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Package 552/609HostnameOS / ArchBUILDCHECKBUILD BIN
spade 1.6.0
Michael Linderman
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/spade
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: spade
Version: 1.6.0
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings spade_1.6.0.tar.gz
StartedAt: 2013-03-25 05:05:32 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 05:09:02 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 210.1 seconds
RetCode: 0
Status:  OK 
CheckDir: spade.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/spade.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spade/DESCRIPTION’ ... OK
* this is package ‘spade’ version ‘1.6.0’
* 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 ‘spade’ can be installed ... OK
* checking installed package size ... 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 for left-over 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
SPADE.driver 147.229  0.636  99.261
* 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

spade.Rcheck/00install.out:

* installing *source* package ‘spade’ ...
configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking for gcc -std=gnu99 option to support OpenMP... -fopenmp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking parallel/algorithm usability... yes
checking parallel/algorithm presence... yes
checking for parallel/algorithm... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_PARALLEL_ALGORITHM=1 -DHAVE_PARALLEL_STL=1 -fpic  -g -O2  -Wall -c cluster.cc -o cluster.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_PARALLEL_ALGORITHM=1 -DHAVE_PARALLEL_STL=1 -fpic  -g -O2  -Wall -c downsample.cc -o downsample.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_PARALLEL_ALGORITHM=1 -DHAVE_PARALLEL_STL=1 -fpic  -g -O2  -Wall -c spade.cc -o spade.o
spade.cc: In function ‘void R_init_spade(DllInfo*)’:
spade.cc:8:31: warning: unused variable ‘_CallFun’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_PARALLEL_ALGORITHM=1 -DHAVE_PARALLEL_STL=1 -fpic  -g -O2  -Wall -c upsample.cc -o upsample.o
g++ -shared -L/usr/local/lib64 -o spade.so cluster.o downsample.o spade.o upsample.o -fopenmp -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/spade.Rcheck/spade/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘SPADE.Rnw’ 
** testing if installed package can be loaded

* DONE (spade)

spade.Rcheck/spade-Ex.timings:

nameusersystemelapsed
SPADE.FCSToTree0.0000.0000.001
SPADE.addClusterToFCS000
SPADE.addDensityToFCS000
SPADE.annotateGraph000
SPADE.downsampleFCS000
SPADE.driver147.229 0.636 99.261
SPADE.flattenAnnotations000
SPADE.installPlugin000
SPADE.layout.arch000
SPADE.markerMedians0.0000.0000.001
SPADE.plot.trees000
SPADE.read.FCS0.0600.0000.071
SPADE.write.graph000