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BioC 3.6: CHECK report for PLPE on tokay1

This page was generated on 2017-08-16 13:28:11 -0400 (Wed, 16 Aug 2017).

Package 1008/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PLPE 1.37.0
Soo-heang Eo
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PLPE
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PLPE
Version: 1.37.0
Command: rm -rf PLPE.buildbin-libdir PLPE.Rcheck && mkdir PLPE.buildbin-libdir PLPE.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PLPE.buildbin-libdir PLPE_1.37.0.tar.gz >PLPE.Rcheck\00install.out 2>&1 && cp PLPE.Rcheck\00install.out PLPE-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=PLPE.buildbin-libdir --install="check:PLPE-install.out" --force-multiarch --no-vignettes --timings PLPE_1.37.0.tar.gz
StartedAt: 2017-08-16 01:34:05 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:34:53 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 48.1 seconds
RetCode: 0
Status:  OK  
CheckDir: PLPE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PLPE.buildbin-libdir PLPE.Rcheck && mkdir PLPE.buildbin-libdir PLPE.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PLPE.buildbin-libdir PLPE_1.37.0.tar.gz >PLPE.Rcheck\00install.out 2>&1 && cp PLPE.Rcheck\00install.out PLPE-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=PLPE.buildbin-libdir --install="check:PLPE-install.out" --force-multiarch --no-vignettes --timings PLPE_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/PLPE.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PLPE/DESCRIPTION' ... OK
* this is package 'PLPE' version '1.37.0'
* 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
** 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' 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.
* 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'.

base.error.paired: no visible global function definition for 'na.omit'
base.error.paired: no visible global function definition for 'quantile'
base.error.paired: no visible global function definition for 'var'
base.error.paired: no visible global function definition for 'median'
base.error.paired: no visible global function definition for
  'smooth.spline'
base.error.paired: no visible global function definition for
  'fixbounds.predict.smooth.spline'
generate.null: no visible global function definition for 'quantile'
generate.null: no visible global function definition for 'median'
lpe.paired.default: no visible binding for global variable 'median'
lpe.paired.default: no visible binding for global variable 'var'
lpe.paired.default: no visible binding for global variable 't.test'
lpe.paired.default: no visible global function definition for 'pnorm'
lpe.paired.default: no visible global function definition for 'lm'
lpe.paired.fdr.default: no visible global function definition for
  'quantile'
summary.lpe.paired: no visible global function definition for 'head'
summary.lpe.paired.fdr: no visible global function definition for
  'head'
Undefined global functions or variables:
  fixbounds.predict.smooth.spline head lm median na.omit pnorm quantile
  smooth.spline t.test var
Consider adding
  importFrom("stats", "lm", "median", "na.omit", "pnorm", "quantile",
             "smooth.spline", "t.test", "var")
  importFrom("utils", "head")
to your NAMESPACE file.
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
* DONE

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-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_1.37.0.zip
* DONE (PLPE)

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

nameusersystemelapsed
lpe.paired0.040.020.05
lpe.paired.default0.20.00.2
lpe.paired.fdr0.160.000.15
lpe.paired.fdr.default0.200.000.21
print.lpe.paired0.030.000.03
summary.lpe.paired0.040.000.03

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

nameusersystemelapsed
lpe.paired0.090.000.09
lpe.paired.default0.270.020.29
lpe.paired.fdr0.210.000.22
lpe.paired.fdr.default0.30.00.3
print.lpe.paired0.050.000.04
summary.lpe.paired0.060.010.08