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Package 237/631HostnameOS / ArchBUILDCHECKBUILD BIN
genefu 1.9.0
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genefu
Last Changed Rev: 70052 / Revision: 72575
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: genefu
Version: 1.9.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings genefu_1.9.0.tar.gz
StartedAt: 2013-01-16 02:44:31 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 02:46:16 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 105.3 seconds
RetCode: 0
Status:  OK 
CheckDir: genefu.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/genefu.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.9.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
prepare_Rd: modelOvcAngioganic.Rd:20-21: Dropping empty section \references
prepare_Rd: sigAngiogenic.Rd:20-21: Dropping empty section \references
prepare_Rd: sigOvcAngiogenic.Rd:20-22: Dropping empty section \references
prepare_Rd: sigOvcCrijns.Rd:20-21: Dropping empty section \references
prepare_Rd: sigOvcSpentzos.Rd:20-21: Dropping empty section \references
prepare_Rd: sigOvcTCGA.Rd:20-21: Dropping empty section \references
prepare_Rd: sigOvcYoshihara.Rd:19-20: Dropping empty section \references
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘multilevel’, ‘dplR’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-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
   ‘genefu.Rnw’ 
** testing if installed package can be loaded

* DONE (genefu)

genefu.Rcheck/genefu-Ex.timings:

nameusersystemelapsed
bimod0.6640.0160.684
boxplotplus20.0200.0000.019
compare.proto.cor1.5120.0121.527
compute.pairw.cor.meta1.9960.0162.017
compute.proto.cor.meta1.1800.0081.188
cordiff.dep0.1840.0040.188
expos0.0040.0000.005
fuzzy.ttest0.0160.0000.016
gene700.4520.0000.456
gene760.0680.0040.072
geneid.map0.1440.0080.156
genius0.4840.0040.486
ggi0.1520.0040.153
intrinsic.cluster0.3560.0040.362
intrinsic.cluster.predict0.3040.0040.309
map.datasets1.0600.0121.072
mod10.0160.0040.023
mod20.0160.0040.021
modelOvcAngioganic0.0200.0000.021
nkis0.020.000.02
npi0.0280.0000.027
oncotypedx0.3240.0080.338
ovcAngiogenic0.1320.0000.129
ovcCrijns0.1280.0000.127
ovcTCGA0.4080.0000.411
ovcYoshihara0.1400.0000.141
pam500.0400.0000.041
pik3cags0.120.000.12
ps.cluster0.9800.0040.983
read.m.file0.0760.0040.083
rename.duplicate0.020.000.02
rescale0.0720.0000.079
scmgene.robust0.0240.0000.023
scmod1.robust0.0400.0040.040
scmod2.robust0.0520.0040.056
sig.gene700.0360.0000.036
sig.gene760.0240.0000.023
sig.genius0.0440.0000.045
sig.ggi0.0080.0040.011
sig.oncotypedx0.0080.0000.009
sig.pik3cags0.0120.0000.010
sig.score0.1040.0000.104
sig.tamr130.0200.0000.016
sigAngiogenic0.0200.0000.017
sigOvcAngiogenic0.0040.0000.010
sigOvcCrijns0.0200.0000.017
sigOvcSpentzos0.0200.0000.018
sigOvcTCGA0.0200.0000.019
sigOvcYoshihara0.0200.0000.024
ssp20030.0320.0040.040
ssp20060.0280.0040.039
st.gallen0.0160.0000.031
stab.fs0.2600.0000.257
stab.fs.ranking1.5530.0241.573
strescR0.0080.0040.013
subtype.cluster0.6520.0080.662
subtype.cluster.predict0.2400.0120.250
tamr130.1280.0000.126
tbrm0.1840.0000.186
vdxs0.0080.0000.011
weighted.meanvar0.0080.0000.008
write.m.file0.0080.0000.010