BioC 3.2: BUILD report for genefu on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data genefu
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* checking for file ‘genefu/DESCRIPTION’ ... OK
* preparing ‘genefu’:
* 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 ...

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\T1/ptm/m/n/10 Kains \T1/fi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/fi4/m/n/10 <markus.schroeder@ucdconnect.ie>  
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 []  \T1/fi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
rroni", "BH", "BY", "fdr"))[] 
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[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
omics Con-sor-tium us-ing Affymetrix hgu133plus2

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[]\T1/ptm/m/n/10 International Ge-nomics Con-sor-tium, [][]$\T1/fi4/m/n/10 http
 : / / www . intgen . org / research-[]services / biobanking-[]experience /
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
 11\T1/ptm/m/n/10 (2):R18 
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[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
 and probes in columns,

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[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
 named "En-trez-Gene.ID",
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 []\T1/fi4/m/n/10 "pam50", "ssp2006", "ssp2003", "intClust", "AIMS"), data, ann
ot, do.mapping = FALSE)[] 
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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE 
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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
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 []\T1/fi4/m/n/9 ovcCrijns.nkis <- ovcCrijns(data=data.nkis, annot=annot.nkis, 
gmap="entrezgene", do.mapping=TRUE)[] 
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 []\T1/fi4/m/n/9 ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap
="entrezgene", do.mapping=TRUE)[] 
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 []\T1/fi4/m/n/10 gmap = c("entrezgene", "ensembl_gene_id", "hgnc_symbol", "uni
gene", "refseq_mrna"),[] 

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[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the 
gene ex-pres-sions (see [][]\T1/fi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ). 
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 []\T1/fi4/m/n/9 tt <- data.frame(matrix(NA, nrow=3, ncol=3, dimnames=list(1:3,
 paste("column", 1:3, sep="."))),[] 
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[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][] 
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
 11\T1/ptm/m/n/10 (2):R18 
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
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[][][]\T1/fi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
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[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
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Saving output to ‘/private/tmp/RtmpJlI8BM/Rbuild8f4025df88e3/genefu/build/genefu.pdf’ ...
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* building ‘genefu_2.2.0.tar.gz’
BioC 3.2: BUILD report for genefu on oaxaca

Summary

Command output
