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BioC 3.0: CHECK report for genefu on perceval

This page was generated on 2015-04-10 09:55:46 -0700 (Fri, 10 Apr 2015).

Package 347/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 1.16.0
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/genefu
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: genefu
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefu_1.16.0.tar.gz
StartedAt: 2015-04-10 01:50:53 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:54:23 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 210.5 seconds
RetCode: 0
Status:  OK 
CheckDir: genefu.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefu_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/genefu.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genefu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genefu’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genefu’ can be installed ... [20s/22s] OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘mclust:::grid1’ ‘mclust:::grid2’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
endoPredict: no visible binding for global variable ‘sig.endoPredict’
gene70: no visible binding for global variable ‘sig.gene70’
gene76: no visible binding for global variable ‘sig.gene76’
genius: no visible binding for global variable ‘scmod1.robust’
genius: no visible binding for global variable ‘sig.genius’
ggi: no visible binding for global variable ‘sig.ggi’
oncotypedx: no visible binding for global variable ‘sig.oncotypedx’
ovcAngiogenic: no visible binding for global variable
  ‘sigOvcAngiogenic’
ovcAngiogenic: no visible binding for global variable
  ‘modelOvcAngiogenic’
ovcCrijns: no visible binding for global variable ‘sigOvcCrijns’
ovcTCGA: no visible binding for global variable ‘sigOvcTCGA’
ovcYoshihara: no visible binding for global variable ‘sigOvcYoshihara’
pik3cags: no visible binding for global variable ‘sig.pik3cags’
rorS: no visible binding for global variable ‘pam50’
subtype.cluster: no visible global function definition for ‘unmap’
subtype.cluster: no visible global function definition for
  ‘mclust.options’
subtype.cluster.predict: no visible global function definition for
  ‘unmap’
tamr13: no visible binding for global variable ‘sig.tamr13’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘dplR’, ‘multilevel’
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/23s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/genefu.Rcheck/00check.log’
for details.

genefu.Rcheck/00install.out:

* installing *source* package ‘genefu’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genefu)

genefu.Rcheck/genefu-Ex.timings:

nameusersystemelapsed
bimod0.7110.0260.736
boxplotplus20.0090.0020.011
compare.proto.cor1.1160.0321.711
compute.pairw.cor.meta1.9580.0492.017
compute.proto.cor.meta0.8410.0230.864
cordiff.dep0.0180.0050.022
endoPredict0.0390.0020.041
expos0.0010.0000.002
fuzzy.ttest0.0030.0000.003
gene700.4740.0100.484
gene760.0590.0020.062
geneid.map0.1410.0060.148
genius0.6170.0100.628
ggi0.0950.0040.100
intrinsic.cluster0.4070.0220.405
intrinsic.cluster.predict0.4980.0190.518
map.datasets0.8080.0180.828
mod10.0020.0010.002
mod20.0020.0000.003
modelOvcAngiogenic0.0020.0000.002
nkis0.0010.0000.002
npi0.0080.0030.011
oncotypedx0.1060.0100.117
ovcAngiogenic0.1330.0040.139
ovcCrijns0.4060.0040.412
ovcTCGA0.3760.0050.382
ovcYoshihara0.0950.0060.099
pam500.0200.0020.021
pik3cags0.0960.0020.098
power.cor0.0010.0010.001
ps.cluster1.1240.0261.127
read.m.file0.0480.0030.051
rename.duplicate0.0030.0000.003
rescale0.0510.0020.065
rorS0.5690.0130.584
scmgene.robust0.0050.0010.007
scmod1.robust0.0070.0000.008
scmod2.robust0.0070.0000.007
setcolclass.df0.0040.0000.005
sig.endoPredict0.0050.0000.005
sig.gene700.0060.0010.008
sig.gene760.0080.0010.009
sig.genius0.0470.0090.057
sig.ggi0.0080.0010.009
sig.oncotypedx0.0040.0000.005
sig.pik3cags0.0040.0010.005
sig.score0.1110.0060.118
sig.tamr130.0080.0030.010
sigOvcAngiogenic0.0090.0010.010
sigOvcCrijns0.0090.0010.009
sigOvcSpentzos0.0090.0010.010
sigOvcTCGA0.0100.0010.011
sigOvcYoshihara0.0090.0010.011
spearmanCI0.0010.0000.001
ssp20030.0270.0020.030
ssp20060.0330.0020.035
st.gallen0.0110.0030.012
stab.fs0.2840.0040.291
stab.fs.ranking1.5530.0561.613
strescR0.0010.0000.002
subtype.cluster0.9520.0391.058
subtype.cluster.predict0.5100.0120.539
tamr130.0650.0030.069
tbrm0.0010.0000.001
vdxs0.0020.0010.003
weighted.meanvar0.0010.0000.001
write.m.file0.0020.0010.002