Check results for 'anchors'

using R version 2.15.0 (2012-03-30)
using platform: i386-apple-darwin9.8.0 (32-bit)
using session charset: ASCII
checking for file 'anchors/DESCRIPTION' ... OK
this is package 'anchors' version '3.0-7'
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 whether package 'anchors' can be installed ... OK
checking installed package size ... OK
checking package directory ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking DESCRIPTION meta-information ... OK
checking top-level 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 'x86_64'
** 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
File 'anchors/R/load.first.R':
.onAttach calls:
cat("\n## anchors (Version ", ver, ", Build Date: ", builddate, ")\n", sep = "")
cat("## See http://wand.stanford.edu/anchors for additional documentation and support.\n\n", sep = "")

Package startup functions should use 'packageStartupMessage' to
generate messages.
See section 'Good practice' in ?.onAttach.

.onAttach: warning in packageDescription("anchors", lib = mylib):
partial argument match of 'lib' to 'lib.loc'
anchors.order.calc: warning in rank(data$z0[i, ], ties = "min"):
partial argument match of 'ties' to 'ties.method'
chopit: warning in anchors.chopit.fit(data = adata, parm = parm, count
= count, opt = options): partial argument match of 'opt' to 'options'
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 contents of 'data' directory ... OK
checking data for non-ASCII characters ... OK
checking data for ASCII and uncompressed saves ... OK
checking line endings in C/C++/Fortran sources/headers ... OK
checking line endings in Makefiles ... OK
checking for portable compilation flags in Makevars ... OK
checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
checking compiled code ... OK
checking sizes of PDF files under 'inst/doc' ... OK
checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
'Makefile', 'anchors.tex', 'apsr2001.bst'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x86_64' ... OK
checking for unstated dependencies in tests ... OK
checking tests ...
** running tests for arch 'i386' OK
Running 'chopit.R'
Comparing 'chopit.Rout' to 'chopit.Rout.save' ...15c15
< ## rgenoud (Version 5.7-3, Build Date: 2011-05-04)
---
> ## rgenoud (Version 5.7-1, Build Date: 2010-08-26)
139c139
< [6] 3.404366e-05 1.620102e-05 1.464629e-03 1.804596e-05 2.864445e-04
---
> [6] 3.404366e-05 1.620102e-05 1.464629e-03 1.804597e-05 2.864445e-04
141,143c141,143
< [16] 2.466399e-06 4.791234e-06 1.320843e-04 1.598640e-06 1.507675e-05
< [21] -1.356460e-06 -2.332286e-06 -2.967051e-06 -3.090504e-06 -2.468684e-06
< [26] -8.169708e-06 -8.479025e-06 -4.477243e-06 -3.743376e-06 -2.198867e-06
---
> [16] 2.466399e-06 4.791235e-06 1.320844e-04 1.598641e-06 1.507675e-05
> [21] -1.356460e-06 -2.332286e-06 -2.967052e-06 -3.090505e-06 -2.468684e-06
> [26] -8.169708e-06 -8.479026e-06 -4.477243e-06 -3.743376e-06 -2.198868e-06
230c230
< [6] 3.404366e-05 1.620102e-05 1.464629e-03 1.804596e-05 2.864445e-04
---
> [6] 3.404366e-05 1.620102e-05 1.464629e-03 1.804597e-05 2.864445e-04
232,234c232,234
< [16] 2.466399e-06 4.791234e-06 1.320843e-04 1.598640e-06 1.507675e-05
< [21] -1.356460e-06 -2.332286e-06 -2.967051e-06 -3.090504e-06 -2.468684e-06
< [26] -8.169708e-06 -8.479025e-06 -4.477243e-06 -3.743376e-06 -2.198867e-06
---
> [16] 2.466399e-06 4.791235e-06 1.320844e-04 1.598641e-06 1.507675e-05
> [21] -1.356460e-06 -2.332286e-06 -2.967052e-06 -3.090505e-06 -2.468684e-06
> [26] -8.169708e-06 -8.479026e-06 -4.477243e-06 -3.743376e-06 -2.198868e-06
Running 'unit.anchors.R'
