cn.farms 1.2.0
Andreas Mitterecker
| Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/cn.farms | | Last Changed Rev: 59920 / Revision: 61898 | | Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | ERROR |
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/cn.farms.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cn.farms/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cn.farms' version '1.2.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'cn.farms' can be installed ... OK
* checking installed package size ... 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 package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... OK
* checking Rd files ... OK
* 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 Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package 'cn.farms' ...
** libs
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_cnfarms.c -o R_init_cnfarms.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
laplace.cpp:420:6: warning: unused variable 'method'
laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)':
laplace.cpp:197:9: warning: 'I1left' may be used uninitialized in this function
laplace.cpp:198:9: warning: 'I1right' may be used uninitialized in this function
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sparse_farms.c -o sparse_farms.o
sparse_farms.c: In function 'normData':
sparse_farms.c:191:10: warning: unused variable 'k'
sparse_farms.c:191:6: warning: unused variable 'i'
sparse_farms.c: In function 'sparseFarmsC':
sparse_farms.c:262:41: warning: unused variable 'invpPsi'
sparse_farms.c:259:9: warning: unused variable 'sumhelp'
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/cn.farms.Rcheck/cn.farms/libs/x64
** R
** demo
** inst
** preparing package for lazy loading
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
- Probesets: 20,000
- Samples..: 100
- Path.....: D:/biocbld/BBS-2˜1.9-B/meat/CNFARM˜1.RCH/00_PKG˜1/CNDCC1˜1.FAR
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Load 'snow'
- Use options(cluster=makeCluster(...))
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Use options(cluster=makeCluster(...))
================================================================================
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'cn.farms.Rnw'
** testing if installed package can be loaded
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
- Probesets: 20,000
- Samples..: 100
- Path.....: D:/biocbld/BBS-2˜1.9-B/meat/CNFARM˜1.RCH/00_PKG˜1/CNDCC1˜1.FAR
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Load 'snow'
- Use options(cluster=makeCluster(...))
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Use options(cluster=makeCluster(...))
================================================================================
* DONE (cn.farms)