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BUILD report for genefu on merida2

This page was generated on 2019-04-09 13:25:46 -0400 (Tue, 09 Apr 2019).

Package 619/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 2.15.0
Benjamin Haibe-Kains
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/genefu
Branch: master
Last Commit: 6244700
Last Changed Date: 2019-03-27 15:03:09 -0400 (Wed, 27 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK [ OK ] OK  OK 

Summary

Package: genefu
Version: 2.15.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data genefu
StartedAt: 2019-04-08 20:10:36 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 20:12:45 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 128.7 seconds
RetCode: 0
Status:  OK 
PackageFile: genefu_2.15.0.tar.gz
PackageFileSize: 4.881 MiB

Command output

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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 ...

This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex)
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entering extended mode
LaTeX2e <2016/03/31>
Babel <3.9r> and hyphenation patterns for 83 language(s) loaded.
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\T1/ptm/m/n/10 doo, Natchar Ratanasirigulchai, Markus S. Schroeder, Laia Pare, 
Joel S. Parker, Aleix Prat, and Ben- 
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 []\T1/zi4/m/n/9 predout <- claudinLow(x=train$xd, classes=as.matrix(train$clas
ses$Group,ncol=1), y=test$xd)[] 
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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/ptm/m/n/10 International Ge-nomics Con-sor-tium, [][]$\T1/zi4/m/n/10 http
 : / / www . intgen . org / research-[]services / biobanking-[]experience /
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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/zi4/m/n/10 ihc4(ER, PGR, HER2, Ki67,age,size,grade,node,ana,scoreWithCli
nical=FALSE, na.rm = FALSE)[] 
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, size=count,replace=TRUE),[] 

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 []\T1/zi4/m/n/9 age=demo.nkis[,"age"],size=demo.nkis[ ,"size"],grade=demo.nkis
[ ,"grade"],node=demo.nkis[ ,"node"],[] 
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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,
[28]
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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/ptm/m/n/10 character string con-tain-ing the \T1/zi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/zi4/m/n/10 do.mapping=TRUE 
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 []\T1/zi4/m/n/9 ovcCrijns.nkis <- ovcCrijns(data=data.nkis, annot=annot.nkis, 
gmap="entrezgene", do.mapping=TRUE)[] 
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 []\T1/zi4/m/n/9 ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap
="entrezgene", do.mapping=TRUE)[] 
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 []\T1/zi4/m/n/10 gmap = c("entrezgene", "ensembl_gene_id", "hgnc_symbol", "uni
gene", "refseq_mrna"),[] 

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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/zi4/m/n/10 biomaRt \T1/p
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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/zi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ). 
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 []\T1/zi4/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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[][][]$\T1/zi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][] 
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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/zi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
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[][][]$\T1/zi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
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[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
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[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
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[][][]$\T1/zi4/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/zi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
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[][][]$\T1/zi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
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\T1/ptm/m/n/10 doo, Natchar Ratanasirigulchai, Markus S. Schroeder, Laia Pare, 
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[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
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[]\T1/ptm/m/n/10 International Ge-nomics Con-sor-tium, [][]$\T1/zi4/m/n/10 http
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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 
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[][][]$\T1/zi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
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[][][]\T1/zi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 intrinsic.clu
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[][][]$\T1/zi4/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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xlive/2016/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2
016/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2016/texmf-
dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts
/type1/urw/times/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/type1/urw
/times/utmri8a.pfb>
Output written on Rd2.pdf (85 pages, 291969 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/RtmpVsjwW7/Rbuild174d3186ab1d7/genefu/build/genefu.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 ‘genefu_2.15.0.tar.gz’