CHECK report for xcms on derby

Package: xcms

Version: 1.5.2

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check xcms_1.5.2.tar.gz

RetCode: 0

Time: 333.9 seconds

Status: WARNINGS

CheckDir: xcms.Rcheck

Warnings: 4

* checking for working latex ... OK
* using log directory '/Users/biocbuild/1.9d/Rpacks/xcms.Rcheck'
* using R version 2.4.0 alpha (2006-09-07 r39185)
* checking for file 'xcms/DESCRIPTION' ... OK
* this is package 'xcms' version '1.5.2'
* checking package dependencies ... WARNING
package 'methods' is used but not declared
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking if this is a source package ... OK
* checking whether package 'xcms' can be installed ... 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 syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking S3 generic/method consistency ... WARNING
Error in get(tname, envir = env) : recursive default argument reference
Error in as.environment(pos) : no item called "newtable" on the search list
Error: .onLoad failed in 'loadNamespace' for 'methods'
Execution halted
See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Error in get(tname, envir = env) : recursive default argument reference
Error in as.environment(pos) : no item called "newtable" on the search list
Error: .onLoad failed in 'loadNamespace' for 'methods'
Execution halted
See the chapter 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Error in get(tname, envir = env) : recursive default argument reference
Error in as.environment(pos) : no item called "newtable" on the search list
Error: .onLoad failed in 'loadNamespace' for 'methods'
Execution halted
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating xcms-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating xcms-manual.tex ... OK
* checking xcms-manual.tex ... OK

WARNING: There were 4 warnings, see
  /Users/biocbuild/1.9d/Rpacks/xcms.Rcheck/00check.log
for details

* Installing *source* package 'xcms' ...
** libs
** arch - i386
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c base64.c -o base64.o
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c netCDF.c -o netCDF.o
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c ramp.c -o ramp.o
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c rampR.c -o rampR.o
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c util.c -o util.o
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c xcms.c -o xcms.o
gcc-4.0 -arch i386 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so base64.o netCDF.o ramp.o rampR.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf  -L/Library/Frameworks/R.framework/Resources/lib/i386 -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Resources/lib/i386/libRblas.dylib
ld: warning -L: directory name (/sw/lib) does not exist
** arch - ppc
gcc-4.0 -arch ppc -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -c base64.c -o base64.o
gcc-4.0 -arch ppc -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -c netCDF.c -o netCDF.o
gcc-4.0 -arch ppc -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -c ramp.c -o ramp.o
gcc-4.0 -arch ppc -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -c rampR.c -o rampR.o
gcc-4.0 -arch ppc -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -c util.c -o util.o
gcc-4.0 -arch ppc -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -c xcms.c -o xcms.o
gcc-4.0 -arch ppc -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so base64.o netCDF.o ramp.o rampR.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf  -L/Library/Frameworks/R.framework/Resources/lib/ppc -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Resources/lib/ppc/libRblas.dylib
ld: warning -L: directory name (/sw/lib) does not exist
** R
** inst
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'xcms'
     Formats: text html latex example 
  SSgauss                           text    html    latex
  c.xcmsSet                         text    html    latex
  clustunique                       text    html    latex
  colMax                            text    html    latex
  descendZero                       text    html    latex   example
  diffreport-methods                text    html    latex
  doubleMatrix                      text    html    latex
  etg                               text    html    latex
  fillPeaks-methods                 text    html    latex
  filtfft                           text    html    latex
  findEqualGreater                  text    html    latex
  findPeaks-methods                 text    html    latex
  getEIC-methods                    text    html    latex
  getPeaks-methods                  text    html    latex
  getScan-methods                   text    html    latex
  getSpec-methods                   text    html    latex
  group-methods                     text    html    latex
  groupnames-methods                text    html    latex
  groupval-methods                  text    html    latex
  image.xcmsRaw                     text    html    latex
  medianFilter                      text    html    latex   example
  na.flatfill                       text    html    latex
  netCDF                            text    html    latex
  panel.cor                         text    html    latex
  plot-methods                      text    html    latex
  plotChrom-methods                 text    html    latex
  plotPeaks-methods                 text    html    latex
  plotRaw-methods                   text    html    latex
  plotScan-methods                  text    html    latex
  plotSpec-methods                  text    html    latex
  plotSurf-methods                  text    html    latex
  plotTIC-methods                   text    html    latex
  plotrt-methods                    text    html    latex
  profGenerate                      text    html    latex
  profMedFilt-methods               text    html    latex
  profMethod-methods                text    html    latex
  profRange-methods                 text    html    latex
  profStep-methods                  text    html    latex
  pval                              text    html    latex
  ramp                              text    html    latex
  rectUnique                        text    html    latex   example
  retcor-methods                    text    html    latex
  retexp                            text    html    latex
  sampnames-methods                 text    html    latex
  specNoise                         text    html    latex
  specPeaks                         text    html    latex
  split.xcmsSet                     text    html    latex
  xcmsEIC-class                     text    html    latex
  xcmsRaw-class                     text    html    latex
  xcmsRaw                           text    html    latex
  xcmsSet-class                     text    html    latex
  xcmsSet                           text    html    latex
** building package indices ...
* DONE (xcms)

Package 204/205	OS	Arch	BUILD	CHECK	BUILD BIN
xcms 1.5.2 Colin A. Smith	Linux (SUSE 9.2)	x86_64	OK	WARNINGS
	Linux (SUSE 9.2)	i686	OK	WARNINGS
	Solaris 2.9	sparc	ERROR	skipped
	Linux (SUSE 10.0)	x86_64	OK	WARNINGS
	Windows Server 2003	x86_64	OK	WARNINGS	OK
	Windows XP	i686	OK	WARNINGS	skipped
	Mac OS X (10.4.6)	i686	OK	[ WARNINGS ]

xcms

1.5.2

Command output