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| Package 188/188 | OS | Arch | BUILD | CHECK | BUILD BIN |
xcms1.6.0Colin 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 |
| Package: xcms |
| Version: 1.6.0 |
| Command: /loc/biocbuild/1.9d/R/bin/R CMD check xcms_1.6.0.tar.gz |
| RetCode: 0 |
| Time: 378.9 seconds |
| Status: WARNINGS |
| CheckDir: xcms.Rcheck |
| Warnings: 4 |
* checking for working latex ... OK * using log directory '/extra/loc/biocbuild/1.9d/Rpacks/xcms.Rcheck' * using R version 2.4.0 (2006-10-03) * checking for file 'xcms/DESCRIPTION' ... OK * this is package 'xcms' version '1.6.0' * 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 /extra/loc/biocbuild/1.9d/Rpacks/xcms.Rcheck/00check.log for details
xcms.Rcheck/00install.out:
* Installing *source* package 'xcms' ...
** libs
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c base64.c -o base64.o
base64.c:18: warning: `encode_group' defined but not used
base64.c:46: warning: `decode_group' defined but not used
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c netCDF.c -o netCDF.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c ramp.c -o ramp.o
ramp.c: In function `readPeaks':
ramp.c:998: warning: dereferencing type-punned pointer will break strict-aliasing rules
ramp.c:1011: warning: dereferencing type-punned pointer will break strict-aliasing rules
ramp.c:1109: warning: dereferencing type-punned pointer will break strict-aliasing rules
ramp.c:1120: warning: dereferencing type-punned pointer will break strict-aliasing rules
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c rampR.c -o rampR.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c util.c -o util.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c xcms.c -o xcms.o
xcms.c: In function `ProfBinLin':
xcms.c:11: warning: `xpre' might be used uninitialized in this function
xcms.c:11: warning: `ypre' might be used uninitialized in this function
xcms.c: In function `ProfBinLinBase':
xcms.c:62: warning: `ipre' might be used uninitialized in this function
gcc -shared -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
** 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)