- using R Under development (unstable) (2012-08-14 r60253)
- using platform: x86_64-unknown-linux-gnu (64-bit)
- using session charset: UTF-8
- 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 for hidden files and directories ... NOTE
Found the following hidden files and directories:
inst/doc.tmp/.Renviron
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
- 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
- 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 ... 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 ... OK
- checking for unstated dependencies in tests ... OK
- checking tests ... OK
Running ‘chopit.R’
Comparing ‘chopit.Rout’ to ‘chopit.Rout.save’ ...15c15
< ## rgenoud (Version 5.7-8, Build Date: 2012-06-03)
---
> ## rgenoud (Version 5.7-1, Build Date: 2010-08-26)
17,22d16
< ## Please cite software as:
< ## Walter Mebane, Jr. and Jasjeet S. Sekhon. 2011.
< ## ``Genetic Optimization Using Derivatives: The rgenoud package for R.''
< ## Journal of Statistical Software, 42(11): 1-26.
< ##
<
Running ‘unit.anchors.R’
Comparing ‘unit.anchors.Rout’ to ‘unit.anchors.Rout.save’ ...12c12
< ## rgenoud (Version 5.7-8, Build Date: 2012-06-03)
---
> ## rgenoud (Version 5.7-1, Build Date: 2010-08-26)
14,19d13
< ## Please cite software as:
< ## Walter Mebane, Jr. and Jasjeet S. Sekhon. 2011.
< ## ``Genetic Optimization Using Derivatives: The rgenoud package for R.''
< ## Journal of Statistical Software, 42(11): 1-26.
< ##
<
Running ‘unit.cpolr.R’
Comparing ‘unit.cpolr.Rout’ to ‘unit.cpolr.Rout.save’ ...4c4
< ## rgenoud (Version 5.7-8, Build Date: 2012-06-03)
---
> ## rgenoud (Version 5.7-1, Build Date: 2010-08-26)
6,11d5
< ## Please cite software as:
< ## Walter Mebane, Jr. and Jasjeet S. Sekhon. 2011.
< ## ``Genetic Optimization Using Derivatives: The rgenoud package for R.''
< ## Journal of Statistical Software, 42(11): 1-26.
< ##
<
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking running R code from vignettes ... [14s/14s] OK
- checking re-building of vignette PDFs ... NOTE
Error in re-building vignettes:
...
ex loaded) Xy-pic pdf driver: `rotate' extension support
(/vols/Linux_Fedora-64/F16/texlive/2012/texmf-dist/tex/generic/xypic/xypdf-ro.t
ex loaded) loaded)) (/data/blackswan/ripley/texmf/tex/latex/forR/html.sty
! LaTeX Error: No counter 'chapter' defined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.117 ...[part]\else\newcounter{lsection}[chapter]
\fi
?
! Emergency stop.
...
l.117 ...[part]\else\newcounter{lsection}[chapter]
\fi
! ==> Fatal error occurred, no output PDF file produced!
Transcript written on anchors.log.
make[1]: *** [anchors.pdf] Error 1
make[1]: Leaving directory `/data/blackswan/ripley/R/packages/tests-devel/anchors.Rcheck/vign_test/anchors/inst/doc'
Error in buildVignettes(dir = "/data/blackswan/ripley/R/packages/tests-devel/anchors.Rcheck/vign_test/anchors") :
running 'make' failed
Execution halted
- checking PDF version of manual ... OK
NOTE: There were 4 notes.
See
‘/data/blackswan/ripley/R/packages/tests-devel/anchors.Rcheck/00check.log’
for details.