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BioC 2.12: BUILD report for genefu on petty

This page was generated on 2013-10-09 09:39:58 -0700 (Wed, 09 Oct 2013).

Package 253/671HostnameOS / ArchBUILDCHECKBUILD BIN
genefu 1.10.0
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/genefu
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64 [ OK ] OK  OK 

Summary

Package: genefu
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data genefu
StartedAt: 2013-10-08 20:45:44 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 20:46:50 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 66.5 seconds
RetCode: 0
Status:  OK 
PackageFile: genefu_1.10.0.tar.gz
PackageFileSize: 4.441 MiB

Command output

* 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 ...

This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012)
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entering extended mode
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LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2012-05-30, ngerman-x-2012-05-30, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h
ungarian, icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, ma
rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, 
kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk,
 polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s
lovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, 
welsh, loaded.
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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/fi4/m/n/10 fuzzy.ttest(x, w1, w2, alternative=c("two.sided", "less", "gr
eater"), check.w = TRUE, na.rm = FALSE)[] 

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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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[][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
[]$http : / / www . nicebread . de / blog / files / fc02e1635792cb0f2b3cbd1f7e6
c580b-[]10 .

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 []\T1/fi4/m/n/9 randst <- apply(rands, 1, function(x, xx, ww1, ww2) { return(f
uzzy.ttest(x=xx, w1=ww1[x], w2=ww2[x])[2]) }, xx=xx, ww1=ww1, ww2=ww2)[] 
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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/fi4/m/n/10 map.datasets(datas, annots, do.mapping = FALSE, mapping.coln 
= "EntrezGene.ID", mapping, verbose = FALSE)[] 

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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 ovcAngiogenic(data, annot, hgs, gmap = c("entrezgene", "ensem
bl_gene_id", "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = 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 
[29]
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 []\T1/fi4/m/n/9 ovcAngiogenic.nkis <- ovcAngiogenic(data=data.nkis, annot=anno
t.nkis, gmap="entrezgene", do.mapping=TRUE)[] 
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 []\T1/fi4/m/n/10 ovcCrijns(data, annot, hgs, gmap = c("entrezgene", "ensembl_g
ene_id", "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)[] 
[30]
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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/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/10 ovcTCGA(data, annot, gmap = c("entrezgene", "ensembl_gene_id"
, "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)[] 

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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 ovcYoshihara(data, annot, hgs, gmap = c("entrezgene", "ensemb
l_gene_id", "hgnc_symbol", "unigene", "refseq_mrna"), do.mapping = FALSE, verbo
se = FALSE)[] 

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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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[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][] 
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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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[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
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[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
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[][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
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[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
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[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
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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
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[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
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rroni", "BH", "BY", "fdr"))[] 
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[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
omics Con-sor-tium us-ing Affymetrix hgu133plus2
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[][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
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[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
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[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
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[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the 
gene ex-pres-sions (see [][]\T1/fi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ). 
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[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][] 
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
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[][][]\T1/fi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 intrinsic.clu
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[][][]$\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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