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This page was generated on 2016-09-21 03:46:41 -0700 (Wed, 21 Sep 2016).
| Package 1219/1257 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| TRONCO 2.5.2 BIMIB Group
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK |  | |||||
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | | |||||
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
| 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 |
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###
### 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
###
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* 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:
| name | user | system | elapsed | |
| TCGA.multiple.samples | 0.02 | 0.00 | 0.02 | |
| TCGA.remove.multiple.samples | 0.03 | 0.00 | 0.03 | |
| TCGA.shorten.barcodes | 0.01 | 0.00 | 0.01 | |
| annotate.description | 0.02 | 0.00 | 0.02 | |
| annotate.stages | 0.01 | 0.00 | 0.02 | |
| as.adj.matrix | 0.00 | 0.02 | 0.01 | |
| as.alterations | 0.02 | 0.00 | 0.02 | |
| as.bootstrap.scores | 0.06 | 0.00 | 0.06 | |
| as.colors | 0 | 0 | 0 | |
| as.confidence | 0.02 | 0.01 | 0.03 | |
| as.description | 0 | 0 | 0 | |
| as.events | 0 | 0 | 0 | |
| as.events.in.patterns | 0.01 | 0.00 | 0.02 | |
| as.events.in.sample | 0 | 0 | 0 | |
| as.gene | 0.02 | 0.00 | 0.01 | |
| as.genes | 0 | 0 | 0 | |
| as.genes.in.patterns | 0.01 | 0.00 | 0.02 | |
| as.genotypes | 0.00 | 0.02 | 0.01 | |
| as.hypotheses | 0.00 | 0.01 | 0.02 | |
| as.joint.probs | 0.00 | 0.04 | 0.03 | |
| as.kfold.eloss | 0.11 | 0.00 | 0.11 | |
| as.kfold.posterr | 0.08 | 0.01 | 0.09 | |
| as.kfold.prederr | 0.13 | 0.00 | 0.13 | |
| as.marginal.probs | 0.01 | 0.00 | 0.01 | |
| as.models | 0.02 | 0.02 | 0.03 | |
| as.parameters | 0 | 0 | 0 | |
| as.pathway | 0.01 | 0.00 | 0.02 | |
| as.patterns | 0 | 0 | 0 | |
| as.samples | 0.02 | 0.00 | 0.02 | |
| as.selective.advantage.relations | 0.15 | 0.00 | 0.15 | |
| as.stages | 0 | 0 | 0 | |
| as.types | 0 | 0 | 0 | |
| as.types.in.patterns | 0 | 0 | 0 | |
| change.color | 0.02 | 0.00 | 0.01 | |
| consolidate.data | 0.03 | 0.00 | 0.03 | |
| delete.event | 0.01 | 0.00 | 0.02 | |
| delete.gene | 0.02 | 0.00 | 0.01 | |
| delete.hypothesis | 0.03 | 0.01 | 0.05 | |
| delete.model | 0 | 0 | 0 | |
| delete.pattern | 0.01 | 0.00 | 0.02 | |
| delete.samples | 0.00 | 0.02 | 0.01 | |
| delete.type | 0.02 | 0.00 | 0.02 | |
| duplicates | 0 | 0 | 0 | |
| enforce.numeric | 0.02 | 0.00 | 0.01 | |
| enforce.string | 0 | 0 | 0 | |
| events.selection | 0 | 0 | 0 | |
| export.graphml | 0.27 | 0.00 | 0.26 | |
| export.mutex | 0 | 0 | 0 | |
| has.duplicates | 0.01 | 0.00 | 0.02 | |
| has.model | 0 | 0 | 0 | |
| has.stages | 0.00 | 0.01 | 0.01 | |
| import.GISTIC | 0 | 0 | 0 | |
| import.MAF | 0.10 | 0.02 | 0.11 | |
| intersect.datasets | 0 | 0 | 0 | |
| is.compliant | 0.01 | 0.00 | 0.02 | |
| join.events | 0 | 0 | 0 | |
| join.types | 0.08 | 0.00 | 0.07 | |
| keysToNames | 0 | 0 | 0 | |
| nameToKey | 0.01 | 0.00 | 0.02 | |
| nevents | 0 | 0 | 0 | |
| ngenes | 0 | 0 | 0 | |
| nhypotheses | 0 | 0 | 0 | |
| npatterns | 0 | 0 | 0 | |
| nsamples | 0 | 0 | 0 | |
| ntypes | 0 | 0 | 0 | |
| oncoprint.cbio | 0.00 | 0.01 | 0.01 | |
| order.frequency | 0.02 | 0.00 | 0.02 | |
| pheatmap | 0.06 | 0.00 | 0.06 | |
| rank.recurrents | 0.01 | 0.00 | 0.01 | |
| rename.gene | 0 | 0 | 0 | |
| rename.type | 0 | 0 | 0 | |
| samples.selection | 0.02 | 0.00 | 0.02 | |
| trim | 0 | 0 | 0 | |
| tronco.bootstrap | 0.30 | 0.05 | 25.91 | |
| tronco.caprese | 0.15 | 0.00 | 0.16 | |
| tronco.capri | 2.79 | 0.02 | 2.81 | |
| tronco.kfold.eloss | 0.24 | 0.00 | 0.23 | |
