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BioC 3.4: CHECK report for TRONCO on moscato1

This page was generated on 2016-09-21 03:46:41 -0700 (Wed, 21 Sep 2016).

Package 1219/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TRONCO 2.5.2
BIMIB Group
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TRONCO
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TRONCO
Version: 2.5.2
Command: rm -rf TRONCO.buildbin-libdir TRONCO.Rcheck && mkdir TRONCO.buildbin-libdir TRONCO.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TRONCO.buildbin-libdir TRONCO_2.5.2.tar.gz >TRONCO.Rcheck\00install.out 2>&1 && cp TRONCO.Rcheck\00install.out TRONCO-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=TRONCO.buildbin-libdir --install="check:TRONCO-install.out" --force-multiarch --no-vignettes --timings TRONCO_2.5.2.tar.gz
StartedAt: 2016-09-20 17:57:34 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 18:06:53 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 559.0 seconds
RetCode: 0
Status:  OK  
CheckDir: TRONCO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf TRONCO.buildbin-libdir TRONCO.Rcheck && mkdir TRONCO.buildbin-libdir TRONCO.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TRONCO.buildbin-libdir TRONCO_2.5.2.tar.gz >TRONCO.Rcheck\00install.out 2>&1 && cp TRONCO.Rcheck\00install.out TRONCO-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=TRONCO.buildbin-libdir --install="check:TRONCO-install.out" --force-multiarch --no-vignettes --timings TRONCO_2.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/TRONCO.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TRONCO/DESCRIPTION' ... OK
* this is package 'TRONCO' version '2.5.2'
* package encoding: UTF-8
* 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 'TRONCO' can be installed ... OK
* checking installed package size ... OK
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
tronco.kfold.posterr 0.36   0.11    7.71
tronco.kfold.prederr 0.28   0.07    6.75
tronco.bootstrap     0.30   0.05   25.91
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
tronco.kfold.posterr 0.28   0.07    7.21
tronco.bootstrap     0.26   0.03   30.60
tronco.kfold.prederr 0.21   0.04    7.56
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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

Status: OK

TRONCO.Rcheck/00install.out:


install for i386

* installing *source* package 'TRONCO' ...
** 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 'TRONCO' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TRONCO' as TRONCO_2.5.2.zip
* DONE (TRONCO)

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

nameusersystemelapsed
TCGA.multiple.samples0.020.000.02
TCGA.remove.multiple.samples0.030.000.03
TCGA.shorten.barcodes0.010.000.01
annotate.description0.020.000.02
annotate.stages0.010.000.02
as.adj.matrix0.000.020.01
as.alterations0.020.000.02
as.bootstrap.scores0.060.000.06
as.colors000
as.confidence0.020.010.03
as.description000
as.events000
as.events.in.patterns0.010.000.02
as.events.in.sample000
as.gene0.020.000.01
as.genes000
as.genes.in.patterns0.010.000.02
as.genotypes0.000.020.01
as.hypotheses0.000.010.02
as.joint.probs0.000.040.03
as.kfold.eloss0.110.000.11
as.kfold.posterr0.080.010.09
as.kfold.prederr0.130.000.13
as.marginal.probs0.010.000.01
as.models0.020.020.03
as.parameters000
as.pathway0.010.000.02
as.patterns000
as.samples0.020.000.02
as.selective.advantage.relations0.150.000.15
as.stages000
as.types000
as.types.in.patterns000
change.color0.020.000.01
consolidate.data0.030.000.03
delete.event0.010.000.02
delete.gene0.020.000.01
delete.hypothesis0.030.010.05
delete.model000
delete.pattern0.010.000.02
delete.samples0.000.020.01
delete.type0.020.000.02
duplicates000
enforce.numeric0.020.000.01
enforce.string000
events.selection000
export.graphml0.270.000.26
export.mutex000
has.duplicates0.010.000.02
has.model000
has.stages0.000.010.01
import.GISTIC000
import.MAF0.100.020.11
intersect.datasets000
is.compliant0.010.000.02
join.events000
join.types0.080.000.07
keysToNames000
nameToKey0.010.000.02
nevents000
ngenes000
nhypotheses000
npatterns000
nsamples000
ntypes000
oncoprint.cbio0.000.010.01
order.frequency0.020.000.02
pheatmap0.060.000.06
rank.recurrents0.010.000.01
rename.gene000
rename.type000
samples.selection0.020.000.02
trim000
tronco.bootstrap 0.30 0.0525.91
tronco.caprese0.150.000.16
tronco.capri2.790.022.81
tronco.kfold.eloss0.240.000.23
tronco.kfold.posterr0.360.117.71
tronco.kfold.prederr0.280.076.75
tronco.mst.chowliu2.230.002.23
tronco.mst.edmonds1.890.001.98
tronco.mst.prim2.850.022.87
tronco.plot0.190.020.53
view000
which.samples0.010.000.02

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

nameusersystemelapsed
TCGA.multiple.samples0.020.020.03
TCGA.remove.multiple.samples0.020.000.01
TCGA.shorten.barcodes0.000.020.02
annotate.description000
annotate.stages000
as.adj.matrix0.020.000.02
as.alterations000
as.bootstrap.scores0.090.000.09
as.colors000
as.confidence0.000.010.02
as.description0.020.000.02
as.events000
as.events.in.patterns000
as.events.in.sample0.010.000.01
as.gene000
as.genes0.020.000.02
as.genes.in.patterns000
as.genotypes0.010.000.01
as.hypotheses0.020.000.02
as.joint.probs0.020.000.01
as.kfold.eloss0.120.000.13
as.kfold.posterr0.080.000.08
as.kfold.prederr0.150.020.17
as.marginal.probs000
as.models0.020.010.03
as.parameters000
as.pathway0.020.000.01
as.patterns000
as.samples000
as.selective.advantage.relations0.170.000.17
as.stages0.020.000.02
as.types000
as.types.in.patterns000
change.color000
consolidate.data0.050.000.05
delete.event0.000.020.02
delete.gene0.020.000.01
delete.hypothesis0.010.010.03
delete.model000
delete.pattern0.020.000.01
delete.samples0.010.000.02
delete.type000
duplicates0.020.000.01
enforce.numeric000
enforce.string000
events.selection0.000.010.02
export.graphml0.250.001.06
export.mutex0.010.000.02
has.duplicates000
has.model000
has.stages0.000.020.01
import.GISTIC0.020.000.02
import.MAF0.110.000.11
intersect.datasets000
is.compliant0.010.000.01
join.events000
join.types0.080.020.10
keysToNames000
nameToKey0.020.000.01
nevents000
ngenes000
nhypotheses0.010.000.02
npatterns000
nsamples000
ntypes0.000.010.01
oncoprint.cbio0.020.000.02
order.frequency0.010.000.01
pheatmap0.080.000.08
rank.recurrents000
rename.gene0.020.000.02
rename.type0.010.000.01
samples.selection0.020.000.02
trim000
tronco.bootstrap 0.26 0.0330.60
tronco.caprese0.230.000.23
tronco.capri2.670.032.70
tronco.kfold.eloss0.280.000.28
tronco.kfold.posterr0.280.077.21
tronco.kfold.prederr0.210.047.56
tronco.mst.chowliu1.960.001.97
tronco.mst.edmonds1.960.001.97
tronco.mst.prim2.950.002.95
tronco.plot0.220.000.22
view000
which.samples000