BioC 2.13: CHECK report for graphite on moscato1
This page was generated on 2014-04-05 09:50:27 -0700 (Sat, 05 Apr 2014).
graphite 1.8.1 Gabriele Sales
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/graphite | Last Changed Rev: 82840 / Revision: 88450 | Last Changed Date: 2013-11-03 12:15:06 -0800 (Sun, 03 Nov 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: graphite
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Version: 1.8.1
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Command: rm -rf graphite.buildbin-libdir && mkdir graphite.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=graphite.buildbin-libdir graphite_1.8.1.tar.gz >graphite-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=graphite.buildbin-libdir --install="check:graphite-install.out" --force-multiarch --no-vignettes --timings graphite_1.8.1.tar.gz && mv graphite.buildbin-libdir/* graphite.Rcheck/ && rmdir graphite.buildbin-libdir
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StartedAt: 2014-04-05 04:25:12 -0700 (Sat, 05 Apr 2014)
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EndedAt: 2014-04-05 04:30:22 -0700 (Sat, 05 Apr 2014)
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EllapsedTime: 310.4 seconds
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RetCode: 0
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Status: OK
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CheckDir: graphite.Rcheck
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Warnings: 0
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Command output
* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/graphite.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 'graphite/DESCRIPTION' ... OK
* this is package 'graphite' version '1.8.1'
* 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 'graphite' 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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... 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 ... NOTE
Note: found 16 marked UTF-8 strings
* 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':
'graphite.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [67s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
runClipperMulti 29.84 0.05 29.89
runClipper 18.25 0.20 18.45
runSPIA 6.68 0.10 7.17
** running examples for arch 'x64' ... [73s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
runClipperMulti 33.09 0.03 33.12
runClipper 18.68 0.19 18.86
runSPIA 7.94 0.05 8.89
* 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 3 notes.
See
'D:/biocbld/bbs-2.13-bioc/meat/graphite.Rcheck/00check.log'
for details.
graphite.Rcheck/00install.out:
install for i386
* installing *source* package 'graphite' ...
** 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 'graphite' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'graphite' as graphite_1.8.1.zip
* DONE (graphite)
graphite.Rcheck/examples_i386/graphite-Ex.timings:
name | user | system | elapsed
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convertIdentifiers | 1.89 | 0.04 | 1.91 |
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cytoscapePlot | 0 | 0 | 0 |
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pathwayGraph | 0.02 | 0.00 | 0.02 |
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runClipper | 18.25 | 0.20 | 18.45 |
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runClipperMulti | 29.84 | 0.05 | 29.89 |
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runDEGraph | 2.36 | 0.32 | 2.85 |
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runDEGraphMulti | 0.86 | 0.03 | 0.89 |
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runSPIA | 6.68 | 0.10 | 7.17 |
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runTopologyGSA | 1.12 | 0.01 | 1.17 |
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runTopologyGSAMulti | 0.56 | 0.03 | 0.59 |
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graphite.Rcheck/examples_x64/graphite-Ex.timings:
name | user | system | elapsed
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convertIdentifiers | 1.96 | 0.08 | 2.04 |
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cytoscapePlot | 0 | 0 | 0 |
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pathwayGraph | 0.03 | 0.00 | 0.03 |
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runClipper | 18.68 | 0.19 | 18.86 |
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runClipperMulti | 33.09 | 0.03 | 33.12 |
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runDEGraph | 2.60 | 0.27 | 2.87 |
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runDEGraphMulti | 1.05 | 0.01 | 1.06 |
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runSPIA | 7.94 | 0.05 | 8.89 |
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runTopologyGSA | 1.63 | 0.06 | 1.72 |
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runTopologyGSAMulti | 0.68 | 0.00 | 0.67 |
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