| tronco.kfold.posterr | 0.36 | 0.11 | 7.71 | |
| tronco.kfold.prederr | 0.28 | 0.07 | 6.75 | |
| tronco.mst.chowliu | 2.23 | 0.00 | 2.23 | |
| tronco.mst.edmonds | 1.89 | 0.00 | 1.98 | |
| tronco.mst.prim | 2.85 | 0.02 | 2.87 | |
| tronco.plot | 0.19 | 0.02 | 0.53 | |
| view | 0 | 0 | 0 | |
| which.samples | 0.01 | 0.00 | 0.02 | |
TRONCO.Rcheck/examples_x64/TRONCO-Ex.timings:
| name | user | system | elapsed | |
| TCGA.multiple.samples | 0.02 | 0.02 | 0.03 | |
| TCGA.remove.multiple.samples | 0.02 | 0.00 | 0.01 | |
| TCGA.shorten.barcodes | 0.00 | 0.02 | 0.02 | |
| annotate.description | 0 | 0 | 0 | |
| annotate.stages | 0 | 0 | 0 | |
| as.adj.matrix | 0.02 | 0.00 | 0.02 | |
| as.alterations | 0 | 0 | 0 | |
| as.bootstrap.scores | 0.09 | 0.00 | 0.09 | |
| as.colors | 0 | 0 | 0 | |
| as.confidence | 0.00 | 0.01 | 0.02 | |
| as.description | 0.02 | 0.00 | 0.02 | |
| as.events | 0 | 0 | 0 | |
| as.events.in.patterns | 0 | 0 | 0 | |
| as.events.in.sample | 0.01 | 0.00 | 0.01 | |
| as.gene | 0 | 0 | 0 | |
| as.genes | 0.02 | 0.00 | 0.02 | |
| as.genes.in.patterns | 0 | 0 | 0 | |
| as.genotypes | 0.01 | 0.00 | 0.01 | |
| as.hypotheses | 0.02 | 0.00 | 0.02 | |
| as.joint.probs | 0.02 | 0.00 | 0.01 | |
| as.kfold.eloss | 0.12 | 0.00 | 0.13 | |
| as.kfold.posterr | 0.08 | 0.00 | 0.08 | |
| as.kfold.prederr | 0.15 | 0.02 | 0.17 | |
| as.marginal.probs | 0 | 0 | 0 | |
| as.models | 0.02 | 0.01 | 0.03 | |
| as.parameters | 0 | 0 | 0 | |
| as.pathway | 0.02 | 0.00 | 0.01 | |
| as.patterns | 0 | 0 | 0 | |
| as.samples | 0 | 0 | 0 | |
| as.selective.advantage.relations | 0.17 | 0.00 | 0.17 | |
| as.stages | 0.02 | 0.00 | 0.02 | |
| as.types | 0 | 0 | 0 | |
| as.types.in.patterns | 0 | 0 | 0 | |
| change.color | 0 | 0 | 0 | |
| consolidate.data | 0.05 | 0.00 | 0.05 | |
| delete.event | 0.00 | 0.02 | 0.02 | |
| delete.gene | 0.02 | 0.00 | 0.01 | |
| delete.hypothesis | 0.01 | 0.01 | 0.03 | |
| delete.model | 0 | 0 | 0 | |
| delete.pattern | 0.02 | 0.00 | 0.01 | |
| delete.samples | 0.01 | 0.00 | 0.02 | |
| delete.type | 0 | 0 | 0 | |
| duplicates | 0.02 | 0.00 | 0.01 | |
| enforce.numeric | 0 | 0 | 0 | |
| enforce.string | 0 | 0 | 0 | |
| events.selection | 0.00 | 0.01 | 0.02 | |
| export.graphml | 0.25 | 0.00 | 1.06 | |
| export.mutex | 0.01 | 0.00 | 0.02 | |
| has.duplicates | 0 | 0 | 0 | |
| has.model | 0 | 0 | 0 | |
| has.stages | 0.00 | 0.02 | 0.01 | |
| import.GISTIC | 0.02 | 0.00 | 0.02 | |
| import.MAF | 0.11 | 0.00 | 0.11 | |
| intersect.datasets | 0 | 0 | 0 | |
| is.compliant | 0.01 | 0.00 | 0.01 | |
| join.events | 0 | 0 | 0 | |
| join.types | 0.08 | 0.02 | 0.10 | |
| keysToNames | 0 | 0 | 0 | |
| nameToKey | 0.02 | 0.00 | 0.01 | |
| nevents | 0 | 0 | 0 | |
| ngenes | 0 | 0 | 0 | |
| nhypotheses | 0.01 | 0.00 | 0.02 | |
| npatterns | 0 | 0 | 0 | |
| nsamples | 0 | 0 | 0 | |
| ntypes | 0.00 | 0.01 | 0.01 | |
| oncoprint.cbio | 0.02 | 0.00 | 0.02 | |
| order.frequency | 0.01 | 0.00 | 0.01 | |
| pheatmap | 0.08 | 0.00 | 0.08 | |
| rank.recurrents | 0 | 0 | 0 | |
| rename.gene | 0.02 | 0.00 | 0.02 | |
| rename.type | 0.01 | 0.00 | 0.01 | |
| samples.selection | 0.02 | 0.00 | 0.02 | |
| trim | 0 | 0 | 0 | |
| tronco.bootstrap | 0.26 | 0.03 | 30.60 | |
| tronco.caprese | 0.23 | 0.00 | 0.23 | |
| tronco.capri | 2.67 | 0.03 | 2.70 | |
| tronco.kfold.eloss | 0.28 | 0.00 | 0.28 | |
| tronco.kfold.posterr | 0.28 | 0.07 | 7.21 | |
| tronco.kfold.prederr | 0.21 | 0.04 | 7.56 | |
| tronco.mst.chowliu | 1.96 | 0.00 | 1.97 | |
| tronco.mst.edmonds | 1.96 | 0.00 | 1.97 | |
| tronco.mst.prim | 2.95 | 0.00 | 2.95 | |
| tronco.plot | 0.22 | 0.00 | 0.22 | |
| view | 0 | 0 | 0 | |
| which.samples | 0 | 0 | 0 | |