Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O [P] Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.13: CHECK report for PLPE on moscato1

This page was generated on 2014-04-05 09:49:44 -0700 (Sat, 05 Apr 2014).

Package 537/750HostnameOS / ArchBUILDCHECKBUILD BIN
PLPE 1.22.0
Soo-heang Eo
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/PLPE
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 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: PLPE
Version: 1.22.0
Command: rm -rf PLPE.buildbin-libdir && mkdir PLPE.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PLPE.buildbin-libdir PLPE_1.22.0.tar.gz >PLPE-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=PLPE.buildbin-libdir --install="check:PLPE-install.out" --force-multiarch --no-vignettes --timings PLPE_1.22.0.tar.gz && mv PLPE.buildbin-libdir/* PLPE.Rcheck/ && rmdir PLPE.buildbin-libdir
StartedAt: 2014-04-05 05:53:47 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 05:54:38 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 51.8 seconds
RetCode: 0
Status:  OK  
CheckDir: PLPE.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/PLPE.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 'PLPE/DESCRIPTION' ... OK
* this is package 'PLPE' version '1.22.0'
* 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 'PLPE' 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
* 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
'library' or 'require' calls to packages already attached by Depends:
  'Biobase' 'LPE' 'MASS' 'methods'
  Please remove these calls from your code.
Package in Depends field not imported from: 'LPE'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of 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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'PLPE/R/lpe.paired.R':
  .First.lib calls:
    cat("LPEP version 1.0.0 \n")
    require(Biobase)
    require(methods)

Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
* 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 ... NOTE
S3 methods shown with full name in documentation object 'lpe.paired.fdr':
  'lpe.paired.fdr'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'PLPE.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [2s] OK
** running examples for arch 'x64' ... [2s] 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

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/PLPE.Rcheck/00check.log'
for details.

PLPE.Rcheck/00install.out:


install for i386

* installing *source* package 'PLPE' ...
** 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 'PLPE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PLPE' as PLPE_1.22.0.zip
* DONE (PLPE)

PLPE.Rcheck/examples_i386/PLPE-Ex.timings:

nameusersystemelapsed
lpe.paired0.070.020.08
lpe.paired.default0.040.000.05
lpe.paired.fdr0.20.00.2
lpe.paired.fdr.default0.200.000.21
print.lpe.paired0.050.000.05
summary.lpe.paired0.040.000.05

PLPE.Rcheck/examples_x64/PLPE-Ex.timings:

nameusersystemelapsed
lpe.paired0.060.010.07
lpe.paired.default0.060.000.07
lpe.paired.fdr0.220.020.23
lpe.paired.fdr.default0.230.000.23
print.lpe.paired0.090.000.09
summary.lpe.paired0.030.000.03