BioC 3.3: CHECK report for lmdme on windows2.bioconductor.org
This page was generated on 2015-10-27 12:15:05 -0400 (Tue, 27 Oct 2015).
lmdme 1.13.0 Cristobal Fresno
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/lmdme | Last Changed Rev: 109592 / Revision: 109948 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK |  |
Summary
Package: lmdme
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Version: 1.13.0
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Command: rm -rf lmdme.buildbin-libdir lmdme.Rcheck && mkdir lmdme.buildbin-libdir lmdme.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lmdme.buildbin-libdir lmdme_1.13.0.tar.gz >lmdme.Rcheck\00install.out 2>&1 && cp lmdme.Rcheck\00install.out lmdme-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=lmdme.buildbin-libdir --install="check:lmdme-install.out" --force-multiarch --no-vignettes --timings lmdme_1.13.0.tar.gz
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StartedAt: 2015-10-27 03:36:22 -0400 (Tue, 27 Oct 2015)
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EndedAt: 2015-10-27 03:37:47 -0400 (Tue, 27 Oct 2015)
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EllapsedTime: 84.7 seconds
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RetCode: 0
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Status: OK
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CheckDir: lmdme.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 lmdme.buildbin-libdir lmdme.Rcheck && mkdir lmdme.buildbin-libdir lmdme.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lmdme.buildbin-libdir lmdme_1.13.0.tar.gz >lmdme.Rcheck\00install.out 2>&1 && cp lmdme.Rcheck\00install.out lmdme-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=lmdme.buildbin-libdir --install="check:lmdme-install.out" --force-multiarch --no-vignettes --timings lmdme_1.13.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/lmdme.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'lmdme/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lmdme' version '1.13.0'
* 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 'lmdme' 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 ... NOTE
'library' or 'require' call to 'parallel' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in 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 ... NOTE
decomposition,lmdme : <anonymous>: no visible global function
definition for 'plsr'
permutation,formula-data.frame-data.frame: no visible binding for
global variable 'mclapply'
permutation,formula-data.frame-data.frame: no visible global function
definition for 'detectCores'
print,lmdme: no visible global function definition for 'pvalues'
Undefined global functions or variables:
detectCores mclapply plsr pvalues
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [27s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
lmdme-permutation 5.19 0.44 5.63
** running examples for arch 'x64' ... [30s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
lmdme-permutation 6.15 0.39 6.55
* 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: 2 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/lmdme.Rcheck/00check.log'
for details.
lmdme.Rcheck/00install.out:
install for i386
* installing *source* package 'lmdme' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'fitted.values' from package 'stats' in package 'lmdme'
Creating a generic function for 'fitted' from package 'stats' in package 'lmdme'
Creating a generic function for 'coef' from package 'stats' in package 'lmdme'
Creating a generic function for 'coefficients' from package 'stats' in package 'lmdme'
Creating a generic function for 'resid' from package 'stats' in package 'lmdme'
Creating a generic function for 'residuals' from package 'stats' in package 'lmdme'
Creating a generic function for 'print' from package 'base' in package 'lmdme'
Creating a generic function for 'summary' from package 'base' in package 'lmdme'
Creating a new generic function for 'p.adjust' in package 'lmdme'
Creating a generic function for 'biplot' from package 'stats' in package 'lmdme'
Creating a generic function for 'screeplot' from package 'stats' in package 'lmdme'
Creating a generic function for 'loadingplot' from package 'pls' in package 'lmdme'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'lmdme' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'lmdme' as lmdme_1.13.0.zip
* DONE (lmdme)
lmdme.Rcheck/examples_i386/lmdme-Ex.timings:
name | user | system | elapsed
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lmdme-biplot | 2.45 | 0.10 | 2.55 |
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lmdme-decomposition | 2.25 | 0.09 | 2.34 |
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lmdme-getters | 2.19 | 0.19 | 2.38 |
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lmdme-leverage | 2.52 | 0.15 | 2.67 |
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lmdme-lmdme | 2.00 | 0.18 | 2.17 |
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lmdme-loadingplot | 1.97 | 0.15 | 2.13 |
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lmdme-padjust | 2.17 | 0.15 | 2.33 |
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lmdme-permutation | 5.19 | 0.44 | 5.63 |
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lmdme-printshow | 2.04 | 0.13 | 2.17 |
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lmdme-screeplot | 2.11 | 0.12 | 2.23 |
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lmdme.Rcheck/examples_x64/lmdme-Ex.timings:
name | user | system | elapsed
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lmdme-biplot | 2.72 | 0.06 | 2.78 |
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lmdme-decomposition | 2.45 | 0.11 | 2.56 |
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lmdme-getters | 2.78 | 0.17 | 2.95 |
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lmdme-leverage | 2.53 | 0.14 | 2.68 |
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lmdme-lmdme | 2.47 | 0.16 | 2.62 |
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lmdme-loadingplot | 2.47 | 0.11 | 2.58 |
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lmdme-padjust | 2.44 | 0.12 | 2.56 |
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lmdme-permutation | 6.15 | 0.39 | 6.55 |
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lmdme-printshow | 2.16 | 0.16 | 2.31 |
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lmdme-screeplot | 2.22 | 0.09 | 2.31 |
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