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Package 208/208OSArchBUILDCHECKBUILD BIN

xcms

1.7.0

Colin A. Smith
Linux (SUSE 9.2) x86_64 OK  WARNINGS 
Linux (SUSE 10.1) x86_64 OK  WARNINGS 
Linux (SUSE 9.2) i686 OK  WARNINGS 
Solaris 2.9 sparc ERROR skipped
Windows Server 2003 x86_64 OK  WARNINGS  OK 
Windows Server 2003 NA OK [ ERROR ] OK 
Mac OS X (10.4.6) i686 OK  WARNINGS 
Package: xcms
Version: 1.7.0
Command: E:\biocbld\2.0d\R\bin\R.exe CMD check xcms_1.7.0.tar.gz
RetCode: 1
Time: 210.5 seconds
Status: ERROR
CheckDir: xcms.Rcheck
Warnings: NA

Command output

* checking for working latex ... OK
* using log directory 'E:/biocbld/2.0d/Rpacks/xcms.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'xcms/DESCRIPTION' ... OK
* this is package 'xcms' version '1.7.0'
* checking package dependencies ... WARNING
'library' or 'require' calls not declared from:
  rgl
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 ... WARNING
Found the following significant warnings:
  Warning: '\.' is an unrecognized escape in a character string
  Warning: unrecognized escape removed from "\\\."
See 'E:/biocbld/2.0d/Rpacks/xcms.Rcheck/00install.out' for details.
* 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 syntax errors ... WARNING
Warning: '\.' is an unrecognized escape in a character string
Warning: unrecognized escape removed from "\\\."
* 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* 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 ... OK
* 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 ... ERROR
LaTeX errors when creating DVI version.
This typically indicates Rd problems.

xcms.Rcheck/00install.out:

installing R.css in E:/biocbld/2.0d/Rpacks/xcms.Rcheck


---------- Making package xcms ------------
  adding build stamp to DESCRIPTION
  making DLL ...
making base64.d from base64.c
making netCDF.d from netCDF.c
making ramp.d from ramp.c
making rampR.d from rampR.c
making util.d from util.c
making xcms.d from xcms.c
gcc  -I./win -Ie:/biocbld/2.0d/R/include  -Wall -O2 -std=gnu99   -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./win -Ie:/biocbld/2.0d/R/include  -Wall -O2 -std=gnu99   -c netCDF.c -o netCDF.o
gcc  -I./win -Ie:/biocbld/2.0d/R/include  -Wall -O2 -std=gnu99   -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./win -Ie:/biocbld/2.0d/R/include  -Wall -O2 -std=gnu99   -c rampR.c -o rampR.o
gcc  -I./win -Ie:/biocbld/2.0d/R/include  -Wall -O2 -std=gnu99   -c util.c -o util.o
gcc  -I./win -Ie:/biocbld/2.0d/R/include  -Wall -O2 -std=gnu99   -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
windres --include-dir e:/biocbld/2.0d/R/include  -i xcms_res.rc -o xcms_res.o
gcc  -shared -s  -o xcms.dll xcms.def base64.o netCDF.o ramp.o rampR.o util.o xcms.o xcms_res.o  -Le:/biocbld/2.0d/R/bin -L./win -lws2_32 -lnetcdf   -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'xcms'
     Formats: text html latex example chm 
  SSgauss                           text    html    latex           chm
  c.xcmsSet                         text    html    latex           chm
  clustunique                       text    html    latex           chm
  colMax                            text    html    latex           chm
  descendZero                       text    html    latex   example chm
  diffreport-methods                text    html    latex           chm
  doubleMatrix                      text    html    latex           chm
  etg                               text    html    latex           chm
  fillPeaks-methods                 text    html    latex           chm
  filtfft                           text    html    latex           chm
  findEqualGreater                  text    html    latex           chm
  findPeaks-methods                 text    html    latex           chm
  getEIC-methods                    text    html    latex           chm
  getPeaks-methods                  text    html    latex           chm
  getScan-methods                   text    html    latex           chm
  getSpec-methods                   text    html    latex           chm
  group-methods                     text    html    latex           chm
  groupnames-methods                text    html    latex           chm
  groupval-methods                  text    html    latex           chm
  image.xcmsRaw                     text    html    latex           chm
  medianFilter                      text    html    latex   example chm
  na.flatfill                       text    html    latex           chm
  netCDF                            text    html    latex           chm
  panel.cor                         text    html    latex           chm
  plot-methods                      text    html    latex           chm
  plotChrom-methods                 text    html    latex           chm
  plotPeaks-methods                 text    html    latex           chm
  plotRaw-methods                   text    html    latex           chm
  plotScan-methods                  text    html    latex           chm
  plotSpec-methods                  text    html    latex           chm
  plotSurf-methods                  text    html    latex           chm
  plotTIC-methods                   text    html    latex           chm
  plotrt-methods                    text    html    latex           chm
  profGenerate                      text    html    latex           chm
  profMedFilt-methods               text    html    latex           chm
  profMethod-methods                text    html    latex           chm
  profRange-methods                 text    html    latex           chm
  profStep-methods                  text    html    latex           chm
  pval                              text    html    latex           chm
  ramp                              text    html    latex           chm
  rectUnique                        text    html    latex   example chm
  retcor-methods                    text    html    latex           chm
  retexp                            text    html    latex           chm
  sampnames-methods                 text    html    latex           chm
  specNoise                         text    html    latex           chm
  specPeaks                         text    html    latex           chm
  split.xcmsSet                     text    html    latex           chm
  xcmsEIC-class                     text    html    latex           chm
  xcmsRaw-class                     text    html    latex           chm
  xcmsRaw                           text    html    latex           chm
  xcmsSet-class                     text    html    latex           chm
  xcmsSet                           text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\2.0d\Rpacks\xcms.Rcheck\00_pkg_src\xcms\chm\xcms.chm


Compile time: 0 minutes, 1 second
53	Topics
250	Local links
8	Internet links
1	Graphic


Created e:\biocbld\2.0d\Rpacks\xcms.Rcheck\00_pkg_src\xcms\chm\xcms.chm, 72,739 bytes
Compression decreased file by 111,303 bytes.
  preparing package xcms for lazy loading
Warning: '\.' is an unrecognized escape in a character string
Warning: unrecognized escape removed from "\\\."
  adding MD5 sums

* DONE (xcms)