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BUILD report for genefu on veracruz1

This page was generated on 2018-04-12 13:34:13 -0400 (Thu, 12 Apr 2018).

Package 536/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 2.11.2
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/genefu
Branch: RELEASE_3_6
Last Commit: 5a6ba0e
Last Changed Date: 2018-04-10 11:58:08 -0400 (Tue, 10 Apr 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK [ OK ] WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: genefu
Version: 2.11.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data genefu
StartedAt: 2018-04-11 19:35:18 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 19:36:58 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 99.9 seconds
RetCode: 0
Status:  OK 
PackageFile: genefu_2.11.2.tar.gz
PackageFileSize: 4.88 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
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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, [][]$\T1/zi4/m/n/10 http
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
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[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
 and probes in columns,
[27]
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[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
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 []\T1/zi4/m/n/9 ovcCrijns.nkis <- ovcCrijns(data=data.nkis, annot=annot.nkis, 
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[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the 
gene ex-pres-sions (see [][]\T1/zi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ). 
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[][][]$\T1/zi4/m/n/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
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-
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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[][][]$\T1/zi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
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[]\T1/ptm/m/n/10 International Ge-nomics Con-sor-tium, [][]$\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 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the 
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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/
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[][][]$\T1/zi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
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[]\T1/ptm/m/n/10 International Ge-nomics Con-sor-tium, [][]$\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 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
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pdfTeX warning (dest): name{Rfn.weighted.mean} has been referenced but does not
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pdfTeX warning (dest): name{Rfn.t.test} has been referenced but does not exist,
 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.cordif.dep} has been referenced but does not ex
ist, replaced by a fixed one

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

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

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

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

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

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Output written on Rd2.pdf (85 pages, 291113 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/RtmpbFLd2Q/Rbuild83977b7f3994/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_2.11.2.tar.gz’