Comparing 'unit.anchors.Rout' to 'unit.anchors.Rout.save' ...12c12
< ## rgenoud (Version 5.7-3, Build Date: 2011-05-04)
---
> ## rgenoud (Version 5.7-1, Build Date: 2010-08-26)
Running 'unit.cpolr.R'
Comparing 'unit.cpolr.Rout' to 'unit.cpolr.Rout.save' ...4c4
< ## rgenoud (Version 5.7-3, Build Date: 2011-05-04)
---
> ## rgenoud (Version 5.7-1, Build Date: 2010-08-26)
** running tests for arch 'x86_64' OK
Running 'chopit.R'
Comparing 'chopit.Rout' to 'chopit.Rout.save' ...15c15
< ## rgenoud (Version 5.7-3, Build Date: 2011-05-04)
---
> ## rgenoud (Version 5.7-1, Build Date: 2010-08-26)
139c139
< [6] 3.404366e-05 1.620102e-05 1.464629e-03 1.804596e-05 2.864445e-04
---
> [6] 3.404366e-05 1.620102e-05 1.464629e-03 1.804597e-05 2.864445e-04
141,143c141,143
< [16] 2.466399e-06 4.791234e-06 1.320843e-04 1.598640e-06 1.507675e-05
< [21] -1.356460e-06 -2.332286e-06 -2.967051e-06 -3.090504e-06 -2.468684e-06
< [26] -8.169708e-06 -8.479025e-06 -4.477243e-06 -3.743376e-06 -2.198867e-06
---
> [16] 2.466399e-06 4.791235e-06 1.320844e-04 1.598641e-06 1.507675e-05
> [21] -1.356460e-06 -2.332286e-06 -2.967052e-06 -3.090505e-06 -2.468684e-06
> [26] -8.169708e-06 -8.479026e-06 -4.477243e-06 -3.743376e-06 -2.198868e-06
230c230
< [6] 3.404366e-05 1.620102e-05 1.464629e-03 1.804596e-05 2.864445e-04
---
> [6] 3.404366e-05 1.620102e-05 1.464629e-03 1.804597e-05 2.864445e-04
232,234c232,234
< [16] 2.466399e-06 4.791234e-06 1.320843e-04 1.598640e-06 1.507675e-05
< [21] -1.356460e-06 -2.332286e-06 -2.967051e-06 -3.090504e-06 -2.468684e-06
< [26] -8.169708e-06 -8.479025e-06 -4.477243e-06 -3.743376e-06 -2.198867e-06
---
> [16] 2.466399e-06 4.791235e-06 1.320844e-04 1.598641e-06 1.507675e-05
> [21] -1.356460e-06 -2.332286e-06 -2.967052e-06 -3.090505e-06 -2.468684e-06
> [26] -8.169708e-06 -8.479026e-06 -4.477243e-06 -3.743376e-06 -2.198868e-06
Running 'unit.anchors.R'
Comparing 'unit.anchors.Rout' to 'unit.anchors.Rout.save' ...12c12
< ## rgenoud (Version 5.7-3, Build Date: 2011-05-04)
---
> ## rgenoud (Version 5.7-1, Build Date: 2010-08-26)
Running 'unit.cpolr.R'
Comparing 'unit.cpolr.Rout' to 'unit.cpolr.Rout.save' ...4c4
< ## rgenoud (Version 5.7-3, Build Date: 2011-05-04)
---
> ## rgenoud (Version 5.7-1, Build Date: 2010-08-26)
checking for unstated dependencies in vignettes ... OK
checking package vignettes in 'inst/doc' ... OK
checking running R code from vignettes ... OK
checking re-building of vignette PDFs ... NOTE
Error in re-building vignettes:
...
Xy-pic option: Colour extension v.3.3 loaded)
(/usr/local/texlive/2009/texmf-dist/tex/generic/xypic/xymatrix.tex
Xy-pic option: Matrix feature v.3.4 loaded)
(/usr/local/texlive/2009/texmf-dist/tex/generic/xypic/xyarrow.tex
Xy-pic option: Arrow and Path feature v.3.5 path, \ar, loaded)
(/usr/local/texlive/2009/texmf-dist/tex/generic/xypic/xygraph.tex
Xy-pic option: Graph feature v.3.7 loaded) loaded))

! LaTeX Error: File `html.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

Enter file name:
! Emergency stop.
<read *>

l.30 \usepackage
{url}^^M
! ==> Fatal error occurred, no output PDF file produced!
Transcript written on anchors.log.
make: *** [anchors.pdf] Error 1
Error in buildVignettes(dir = "/Volumes/Tiger/Builds/Rdev-web/QA/Simon/packages/leopard-universal/results/2.15/anchors.Rcheck/vign_test/anchors") :
running 'make' failed
Execution halted
checking PDF version of manual ... OK
NOTE: There were 3 notes.
See
'/Volumes/Tiger/Builds/Rdev-web/QA/Simon/packages/leopard-universal/results/2.15/anchors.Rcheck/00check.log'
for details.
elapsed time (check, wall clock): 1:48