1/zi4/m/n/10 Title: MUC12 mRNA expression is an independent marker of pr
ognosis in stage II and stage III colorectal cancer.[]
[33] [34] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (108.78088pt too wide) in paragraph at lines 1624--1624
[] \T1/zi4/m/n/10 Experimenter name: EXpression Project for Oncology, Interna
tional Genomics Consortium, www.intgen.org[]
[35] [36] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (8.67705pt too wide) in paragraph at lines 1741--1742
[]\T1/ptm/m/n/10 This study aimed to iden-tify a novel biomarker or a tar-get o
f treat-ment for col-orec-tal can-cer (CRC).The
Overfull \hbox (479.78088pt too wide) in paragraph at lines 1754--1754
[] \T1/zi4/m/n/10 Experimenter name: Tsukamoto S, Ishikawa T, Iida S, Ishigur
o M et al.??Clinical significance of osteoprotegerin expression in human colore
ctal cancer.??Clin Cancer Res2011 Apr 15[]
[37]
Overfull \hbox (33.78088pt too wide) in paragraph at lines 1757--1757
[] \T1/zi4/m/n/10 Title: Clinical significance of osteoprotegerin expression
in human colorectal cancer.[]
[38] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [39]
Overfull \hbox (742.78088pt too wide) in paragraph at lines 1856--1856
[] \T1/zi4/m/n/10 Experimenter name: Kogo R, Shimamura T, Mimori K, Kawahara
K et al.??Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modi
fication and is associated with poor prognosis in colorectal cancers.??Cancer R
es??2011 Oct 15[]
Overfull \hbox (320.78088pt too wide) in paragraph at lines 1859--1859
[] \T1/zi4/m/n/10 Title: Long noncoding RNA HOTAIR regulates polycomb-depende
nt chromatin modification and is associated with poor prognosis in colorectal c
ancers.[]
[40]
Underfull \vbox (badness 10000) has occurred while \output is active [41]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (881.78088pt too wide) in paragraph at lines 1983--1983
[] \T1/zi4/m/n/10 Experimenter name: Sveen A,????esen TH,??Rognum TO,??Lothe
RA,??Skotheim RI. Transcriptome instability in colorectal cancer identified by
exon microarray analyses: Associations with splicing factor expression levels a
nd patient survival. Genome Med 2011 May 27[]
Overfull \hbox (428.78088pt too wide) in paragraph at lines 1986--1986
[] \T1/zi4/m/n/10 Title: Transcriptome instability in colorectal cancer ident
ified by exon microarray analyses: Associations with splicing factor expression
levels and patient survival.[]
[42] [43] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [44]
Overfull \hbox (845.78088pt too wide) in paragraph at lines 2106--2106
[] \T1/zi4/m/n/10 Experimenter name: Sveen A, Agesen TH, Nesbakken A, Rognum
TO et al.??Transcriptome instability in colorectal cancer identified by exon mi
croarray analyses: Associations with splicing factor expression levels and pati
ent survival.Genome Med??2011 May 27[]
Overfull \hbox (428.78088pt too wide) in paragraph at lines 2109--2109
[] \T1/zi4/m/n/10 Title: Transcriptome instability in colorectal cancer ident
ified by exon microarray analyses: Associations with splicing factor expression
levels and patient survival.[]
[45] [46] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (731.78088pt too wide) in paragraph at lines 2229--2229
[] \T1/zi4/m/n/10 Experimenter name: Bandr??E,??Malumbres R,??Cubedo E,??Sola
J,??Garc??Foncillas J,??Labarga A. A gene signature of 8 genes could identify
the risk of recurrence and progression in Dukes\TS1/zi4/m/n/10 ' \T1/zi4/m/n/10
B colon cancer patients. Oncol Rep 2007 May[]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2230--2230
[] \T1/zi4/m/n/10 Laboratory: Bandr??E,??Malumbres R,??Cubedo E,??Sola J,??Ga
rc??Foncillas J,??Labarga A 2005[]
Overfull \hbox (207.78088pt too wide) in paragraph at lines 2232--2232
[] \T1/zi4/m/n/10 Title: A gene signature of 8 genes could identify the risk
of recurrence and progression in Dukes\TS1/zi4/m/n/10 ' \T1/zi4/m/n/10 B colon
cancer patients.[]
[47] [48]
Underfull \vbox (badness 10000) has occurred while \output is active [49]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1051.78088pt too wide) in paragraph at lines 2371--2371
[] \T1/zi4/m/n/10 Experimenter name: Vilar E,??Gruber SB,??Rennert G,??Bartni
k CM,??Stenzel SL,??Iniesta MD,??Raskin L,Mukherjee B,??Ahn J,??Moreno V,??Morg
an MA. MRE11 deficiency increases sensitivity to poly(ADP-ribose) polymerase in
hibition in microsatellite unstable colorectal cancers. Cancer Res 2011 Apr 1[]
Overfull \hbox (269.78088pt too wide) in paragraph at lines 2374--2374
