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BioC 2.13: CHECK report for genefu on moscato1

This page was generated on 2014-04-05 09:50:18 -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: rm -rf genefu.buildbin-libdir && mkdir genefu.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genefu.buildbin-libdir genefu_1.12.0.tar.gz >genefu-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=genefu.buildbin-libdir --install="check:genefu-install.out" --force-multiarch --no-vignettes --timings genefu_1.12.0.tar.gz && mv genefu.buildbin-libdir/* genefu.Rcheck/ && rmdir genefu.buildbin-libdir
StartedAt: 2014-04-05 04:02:30 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:04:51 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 141.4 seconds
RetCode: 0
Status:  OK  
CheckDir: genefu.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/genefu.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'genefu' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ...
** running examples for arch 'i386' ... [15s] OK
** running examples for arch 'x64' ... [16s] 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
  'D:/biocbld/bbs-2.13-bioc/meat/genefu.Rcheck/00check.log'
for details.

genefu.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'genefu' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genefu' as genefu_1.12.0.zip
* DONE (genefu)

genefu.Rcheck/examples_i386/genefu-Ex.timings:

nameusersystemelapsed
bimod0.410.020.43
boxplotplus20.010.000.02
compare.proto.cor0.760.000.77
compute.pairw.cor.meta1.340.001.34
compute.proto.cor.meta0.560.000.57
cordiff.dep0.060.000.06
expos000
fuzzy.ttest0.030.000.03
gene700.320.030.36
gene760.070.010.08
geneid.map0.130.030.16
genius0.470.000.47
ggi0.190.020.21
intrinsic.cluster0.510.010.53
intrinsic.cluster.predict0.300.020.32
map.datasets0.50.00.5
mod10.010.000.01
mod20.000.020.01
modelOvcAngioganic0.020.000.01
nkis0.020.000.01
npi0.040.000.03
oncotypedx0.130.000.12
ovcAngiogenic0.140.010.16
ovcCrijns0.140.000.14
ovcTCGA0.480.000.49
ovcYoshihara0.210.020.23
pam500.050.000.05
pik3cags0.140.000.14
ps.cluster1.140.001.14
read.m.file0.120.010.14
rename.duplicate000
rescale0.060.000.06
scmgene.robust000
scmod1.robust0.020.000.02
scmod2.robust0.010.000.01
sig.gene700.020.000.02
sig.gene760.020.000.01
sig.genius0.030.000.03
sig.ggi0.000.020.02
sig.oncotypedx000
sig.pik3cags000
sig.score0.140.000.15
sig.tamr130.020.000.02
sigAngiogenic0.020.000.02
sigOvcAngiogenic0.030.000.03
sigOvcCrijns0.020.000.01
sigOvcSpentzos0.010.000.02
sigOvcTCGA0.000.010.01
sigOvcYoshihara0.020.000.01
ssp20030.050.000.05
ssp20060.050.000.05
st.gallen0.010.020.03
stab.fs0.380.000.38
stab.fs.ranking2.240.002.24
strescR000
subtype.cluster1.040.021.07
subtype.cluster.predict0.320.010.34
tamr130.10.00.1
tbrm0.020.000.02
vdxs0.020.000.02
weighted.meanvar0.020.000.02
write.m.file0.030.000.03

genefu.Rcheck/examples_x64/genefu-Ex.timings:

nameusersystemelapsed
bimod0.590.010.61
boxplotplus20.050.000.04
compare.proto.cor1.130.001.12
compute.pairw.cor.meta1.610.041.64
compute.proto.cor.meta0.730.000.73
cordiff.dep0.020.010.03
expos0.010.000.02
fuzzy.ttest0.020.000.01
gene700.180.000.18
gene760.050.020.06
geneid.map0.090.000.09
genius0.470.010.48
ggi0.080.000.08
intrinsic.cluster0.360.000.36
intrinsic.cluster.predict0.220.000.22
map.datasets0.390.000.39
mod10.010.000.01
mod20.020.000.02
modelOvcAngioganic0.010.000.02
nkis0.000.020.01
npi0.020.000.02
oncotypedx0.100.000.11
ovcAngiogenic0.110.000.11
ovcCrijns0.110.000.11
ovcTCGA0.400.010.42
ovcYoshihara0.080.000.08
pam500.010.000.02
pik3cags0.080.000.08
ps.cluster0.740.000.73
read.m.file0.040.000.05
rename.duplicate000
rescale0.060.000.07
scmgene.robust000
scmod1.robust0.020.000.01
scmod2.robust0.000.020.02
sig.gene70000
sig.gene760.020.000.02
sig.genius0.030.000.03
sig.ggi0.020.000.02
sig.oncotypedx0.010.000.01
sig.pik3cags000
sig.score0.080.010.09
sig.tamr13000
sigAngiogenic0.000.020.02
sigOvcAngiogenic0.020.000.02
sigOvcCrijns0.020.000.02
sigOvcSpentzos0.000.020.01
sigOvcTCGA0.010.000.02
sigOvcYoshihara0.010.000.02
ssp20030.030.000.05
ssp20060.030.000.03
st.gallen0.000.010.02
stab.fs0.340.000.35
stab.fs.ranking2.640.022.65
strescR0.010.000.01
subtype.cluster0.730.010.75
subtype.cluster.predict0.350.000.35
tamr130.10.00.1
tbrm0.020.000.01
vdxs000
weighted.meanvar000
write.m.file0.000.020.02