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| Package 204/205 | OS | Arch | BUILD | CHECK | BUILD BIN |
xcms1.5.2Colin 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 ] |
| 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
xcms.Rcheck/00install.out:
* 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)