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BioC 2.12: CHECK report for lmdme on moscato2

This page was generated on 2013-10-09 09:39:11 -0700 (Wed, 09 Oct 2013).

Package 367/671HostnameOS / ArchBUILDCHECKBUILD BIN
lmdme 1.2.1
Cristobal Fresno
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/lmdme
Last Changed Rev: 76154 / Revision: 81334
Last Changed Date: 2013-04-30 10:54:26 -0700 (Tue, 30 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: lmdme
Version: 1.2.1
Command: rm -rf lmdme.buildbin-libdir && mkdir lmdme.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lmdme.buildbin-libdir lmdme_1.2.1.tar.gz >lmdme-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=lmdme.buildbin-libdir --install="check:lmdme-install.out" --force-multiarch --no-vignettes --timings lmdme_1.2.1.tar.gz && mv lmdme.buildbin-libdir/* lmdme.Rcheck/ && rmdir lmdme.buildbin-libdir
StartedAt: 2013-10-09 02:49:26 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:53:52 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 266.4 seconds
RetCode: 0
Status:  OK  
CheckDir: lmdme.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/lmdme.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-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 '1.2.1'
* 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 'lmdme' can be installed ... OK
* checking installed package size ... OK
* checking package 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
* 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 for unstated 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 ... NOTE
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'
* 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 examples ...
** running examples for arch 'i386' ... [105s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
lmdme-permutation   23.10   1.16   24.28
lmdme-biplot        10.03   0.45   10.53
lmdme-leverage       9.02   0.25    9.27
lmdme-padjust        8.88   0.20    9.08
lmdme-getters        8.79   0.25    9.04
lmdme-printshow      8.61   0.34    8.95
lmdme-screeplot      8.06   0.06    8.12
lmdme-lmdme          7.91   0.15    8.06
lmdme-loadingplot    7.92   0.14    8.06
lmdme-decomposition  7.40   0.36    7.77
** running examples for arch 'x64' ... [108s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
lmdme-permutation   25.09   1.35   26.44
lmdme-decomposition  9.98   0.50   10.48
lmdme-biplot         9.92   0.33   10.25
lmdme-padjust        9.64   0.19    9.86
lmdme-getters        8.71   0.28    8.99
lmdme-leverage       8.02   0.23    8.69
lmdme-printshow      7.58   0.35    7.93
lmdme-loadingplot    7.71   0.19    7.90
lmdme-screeplot      7.72   0.11    7.83
lmdme-lmdme          7.52   0.22    7.76
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.12-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_1.2.1.zip
* DONE (lmdme)