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Package 100/479HostnameOS / ArchBUILDCHECKBUILD BIN
cn.farms 1.1.2
Andreas Mitterecker
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cn.farms
Last Changed Rev: 55652 / Revision: 56603
Last Changed Date: 2011-05-17 16:01:16 -0700 (Tue, 17 May 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 (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: cn.farms
Version: 1.1.2
Command: mkdir cn.farms.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cn.farms.buildbin-libdir cn.farms_1.1.2.tar.gz >cn.farms-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=cn.farms.buildbin-libdir --install="check:cn.farms-install.out" --force-multiarch --no-vignettes --timings cn.farms_1.1.2.tar.gz && mv cn.farms.buildbin-libdir/* cn.farms.Rcheck/ && rmdir cn.farms.buildbin-libdir
StartedAt: 2011-07-07 04:40:46 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 04:43:57 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 191.0 seconds
RetCode: 0
Status:  OK  
CheckDir: cn.farms.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/cn.farms.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-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 '1.1.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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
* loading checks for arch 'i386'
** 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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 examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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

cn.farms.Rcheck/00install.out:


install for i386

* installing *source* package 'cn.farms' ...
** libs
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_cnfarms.c -o R_init_cnfarms.o
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:244:6: warning: unused variable 'method'
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -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'
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/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/i386
** R
** demo
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: tools
Loading required package: bit
Loading package bit1.1-7

package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)

creators: bit bitwhich

coercion: as.logical as.integer as.bit as.bitwhich which

operator: ! & | xor != == 

querying: print length any all min max range sum summary

bit access: length<- [ [<- [[ [[<-

for more help type ?bit


Attaching package: 'bit'

The following object(s) are masked from 'package:base':

    xor

Loading package ff2.2-2
- getOption("fftempdir")=="D:/biocbld/bbs-2.9-bioc/tmpdir/RtmpEdKMiJ"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==37570478.08 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==1878523904 -- consider a different value for tuning your system

Attaching package ff

Attaching package: 'ff'

The following object(s) are masked from 'package:utils':

    write.csv, write.csv2

The following object(s) are masked from 'package:base':

    is.factor, is.ordered

================================================================================
Welcome to oligoClasses version 1.15.9
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
    - Probesets: 20,000
    - Samples..:    100
    - Path.....: D:/biocbld/bbs-2.9-bioc/tmpdir/RtmpEdKMiJ/R.INSTALL16df4ab8/cn.farms
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Loading required package: snow
Parallel computing support for 'oligo/crlmm': Disabled
     - Use options(cluster=makeCluster(...))
================================================================================

**************************************************************************
   The plan to change the data format for CNA object has been postponed   
 in order to ensure backward compatibility with older versions of DNAcopy 
**************************************************************************

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'cn.farms.Rnw' 
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.15.9
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
    - Probesets: 20,000
    - Samples..:    100
    - Path.....: D:/biocbld/bbs-2.9-bioc/tmpdir/RtmpEdKMiJ/R.INSTALL16df4ab8/cn.farms
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Use options(cluster=makeCluster(...))
================================================================================

add DLL for x64

* 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:244:6: warning: unused variable 'method'
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.buildbin-libdir/cn.farms/libs/x64
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.15.9
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
    - Probesets: 20,000
    - Samples..:    100
    - Path.....: D:/biocbld/bbs-2.9-bioc/tmpdir/RtmpaUZyNQ/R.INSTALL3b132043/cn.farms
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Use options(cluster=makeCluster(...))
================================================================================
* MD5 sums
packaged installation of 'cn.farms' as cn.farms_1.1.2.zip

* DONE (cn.farms)

cn.farms.Rcheck/cn.farms-Ex.timings:

nameusersystemelapsed
combineData0.860.000.92
createAnnotation000
distributionDistance0.530.000.53
dnaCopySf0.150.000.16
fragLengCorr4.190.004.26
mlSummarization1.770.041.80
normalizeAverage000
normalizeCels000
normalizeNpData000
plotDendrogram0.270.000.27
plotDensity0.850.000.84
plotEvalIc0.220.000.22
plotRegions0.290.000.29
plotSmoothScatter0.860.001.22
plotViolines0.190.000.19
slSummarization1.710.011.73
sparseFarmsC000
summarizeFarmsExact000
summarizeFarmsGaussian0.020.000.01
summarizeFarmsMethods000
summarizeFarmsVariational000
summarizeWindowBps0.010.000.02
summarizeWindowMethods000
summarizeWindowStd000