xcms 1.21.6
Colin A. Smith
| Bioconductor Changelog | | Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms | | Last Changed Rev: 43393 / Revision: 43434 | | Last Changed Date: 2009-12-04 10:31:08 -0800 (Fri, 04 Dec 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | ERROR | skipped | skipped |
| pelham | Mac OS X Leopard (10.5.8) / i386 | ERROR | skipped | skipped |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/xcms.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-10-22 r50179)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'xcms/DESCRIPTION' ... OK
* this is package 'xcms' version '1.21.6'
* checking package name space information ... OK
* checking package dependencies ... OK
* 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 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 name space can be loaded with stated dependencies ... 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
.onLoad : <anonymous>: no visible global function definition for
'mpi.comm.size'
.onLoad : <anonymous>: no visible global function definition for
'mpi.close.Rslaves'
.onLoad : <anonymous>: no visible global function definition for
'mpi.finalize'
KeggSearch: no visible binding for global variable 'masfile'
KeggSearch: no visible binding for global variable 'type'
patternVsRowScore: no visible global function definition for 'nn2'
running: multiple local function definitions for 'funct' with different
formal arguments
xcmsPapply: no visible global function definition for 'mpi.comm.size'
xcmsPapply: no visible global function definition for
'mpi.spawn.Rslaves'
xcmsPapply: no visible global function definition for 'mpi.comm.rank'
xcmsPapply : papply_int_slavefunction: no visible global function
definition for 'mpi.send.Robj'
xcmsPapply : papply_int_slavefunction: no visible global function
definition for 'mpi.recv.Robj'
xcmsPapply : papply_int_slavefunction: no visible global function
definition for 'mpi.any.source'
xcmsPapply : papply_int_slavefunction: no visible global function
definition for 'mpi.any.tag'
xcmsPapply : papply_int_slavefunction: no visible global function
definition for 'mpi.get.sourcetag'
xcmsPapply: no visible global function definition for
'mpi.bcast.Robj2slave'
xcmsPapply: no visible global function definition for 'mpi.bcast.cmd'
xcmsPapply: no visible global function definition for 'mpi.recv.Robj'
xcmsPapply: no visible global function definition for 'mpi.any.source'
xcmsPapply: no visible global function definition for 'mpi.any.tag'
xcmsPapply: no visible global function definition for
'mpi.get.sourcetag'
xcmsPapply: no visible global function definition for 'mpi.send.Robj'
xcmsSet: no visible global function definition for 'mpi.spawn.Rslaves'
xcmsSet: no visible global function definition for 'mpi.comm.size'
xcmsSet: no visible global function definition for 'mpi.comm.rank'
xcmsSet: no visible global function definition for 'mpi.close.Rslaves'
* checking Rd files ... NOTE
prepare_Rd: collect-methods.Rd:63-64: Dropping empty section \seealso
prepare_Rd: split.xcmsRaw.Rd:18-20: Dropping empty section \usage
prepare_Rd: split.xcmsSet.Rd:19-21: Dropping empty section \usage
prepare_Rd: xcmsRaw.Rd:46-48: Dropping empty section \note
prepare_Rd: xcmsSet.Rd:41-43: 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking tests ...
Running 'doRUnit.R'
OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* install options are ' --no-html'
* installing *source* package 'xcms' ...
** libs
making DLL ...
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -c obiwarp/xcms_obiwarp.cpp -o obiwarp/xcms_obiwarp.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O3 -Wall -std=gnu99 -c mzClust_hclust.c -o mzClust_hclust.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O3 -Wall -std=gnu99 -c mzROI.c -o mzROI.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O3 -Wall -std=gnu99 -c netCDF.c -o netCDF.o
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -c ramp_base64.cpp -o ramp_base64.o
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -c ramp.cpp -o ramp.o
ramp.cpp:64:1: warning: "S_ISDIR" redefined
In file included from ramp.h:59,
from ramp.cpp:34:
c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/sys/stat.h:68:1: warning: this is the location of the previous definition
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -c rampR.cpp -o rampR.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O3 -Wall -std=gnu99 -c util.c -o util.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O3 -Wall -std=gnu99 -c xcms.c -o xcms.o
g++ -shared -s -o xcms.dll tmp.def obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwarp.o mzClust_hclust.o mzROI.o netCDF.o ramp_base64.o ramp.o rampR.o util.o xcms.o -L./win -lws2_32 -lnetcdf -lz -Le:/biocbld/bbs-2.6-bioc/R/bin -lR
... done
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** MD5 sums
* DONE (xcms)