BioC 3.1: CHECK report for CGHbase on moscato2
This page was generated on 2015-10-09 09:28:17 -0700 (Fri, 09 Oct 2015).
CGHbase 1.28.0 Mark van de Wiel
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/CGHbase | Last Changed Rev: 102591 / Revision: 109384 | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK |  |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |  |
Summary
Package: CGHbase
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Version: 1.28.0
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Command: rm -rf CGHbase.buildbin-libdir CGHbase.Rcheck && mkdir CGHbase.buildbin-libdir CGHbase.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CGHbase.buildbin-libdir CGHbase_1.28.0.tar.gz >CGHbase.Rcheck\00install.out 2>&1 && cp CGHbase.Rcheck\00install.out CGHbase-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=CGHbase.buildbin-libdir --install="check:CGHbase-install.out" --force-multiarch --no-vignettes --timings CGHbase_1.28.0.tar.gz
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StartedAt: 2015-10-09 00:08:04 -0700 (Fri, 09 Oct 2015)
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EndedAt: 2015-10-09 00:09:12 -0700 (Fri, 09 Oct 2015)
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EllapsedTime: 67.7 seconds
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RetCode: 0
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Status: OK
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CheckDir: CGHbase.Rcheck
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Warnings: 0
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Command output
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### Running command:
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### rm -rf CGHbase.buildbin-libdir CGHbase.Rcheck && mkdir CGHbase.buildbin-libdir CGHbase.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CGHbase.buildbin-libdir CGHbase_1.28.0.tar.gz >CGHbase.Rcheck\00install.out 2>&1 && cp CGHbase.Rcheck\00install.out CGHbase-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=CGHbase.buildbin-libdir --install="check:CGHbase-install.out" --force-multiarch --no-vignettes --timings CGHbase_1.28.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/CGHbase.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CGHbase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CGHbase' version '1.28.0'
* 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 'CGHbase' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Package in Depends field not imported from: 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': 'Biobase:::assayDataElement'
See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'Biobase:::assayDataDims'
See the note in ?`:::` about the use of this operator.
* 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 examples ...
** running examples for arch 'i386' ... [2s] OK
** running examples for arch 'x64' ... [3s] OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'E:/biocbld/bbs-3.1-bioc/meat/CGHbase.Rcheck/00check.log'
for details.
CGHbase.Rcheck/00install.out:
install for i386
* installing *source* package 'CGHbase' ...
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
install for x64
* installing *source* package 'CGHbase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CGHbase' as CGHbase_1.28.0.zip
* DONE (CGHbase)
CGHbase.Rcheck/examples_i386/CGHbase-Ex.timings:
name | user | system | elapsed
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class.cghCall | 0.06 | 0.00 | 0.06 |
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class.cghRaw | 0.28 | 0.00 | 0.28 |
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class.cghRegions | 0.27 | 0.00 | 0.27 |
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class.cghSeg | 0.04 | 0.00 | 0.04 |
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copynumber | 0.05 | 0.00 | 0.05 |
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frequencyPlot | 0 | 0 | 0 |
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frequencyPlotCalls | 0 | 0 | 0 |
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make_cghRaw | 0.14 | 0.00 | 0.14 |
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summaryPlot | 0 | 0 | 0 |
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CGHbase.Rcheck/examples_x64/CGHbase-Ex.timings:
name | user | system | elapsed
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class.cghCall | 0.09 | 0.00 | 0.09 |
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class.cghRaw | 0.27 | 0.00 | 0.26 |
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class.cghRegions | 0.32 | 0.00 | 0.31 |
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class.cghSeg | 0.04 | 0.00 | 0.05 |
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copynumber | 0.03 | 0.00 | 0.03 |
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frequencyPlot | 0 | 0 | 0 |
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frequencyPlotCalls | 0 | 0 | 0 |
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make_cghRaw | 0.2 | 0.0 | 0.2 |
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summaryPlot | 0 | 0 | 0 |
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