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BioC 3.5: BUILD report for genefu on oaxaca

This page was generated on 2017-03-04 16:40:50 -0500 (Sat, 04 Mar 2017).

Package 494/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 2.7.0
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genefu
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS 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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK [ OK ] WARNINGS  OK 

Summary

Package: genefu
Version: 2.7.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data genefu
StartedAt: 2017-03-03 17:15:45 -0800 (Fri, 03 Mar 2017)
EndedAt: 2017-03-03 17:19:20 -0800 (Fri, 03 Mar 2017)
EllapsedTime: 214.9 seconds
RetCode: 0
Status:  OK 
PackageFile: genefu_2.7.0.tar.gz
PackageFileSize: 4.828 MiB

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data genefu
###
##############################################################################
##############################################################################


* 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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\T1/ptm/m/n/10 doo, Natchar Ratanasirigulchai, Markus S. Schroder, Laia Pare, J
oel S. Parker, Aleix Prat, and Ben- 
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\T1/ptm/m/n/10 Kains \T1/zi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/zi4/m/n/10 <markus.schroeder@ucdconnect.ie>  
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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)[] 
[22]
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:10, size=count,replace=TRUE),[] 

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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,
[27]
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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/zi4/m/n/10 "pam50", "ssp2006", "ssp2003", "intClust", "AIMS","claudinLow
"), data, annot, do.mapping = FALSE)[] 
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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
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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 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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replaced by a fixed one

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placed by a fixed one

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t, replaced by a fixed one

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, replaced by a fixed one

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pdfTeX warning (dest): name{Rfn.Mclust} has been referenced but does not exist,
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Output written on Rd2.pdf (80 pages, 261468 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/RtmpjjO8cA/Rbuild15c0229bb53a/genefu/build/genefu.pdf’ ...
Done
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘genefu_2.7.0.tar.gz’