* using log directory 'd:/Rcompile/CRANpkg/local/2.12/Rknots.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* checking for file 'Rknots/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rknots' version '1.1'
* checking package dependencies ... NOTE
Package suggested but not available for checking: bio3d
* checking if this is a source package ... OK
* checking whether package 'Rknots' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... 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 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
fileImport: no visible global function definition for 'read.pdb'
* checking Rd files ... NOTE
prepare_Rd: AlexanderBriggs.Rd:24-26: Dropping empty section \details
prepare_Rd: AlexanderBriggs.Rd:43-45: Dropping empty section \note
prepare_Rd: HOMFLY2mirror.Rd:22-24: Dropping empty section \details
prepare_Rd: HOMFLY2mirror.Rd:25-29: Dropping empty section \value
prepare_Rd: HOMFLY2mirror.Rd:42-44: Dropping empty section \note
prepare_Rd: PCAProjection.Rd:21-23: Dropping empty section \details
prepare_Rd: PCAProjection.Rd:46-48: Dropping empty section \note
prepare_Rd: Rknots-internal.Rd:67-68: Dropping empty section \usage
prepare_Rd: Rknots-internal.Rd:74-78: Dropping empty section \value
prepare_Rd: Rknots-internal.Rd:85-87: Dropping empty section \note
prepare_Rd: Rknots-internal.Rd:82-84: Dropping empty section \author
prepare_Rd: Rknots-internal.Rd:79-81: Dropping empty section \references
prepare_Rd: Rknots-internal.Rd:91-93: Dropping empty section \seealso
prepare_Rd: Rknots-internal.Rd:94-95: Dropping empty section \examples
prepare_Rd: Rknots-package.Rd:63-66: Dropping empty section \seealso
prepare_Rd: Rolfsen.table.Rd:26-28: Dropping empty section \details
prepare_Rd: buildLsw.Rd:34-36: Dropping empty section \details
prepare_Rd: buildLsw.Rd:37-41: Dropping empty section \value
prepare_Rd: buildLsw.Rd:52-54: Dropping empty section \note
prepare_Rd: buildLsw.Rd:58-60: Dropping empty section \seealso
prepare_Rd: buildLzero.Rd:34-36: Dropping empty section \details
prepare_Rd: buildLzero.Rd:37-41: Dropping empty section \value
prepare_Rd: buildLzero.Rd:52-54: Dropping empty section \note
prepare_Rd: buildLzero.Rd:58-60: Dropping empty section \seealso
prepare_Rd: centroidClosure.Rd:29-31: Dropping empty section \details
prepare_Rd: centroidClosure.Rd:48-50: Dropping empty section \note
prepare_Rd: centroidClosure.Rd:54-56: Dropping empty section \seealso
prepare_Rd: fileImport.Rd:59-61: Dropping empty section \seealso
prepare_Rd: findGaps.Rd:44-46: Dropping empty section \note
prepare_Rd: findGaps.Rd:37-39: Dropping empty section \references
prepare_Rd: findKnot.Rd:30-32: Dropping empty section \details
prepare_Rd: findKnot.Rd:52-54: Dropping empty section \note
prepare_Rd: findProteinKnot.Rd:32-34: Dropping empty section \details
prepare_Rd: grm.Rd:57-59: Dropping empty section \note
prepare_Rd: link.table.Rd:21-23: Dropping empty section \details
prepare_Rd: linkingNumber.Rd:54-56: Dropping empty section \note
prepare_Rd: msr.Rd:60-62: Dropping empty section \seealso
prepare_Rd: plotKnot3D.Rd:31-33: Dropping empty section \details
prepare_Rd: plotKnot3D.Rd:49-51: Dropping empty section \note
prepare_Rd: plotKnot3D.Rd:42-44: Dropping empty section \references
prepare_Rd: plotKnotDiagram.Rd:33-35: Dropping empty section \details
prepare_Rd: plotKnotDiagram.Rd:55-58: Dropping empty section \note
prepare_Rd: plotKnotDiagram.Rd:62-64: Dropping empty section \seealso
prepare_Rd: polyConversion.Rd:35-39: Dropping empty section \value
prepare_Rd: polyConversion.Rd:52-54: Dropping empty section \note
prepare_Rd: rMatrix.Rd:41-43: Dropping empty section \note
prepare_Rd: rMatrix.Rd:47-49: Dropping empty section \seealso
prepare_Rd: singleIntersection.Rd:70-72: Dropping empty section \note
prepare_Rd: singleIntersection.Rd:63-65: Dropping empty section \references
prepare_Rd: skeinIterator.Rd:28-30: Dropping empty section \details
prepare_Rd: skeinSign.Rd:47-49: Dropping empty section \note
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking PDF version of manual ... OK