BioC 2.12: CHECK report for spade on lamb2

Package: spade

Version: 1.7.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings spade_1.7.0.tar.gz

StartedAt: 2013-01-16 06:31:34 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 06:35:43 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 248.0 seconds

RetCode: 0

Status: OK

CheckDir: spade.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/spade.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.7.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘spade’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 346.253  0.132  169.94
* 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 ‘spade’ ...
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-2.12-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  -c cluster.cc -o cluster.o
g++ -I/home/biocbuild/bbs-2.12-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  -c downsample.cc -o downsample.o
g++ -I/home/biocbuild/bbs-2.12-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  -c spade.cc -o spade.o
g++ -I/home/biocbuild/bbs-2.12-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  -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-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-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)

name	user	system	elapsed
SPADE.FCSToTree	0.016	0.000	0.014
SPADE.addClusterToFCS	0.016	0.000	0.016
SPADE.addDensityToFCS	0.008	0.000	0.009
SPADE.annotateGraph	0.008	0.004	0.012
SPADE.downsampleFCS	0.012	0.000	0.014
SPADE.driver	346.253	0.132	169.940
SPADE.flattenAnnotations	0.008	0.004	0.011
SPADE.installPlugin	0.004	0.000	0.005
SPADE.layout.arch	0.008	0.000	0.007
SPADE.markerMedians	0.020	0.000	0.016
SPADE.plot.trees	0.008	0.000	0.008
SPADE.read.FCS	0.060	0.000	0.058
SPADE.write.graph	0.012	0.000	0.010

Summary

Command output