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rptR log file (check_x86_64_linux)

Tue Jul 16 20:22:53 2013: Checking package rptR (SVN revision 52) ...
* using log directory ‘/mnt/building/build_2013-07-16-20-05/RF_PKG_CHECK/PKGS/rptR.Rcheck’
* using R version 3.0.1 Patched (2013-07-15 r63328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘rptR/DESCRIPTION’ ... OK
* this is package ‘rptR’ version ‘0.6.405’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Holger Schielzeth ’
New submission
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rptR’ can be installed ... [13s/26s] 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
* 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file ‘/mnt/building/build_2013-07-16-20-05/RF_PKG_CHECK/PKGS/rptR.Rcheck/00_pkg_src/rptR/man/rpt.adj.Rd’:
  \examples lines wider than 105 characters:
     (rpt.Fledge <- rpt.adj(sqrtFledge ~ Age + (1|MaleID), "MaleID", data=Fledglings, datatype="Gaussian", 

Rd file ‘/mnt/building/build_2013-07-16-20-05/RF_PKG_CHECK/PKGS/rptR.Rcheck/00_pkg_src/rptR/man/rpt.binomGLMM.add.Rd’:
  \examples lines wider than 105 characters:
     (rpt.Host <- rpt.binomGLMM.add(HostYN[OwnClutchesBothSeasons==1], FemaleID[OwnClutchesBothSeasons==1]))

Rd file ‘/mnt/building/build_2013-07-16-20-05/RF_PKG_CHECK/PKGS/rptR.Rcheck/00_pkg_src/rptR/man/rpt.binomGLMM.multi.Rd’:
  \usage lines wider than 95 characters:
             rpt.binomGLMM.multi(y, groups, link=c("logit", "probit"), CI=0.95, nboot=1000, npermut=1000)
  \examples lines wider than 105 characters:
     (rpt.Host <- rpt.binomGLMM.multi(HostYN[OwnClutchesBothSeasons==1], FemaleID[OwnClutchesBothSeasons==1],
             FemaleID[OwnClutchesBothSeasons==1], nboot=10, npermut=10))  # reduced number of npermut iterations
     zz = which(ParasitismOR[,1]==0 & ParasitismOR[,2]==0) # some rows have entries 0,0 and need to be removed

Rd file ‘/mnt/building/build_2013-07-16-20-05/RF_PKG_CHECK/PKGS/rptR.Rcheck/00_pkg_src/rptR/man/rpt.poisGLMM.multi.Rd’:
  \usage lines wider than 95 characters:
             rpt.poisGLMM.multi(y, groups, link=c("log", "sqrt"), CI=0.95, nboot=1000, npermut=1000)

Rd file ‘/mnt/building/build_2013-07-16-20-05/RF_PKG_CHECK/PKGS/rptR.Rcheck/00_pkg_src/rptR/man/rpt.remlLMM.adj.Rd’:
  \examples lines wider than 105 characters:
     (rpt.BS <- rpt.remlLMM.adj(Tarsus ~ Sex + (1|BirdID), "BirdID", data=BodySize, nboot=10, npermut=10))
     (rpt.Weight <- rpt.remlLMM.adj(Weight ~ Sex + (1|BirdID), "BirdID", data=BodySize, nboot=10, npermut=10))

These lines will be truncated in the PDF manual.
* 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 ... [33s/62s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
rpt.binomGLMM.add 8.205  0.020  16.335
rpt.mcmcLMM       6.056  0.008  10.519
rpt.poisGLMM.add  5.336  0.012   9.756
print.rpt         3.412  0.020   6.929
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/mnt/building/build_2013-07-16-20-05/RF_PKG_CHECK/PKGS/rptR.Rcheck/00check.log’
for details.

Run time: 377 seconds.

Additional Logs:   00install.out
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