[] \T1/zi4/m/n/10 Title: MRE11 deficiency increases sensitivity to poly(ADP-r
ibose) polymerase inhibition in microsatellite unstable colorectal cancers.[]
[50] [51] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1051.78088pt too wide) in paragraph at lines 2465--2465
[] \T1/zi4/m/n/10 Experimenter name: Vilar E,??Gruber SB,??Rennert G,??Bartni
k CM,??Stenzel SL,??Iniesta MD,??Raskin L,Mukherjee B,??Ahn J,??Moreno V,??Morg
an MA. MRE11 deficiency increases sensitivity to poly(ADP-ribose) polymerase in
hibition in microsatellite unstable colorectal cancers. Cancer Res 2011 Apr 1[]
Overfull \hbox (269.78088pt too wide) in paragraph at lines 2468--2468
[] \T1/zi4/m/n/10 Title: MRE11 deficiency increases sensitivity to poly(ADP-r
ibose) polymerase inhibition in microsatellite unstable colorectal cancers.[]
[52] [53] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (428.78088pt too wide) in paragraph at lines 2559--2559
[] \T1/zi4/m/n/10 Experimenter name: Birnbaum DJ, Laibe S, Ferrari A, Lagarde
A et al.??Expression Profiles in Stage II Colon Cancer According to APC Gene S
tatus.??Transl Oncol??2012 Apr[]
Overfull \hbox (5.78088pt too wide) in paragraph at lines 2562--2562
[] \T1/zi4/m/n/10 Title: Expression Profiles in Stage II Colon Cancer Accordi
ng to APC Gene Status.[]
[54] [55]
Underfull \vbox (badness 10000) has occurred while \output is active [56]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (84.78088pt too wide) in paragraph at lines 2697--2697
[] \T1/zi4/m/n/10 Experimenter name: Bernal M,??Garc??Alcalde F,??Concha ????
Blanco A,??Garrido F,??Ruiz-Cabello F[]
Overfull \hbox (74.78088pt too wide) in paragraph at lines 2698--2698
[] \T1/zi4/m/n/10 Laboratory: Bernal M,??Garc??Alcalde F,??Concha ????Blanco
A,??Garrido F,??Ruiz-Cabello F 2011[]
Overfull \hbox (240.78088pt too wide) in paragraph at lines 2700--2700
[] \T1/zi4/m/n/10 Title: Genome-wide profiling characterizes CRCs with geneti
c instability and specific routes to HLA class I loss and immunoescape[]
[57] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [58]
Overfull \hbox (501.78088pt too wide) in paragraph at lines 2783--2783
[] \T1/zi4/m/n/10 Experimenter name: Tsuji S, Midorikawa Y, Takahashi T, Yagi
K et al.??Potential responders to FOLFOX therapy for colorectal cancer by Rand
om Forests analysis.??Br J Cancer??2012 Jan 3[]
Overfull \hbox (75.78088pt too wide) in paragraph at lines 2786--2786
[] \T1/zi4/m/n/10 Title: Potential responders to FOLFOX therapy for colorecta
l cancer by Random Forests analysis.[]
[59]
Underfull \vbox (badness 10000) has occurred while \output is active [60]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (588.78088pt too wide) in paragraph at lines 2921--2921
[] \T1/zi4/m/n/10 Experimenter name: Bianchini M, Levy E, Zucchini C, Pinski
V et al.??Comparative study of gene expression by cDNA microarray in human colo
rectal cancer tissues and normal mucosa.??Int J Oncol??2006 Jul[]
[61]
Overfull \hbox (176.78088pt too wide) in paragraph at lines 2924--2924
[] \T1/zi4/m/n/10 Title: Comparative study of gene expression by cDNA microar
ray in human colorectal cancer tissues and normal mucosa.[]
[62] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [63]
Overfull \hbox (682.78088pt too wide) in paragraph at lines 3047--3047
[] \T1/zi4/m/n/10 Experimenter name: de Sousa E Melo F, Colak S, Buikhuisen J
, Koster J et al.??Methylation of cancer-stem-cell-associated Wnt target genes
predicts poor prognosis in colorectal cancer patients.??Cell Stem Cell??2011 No
v 4[]
Overfull \hbox (83.78088pt too wide) in paragraph at lines 3050--3050
[] \T1/zi4/m/n/10 Title: Mutations in the Ras-Raf Axis underlie the prognosti
c value of CD133 in colorectal cancer.[]
[64] [65] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [66]
Overfull \hbox (622.78088pt too wide) in paragraph at lines 3157--3157
[] \T1/zi4/m/n/10 Experimenter name: Marisa L, de Reyni??A, Duval A, Selves J
et al.??Gene expression classification of colon cancer into molecular subtypes
: characterization, validation, and prognostic value.??PLoS Med??2013[]
Overfull \hbox (248.78088pt too wide) in paragraph at lines 3160--3160
[] \T1/zi4/m/n/10 Title: Gene expression classification of colon cancer into
molecular subtypes: characterization, validation, and prognostic value.[]
[67]
Underfull \vbox (badness 10000) has occurred while \output is active [68]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [69]
Overfull \hbox (383.78088pt too wide) in paragraph at lines 3311--3311
