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BioC 2.12: CHECK report for genefu on petty

This page was generated on 2013-10-09 09:39:58 -0700 (Wed, 09 Oct 2013).

Package 253/671HostnameOS / ArchBUILDCHECKBUILD BIN
genefu 1.10.0
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/genefu
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: genefu
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefu_1.10.0.tar.gz
StartedAt: 2013-10-08 22:28:18 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:30:54 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 156.6 seconds
RetCode: 0
Status:  OK 
CheckDir: genefu.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/genefu.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'genefu/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genefu' version '1.10.0'
* 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 ... [14s/15s] 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 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
Package unavailable to check Rd xrefs: '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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [25s/25s] 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
  '/Users/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
** testing if installed package can be loaded
* DONE (genefu)

genefu.Rcheck/genefu-Ex.timings:

nameusersystemelapsed
bimod0.8470.0360.892
boxplotplus20.0440.0010.045
compare.proto.cor1.8490.0641.922
compute.pairw.cor.meta2.6180.0752.711
compute.proto.cor.meta1.2120.0471.267
cordiff.dep0.0480.0090.057
expos0.0150.0030.018
fuzzy.ttest0.0380.0060.044
gene700.3570.0210.384
gene760.2510.0110.266
geneid.map0.1530.0210.175
genius0.6150.0310.656
ggi0.1520.0150.167
intrinsic.cluster0.5910.0360.631
intrinsic.cluster.predict0.3910.0200.421
map.datasets0.9780.0321.042
mod10.0150.0050.020
mod20.0160.0030.019
modelOvcAngioganic0.0150.0030.017
nkis0.0160.0030.018
npi0.0290.0060.034
oncotypedx0.1770.0140.194
ovcAngiogenic0.3440.0080.354
ovcCrijns0.2860.0140.304
ovcTCGA0.5470.0210.575
ovcYoshihara0.1570.0140.171
pam500.0550.0030.060
pik3cags0.1360.0160.156
ps.cluster1.2600.0331.291
read.m.file0.0900.0070.097
rename.duplicate0.0140.0030.018
rescale0.0720.0110.083
scmgene.robust0.0250.0020.027
scmod1.robust0.0240.0020.026
scmod2.robust0.0210.0040.025
sig.gene700.0160.0040.020
sig.gene760.0200.0040.024
sig.genius0.0300.0120.043
sig.ggi0.0200.0030.024
sig.oncotypedx0.0230.0040.027
sig.pik3cags0.0160.0020.018
sig.score0.1840.0140.197
sig.tamr130.1460.0070.155
sigAngiogenic0.0170.0050.022
sigOvcAngiogenic0.0160.0050.021
sigOvcCrijns0.0160.0040.021
sigOvcSpentzos0.0160.0040.020
sigOvcTCGA0.0170.0050.023
sigOvcYoshihara0.0170.0050.022
ssp20030.0420.0070.049
ssp20060.0410.0080.050
st.gallen0.0160.0090.027
stab.fs0.4310.0140.449
stab.fs.ranking2.6420.0562.714
strescR0.0040.0020.006
subtype.cluster0.9450.0521.016
subtype.cluster.predict0.3330.0180.357
tamr130.1200.0080.127
tbrm0.1590.0030.164
vdxs0.0070.0050.012
weighted.meanvar0.0060.0040.013
write.m.file0.0080.0040.018