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BioC 3.2: BUILD report for survcomp on oaxaca

This page was generated on 2016-04-23 10:25:07 -0700 (Sat, 23 Apr 2016).

Package 1032/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
survcomp 1.20.0
Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/survcomp
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK [ OK ] OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: survcomp
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data survcomp
StartedAt: 2016-04-22 18:43:32 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 18:43:58 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 25.3 seconds
RetCode: 0
Status:  OK 
PackageFile: survcomp_1.20.0.tar.gz
PackageFileSize: 823.1 KiB

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 survcomp
###
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* checking for file ‘survcomp/DESCRIPTION’ ... OK
* preparing ‘survcomp’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* 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 3.1415926-2.5-1.40.14 (TeX Live 2013)
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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>\T1/ptm
/m/n/10 , Catha- 
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[]\T1/ptm/m/n/10 - Com-pu-ta-tional Bi-ol-ogy and Func-tional Ge-nomics Lab-o-r
a-tory, Dana-Farber Can-cer In-sti-tute, Boston,
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[]\T1/ptm/m/n/10 The func-tion com-bines sev-eral es-ti-ma-tors us-ing meta-ana
lytical for-mula to com-pute a meta-estimate. 
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 []\T1/fi4/m/n/10 concordance.index(x, surv.time, surv.event, cl, weights, comp
pairs=10, strat, alpha = 0.05, outx = TRUE, method = c("conservative", "noether
", "nam"), alternative = c("two.sided", "less", "greater"), na.rm = FALSE)[] 
[10]
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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 \T1/fi4/m/n/10 "two.sided"
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5, method.test = c("logrank", "likelihood.ratio", "wald"), na.rm = FALSE, ...)[
] 
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\T1/ptm/m/n/10 and ran-dom ef-fects meta-analysis for two-sample com-par-isons 
and cu-mu-la-tive meta-analyses. Draws

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 []\T1/fi4/m/n/9 forestplot.surv(labeltext=labeltext, mean=r.mean, lower=r.lowe
r, upper=r.upper, zero=0.5,[] 

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 []    \T1/fi4/m/n/9 align=c("l"), graphwidth=unit(2, "inches"), x.ticks=seq(0.
3,0.8,0.1), xlab=paste( "Forestplot Example", myspace, sep=""),[] 

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 []\T1/fi4/m/n/10 hazard.ratio(x, surv.time, surv.event, weights, strat, alpha 
= 0.05, method.test = c("logrank", "likelihood.ratio", "wald"), na.rm = FALSE, 
...)[] 
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 []\T1/fi4/m/n/10 km.coxph.plot(formula.s, data.s, weight.s, x.label, y.label, 
main.title, sub.title, leg.text, leg.pos = "bottomright", leg.bty = "o", leg.in
set = 0.05, o.text, v.line, h.line, .col = 1:4, .lty = 1, .lwd = 1, show.n.risk
 = FALSE, n.risk.step, n.risk.cex = 0.85, verbose = TRUE, ...)[] 
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 []\T1/fi4/m/n/9 metaplot.surv(mn=c(0.4,0.5,0.6), lower=c(0.35,0.4,0.57), upper
=c(0.45,0.6,0.63), labels=c("A","B","C"), xlim=c(0.2,0.8), boxsize=0.5, zero=0.
5, col=rmeta::meta.colors(box="royalblue",line="darkblue",zero="firebrick"))[] 

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 []\T1/fi4/m/n/10 mrmr.cindex(x, surv.time, surv.event, cl, weights, comppairs=
10, strat, alpha = 0.05, outx = TRUE, method = c("conservative", "noether", "na
m"), alternative = c("two.sided", "less", "greater"), 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 \T1/fi4/m/n/10 "two.sided"
[34]
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 []\T1/fi4/m/n/9 mrmr.cindex(x=xx, surv.time=stime, surv.event=sevent, strat=st
rat, weights=weight, method="noether", comppairs=comppairs)[] 
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omppairs=10, strat, alpha = 0.05, outx = TRUE, method = c("conservative", "noet
her", "nam"), alternative = c("two.sided", "less", "greater"), maxparents, maxn
sol, nboot = 200, na.rm = FALSE)[] 
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e-sis, must be one of \T1/fi4/m/n/10 "two.sided"
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[]\T1/ptm/m/n/10 This dataset con-tains a sub-set of the gene ex-pres-sion, an-
no-ta-tions and clin-i-cal data from the TRANS-

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[]\T1/fi4/m/n/10 exprs(transbig7g)\T1/ptm/m/n/10 : Ma-trix con-tain-ing gene ex
-pres-sions as mea-sured by Affymetrix hgu133a
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Output written on Rd2.pdf (51 pages, 184675 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/Rtmpx7vEEd/Rbuild8fda60ceba7b/survcomp/build/survcomp.pdf’ ...
Done
* creating vignettes ... OK
* cleaning src
* 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 ‘survcomp_1.20.0.tar.gz’