Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R [S] T  U  V  W  X  Y  Z 

BioC 3.5: BUILD report for survcomp on oaxaca

This page was generated on 2017-03-04 16:40:52 -0500 (Sat, 04 Mar 2017).

Package 1248/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
survcomp 1.25.0
Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/survcomp
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  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  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 

Summary

Package: survcomp
Version: 1.25.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data survcomp
StartedAt: 2017-03-03 17:16:06 -0800 (Fri, 03 Mar 2017)
EndedAt: 2017-03-03 17:16:42 -0800 (Fri, 03 Mar 2017)
EllapsedTime: 36.2 seconds
RetCode: 0
Status:  OK 
PackageFile: survcomp_1.25.0.tar.gz
PackageFileSize: 839.1 KiB

Command output

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


* 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 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./Rd2.tex
LaTeX2e <2016/03/31>
Babel <3.9r> and hyphenation patterns for 83 language(s) loaded.
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.10, 2016/02/22 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2016/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2016/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/latexconfig/hyperref.cfg))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 366.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 366.

) (/usr/local/texlive/2016/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2016/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
Overfull \hbox (77.29225pt too wide) in paragraph at lines 22--23
\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>\T1/ptm
/m/n/10 , Catha- 
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \vbox (34.37697pt too high) has occurred while \output is active
[1{/usr/local/texlive/2016/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (7.89719pt too wide) in paragraph at lines 60--61
[]\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,
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [6] [7]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (2.15596pt too wide) in paragraph at lines 382--383
[]\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. 
[8] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (649.78088pt too wide) in paragraph at lines 502--502
 []\T1/zi4/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]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 518--519
[]\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/zi4/m/n/10 "two.sided"
[11] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [12]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (283.78088pt too wide) in paragraph at lines 650--650
 []\T1/zi4/m/n/10 D.index(x, surv.time, surv.event, weights, strat, alpha = 0.0
5, method.test = c("logrank", "likelihood.ratio", "wald"), na.rm = FALSE, ...)[
] 
[13] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [14]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [15] [16]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [17]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [18]
Overfull \hbox (3.50652pt too wide) in paragraph at lines 958--959
\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

Overfull \hbox (1.68091pt too wide) in paragraph at lines 975--975
 []\T1/zi4/m/n/9 forestplot.surv(labeltext=labeltext, mean=r.mean, lower=r.lowe
r, upper=r.upper, zero=0.5,[] 

Overfull \hbox (156.48096pt too wide) in paragraph at lines 976--976
 []    \T1/zi4/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=""),[] 

Overfull \hbox (47.58093pt too wide) in paragraph at lines 977--977
 []    \T1/zi4/m/n/9 col=meta.colors(box="royalblue", line="darkblue", zero="da
rkred"), box.size=bs, clip=c(0.3,0.8))[] 
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (308.78088pt too wide) in paragraph at lines 1042--1042
 []\T1/zi4/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, 
...)[] 
[20] [21] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [22]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [23]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [24] [25]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [26]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [27]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [28]
Overfull \hbox (970.78088pt too wide) in paragraph at lines 1471--1471
 []\T1/zi4/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, ...)[] 
[29] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [30]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [32]
Overfull \hbox (574.98093pt too wide) in paragraph at lines 1713--1713
 []\T1/zi4/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"))[] 

(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [33]
Overfull \hbox (619.78088pt too wide) in paragraph at lines 1727--1727
 []\T1/zi4/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)[] 

Overfull \hbox (14.50804pt too wide) in paragraph at lines 1743--1744
[]\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/zi4/m/n/10 "two.sided"
[34]
Overfull \hbox (143.88092pt too wide) in paragraph at lines 1785--1785
 []\T1/zi4/m/n/9 mrmr.cindex(x=xx, surv.time=stime, surv.event=sevent, strat=st
rat, weights=weight, method="noether", comppairs=comppairs)[] 
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (829.78088pt too wide) in paragraph at lines 1799--1799
 []\T1/zi4/m/n/10 mrmr.cindex.ensemble(x, surv.time, surv.event, cl, weights, c
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)[] 
[35]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1815--1816
[]\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/zi4/m/n/10 "two.sided"
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [36] [37]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [38]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [39]
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [40]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [41]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [42] [43]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [44]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [45]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (0.68686pt too wide) in paragraph at lines 2343--2344
[]\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-

Overfull \hbox (3.21828pt too wide) in paragraph at lines 2350--2351
[]\T1/zi4/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
[46] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [47]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [48]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [49] [50]
No file Rd2.ind.
[51] (./Rd2.aux)

Package rerunfilecheck Warning: File `Rd2.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.

 )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.jackknife} has been referenced but does not exist, replaced by a fixed one


pdfTeX warning (dest): name{Rfn.survivalROC} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.survivalROC.C} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.prodlim} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.plot} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.sbrier} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.wilcox.test} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.survfit} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.metaplot} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.meta.colors} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.t.test} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.normOrder} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.coxph.object} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.summary.coxph} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.coxphCPE} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.phcpe} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rcorr.cens} has been referenced but does not ex
ist, replaced by a fixed one

{/usr/local/texlive/2016/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2016/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2016/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
16/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2016/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/local/te
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 (51 pages, 201109 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/Rtmp4IMDsW/Rbuild15c7c1b7ee6c4/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_1.25.0.tar.gz’