[] \T1/zi4/m/n/10 Experimenter name: Graudens E, Boulanger V, Mollard C, Mari
age-Samson R et al.??Deciphering cellular states of innate tumor drug responses
.??Genome Biol??2006[]
[70] [71] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [72]
Overfull \hbox (483.78088pt too wide) in paragraph at lines 3457--3457
[] \T1/zi4/m/n/10 Experimenter name: Laiho P, Kokko A, Vanharanta S, Salovaar
a R et al.??Serrated carcinomas form a subclass of colorectal cancer with disti
nct molecular basis.??Oncogene2007 Jan 11[]
Overfull \hbox (70.78088pt too wide) in paragraph at lines 3460--3460
[] \T1/zi4/m/n/10 Title: Serrated carcinomas form a subclass of colorectal ca
ncer with distinct molecular basis.[]
[73]
Underfull \vbox (badness 10000) has occurred while \output is active [74]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (425.78088pt too wide) in paragraph at lines 3583--3583
[] \T1/zi4/m/n/10 Experimenter name: Watanabe T, Kobunai T, Sakamoto E, Yamam
oto Y et al.??Gene expression signature for recurrence in stage III colorectal
cancers.??Cancer??2009 Jan 15[]
Overfull \hbox (2.78088pt too wide) in paragraph at lines 3586--3586
[] \T1/zi4/m/n/10 Title: Gene expression signature for recurrence in stage II
I colorectal cancers.[]
[75] [76] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (317.78088pt too wide) in paragraph at lines 3689--3689
[] \T1/zi4/m/n/10 Experimenter name: Profiling project of a panel of tubular
adenoma and serrated adenoma patient material collected in the Academic Medical
Center[]
Overfull \hbox (144.78088pt too wide) in paragraph at lines 3690--3690
[] \T1/zi4/m/n/10 Laboratory: Medema JP,??de Sousa E Melo F,??Vermeulen L,??J
ansen M,??Dekker E,??Van Noesel C,??Fessler E 2013[]
[77] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [78]
Overfull \hbox (189.78088pt too wide) in paragraph at lines 3767--3767
[] \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
of human colon and rectal cancer. Nature 2012, 487:330-337[]
Overfull \hbox (8.78088pt too wide) in paragraph at lines 3770--3770
[] \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[]
[79] [80]
Underfull \vbox (badness 10000) has occurred while \output is active [81]
Underfull \vbox (badness 10000) has occurred while \output is active [82]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [83]
Overfull \hbox (189.78088pt too wide) in paragraph at lines 4000--4000
[] \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
of human colon and rectal cancer. Nature 2012, 487:330-337[]
Overfull \hbox (8.78088pt too wide) in paragraph at lines 4003--4003
[] \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[]
[84]
Underfull \vbox (badness 10000) has occurred while \output is active [85]
Underfull \vbox (badness 10000) has occurred while \output is active [86]
Underfull \vbox (badness 10000) has occurred while \output is active [87]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (189.78088pt too wide) in paragraph at lines 4249--4249
[] \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
of human colon and rectal cancer. Nature 2012, 487:330-337[]
[88]
Overfull \hbox (8.78088pt too wide) in paragraph at lines 4252--4252
[] \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[]
[89]
Underfull \vbox (badness 10000) has occurred while \output is active [90]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [91]
Overfull \hbox (189.78088pt too wide) in paragraph at lines 4418--4418
[] \T1/zi4/m/n/10 Experimenter name: Comprehensive molecular characterization
of human colon and rectal cancer. Nature 2012, 487:330-337[]
Overfull \hbox (8.78088pt too wide) in paragraph at lines 4421--4421
[] \T1/zi4/m/n/10 Title: Comprehensive molecular characterization of human co
lon and rectal cancer.[]
[92] [93]
Underfull \vbox (badness 10000) has occurred while \output is active [94]
Underfull \vbox (badness 10000) has occurred while \output is active [95]
(/tmp/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/Rd2.ind [96]
LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font) using `T1/zi4/m/n' instead on input line 41.
[97] [98])
(/tmp/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/.Rd2pdf2706/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 (98 pages, 247330 bytes).
Transcript written on Rd2.log.
Saving output to ‘/tmp/RtmpEqwac6/Rbuilda922b2dca88/curatedCRCData/build/curatedCRCData.pdf’ ...
Done
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘curatedCRCData_2.8.0.tar.gz’
