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BioC 2.13: CHECK report for genefu on perceval

This page was generated on 2014-04-05 09:52:36 -0700 (Sat, 05 Apr 2014).

Package 283/750HostnameOS / ArchBUILDCHECKBUILD BIN
genefu 1.12.0
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/genefu
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: genefu
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefu_1.12.0.tar.gz
StartedAt: 2014-04-05 01:29:36 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:31:33 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 117.0 seconds
RetCode: 0
Status:  OK 
CheckDir: genefu.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/genefu.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.12.0’
* 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 ... [9s/10s] 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
‘library’ or ‘require’ call to ‘survcomp’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘biomaRt’ ‘survcomp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ‘:::’ calls:
  ‘mclust:::grid1’ ‘mclust:::grid2’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘genefu.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [21s/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

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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
bimod0.6720.0340.772
boxplotplus20.1260.0060.138
compare.proto.cor1.9910.0742.305
compute.pairw.cor.meta2.1280.0462.360
compute.proto.cor.meta1.2930.0451.374
cordiff.dep0.0510.0100.062
expos0.0150.0010.017
fuzzy.ttest0.0550.0030.059
gene700.2620.0200.284
gene760.0910.0070.100
geneid.map0.1190.0220.161
genius0.4350.0240.464
ggi0.1670.0070.175
intrinsic.cluster0.6420.0440.686
intrinsic.cluster.predict0.2920.0300.367
map.datasets1.1780.0521.302
mod10.0170.0030.020
mod20.0170.0030.021
modelOvcAngioganic0.0150.0030.018
nkis0.0160.0030.020
npi0.0250.0060.031
oncotypedx0.1620.0170.200
ovcAngiogenic0.3580.0150.446
ovcCrijns0.1330.0270.176
ovcTCGA0.6190.0220.674
ovcYoshihara0.1310.0200.161
pam500.0420.0060.049
pik3cags0.1460.0100.162
ps.cluster0.9690.0611.036
read.m.file0.0840.0080.093
rename.duplicate0.0210.0010.023
rescale0.0690.0130.085
scmgene.robust0.0180.0040.022
scmod1.robust0.0210.0040.027
scmod2.robust0.0180.0040.022
sig.gene700.0210.0040.026
sig.gene760.0220.0040.028
sig.genius0.0670.0130.084
sig.ggi0.0410.0060.049
sig.oncotypedx0.0290.0040.033
sig.pik3cags0.0250.0040.030
sig.score0.1450.0150.165
sig.tamr130.0210.0060.027
sigAngiogenic0.0250.0030.028
sigOvcAngiogenic0.0370.0030.042
sigOvcCrijns0.0200.0010.021
sigOvcSpentzos0.0220.0070.028
sigOvcTCGA0.0220.0040.027
sigOvcYoshihara0.0240.0050.029
ssp20030.0410.0050.045
ssp20060.0380.0070.050
st.gallen0.0150.0070.029
stab.fs0.2890.0160.340
stab.fs.ranking1.6950.0391.825
strescR0.0040.0020.006
subtype.cluster0.7880.0691.004
subtype.cluster.predict0.4170.0210.468
tamr130.1020.0090.113
tbrm0.0120.0020.014
vdxs0.0220.0030.025
weighted.meanvar0.0240.0020.026
write.m.file0.0210.0030.025