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BioC 2.12: CHECK report for spade on petty

This page was generated on 2013-10-09 09:40:06 -0700 (Wed, 09 Oct 2013).

Package 609/671HostnameOS / ArchBUILDCHECKBUILD BIN
spade 1.8.0
Michael Linderman
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/spade
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: spade
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch spade_1.8.0.tar.gz
StartedAt: 2013-10-08 23:58:03 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-09 00:00:42 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 159.7 seconds
RetCode: 0
Status:  OK 
CheckDir: spade.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/spade.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'spade/DESCRIPTION' ... OK
* this is package 'spade' version '1.8.0'
* 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 ... [17s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [82s/52s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
SPADE.driver 69.98  7.157  47.364
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/spade.Rcheck/00check.log'
for details.

spade.Rcheck/00install.out:

* installing *source* package 'spade' ...
checking for gcc... llvm-gcc-4.2 -arch x86_64 -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 llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... llvm-gcc-4.2 -arch x86_64 -std=gnu99 -E
checking whether we are using the GNU C++ compiler... yes
checking whether llvm-g++-4.2 -arch x86_64 accepts -g... yes
checking how to run the C++ preprocessor... llvm-g++-4.2 -arch x86_64 -E
checking for llvm-gcc-4.2 -arch x86_64 -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... no
checking parallel/algorithm presence... no
checking for parallel/algorithm... no
"Parallel STL not found using default"
configure: creating ./config.status
config.status: creating src/Makevars
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/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 -fPIC  -mtune=core2 -g -O2  -c cluster.cc -o cluster.o
cluster.cc: In function 'void<unnamed>::cluster(const <unnamed>::Data_t*, size_t, size_t, size_t, <unnamed>::Idx_t*)':
cluster.cc:253: warning: iteration variable 'i' is unsigned
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/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 -fPIC  -mtune=core2 -g -O2  -c downsample.cc -o downsample.o
downsample.cc: In function '<unnamed>::Dist_t<unnamed>::compute_median_min_dist(<unnamed>::Data_t*, size_t, size_t, size_t)':
downsample.cc:44: warning: iteration variable 'i' is unsigned
downsample.cc: In function 'void<unnamed>::count_neighbors(<unnamed>::Data_t*, size_t, size_t, <unnamed>::Dist_t, <unnamed>::Dist_t, <unnamed>::Count_t*)':
downsample.cc:74: warning: iteration variable 'i' is unsigned
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/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 -fPIC  -mtune=core2 -g -O2  -c spade.cc -o spade.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/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 -fPIC  -mtune=core2 -g -O2  -c upsample.cc -o upsample.o
upsample.cc: In function 'void<unnamed>::assign_cluster(const <unnamed>::Data_t*, const <unnamed>::Data_t*, <unnamed>::Idx_t*, size_t, size_t, size_t, <unnamed>::Idx_t*)':
upsample.cc:35: warning: iteration variable 'i' is unsigned
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o spade.so cluster.o downsample.o spade.o upsample.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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
** testing if installed package can be loaded
* DONE (spade)

spade.Rcheck/spade-Ex.timings:

nameusersystemelapsed
SPADE.FCSToTree0.0150.0010.017
SPADE.addClusterToFCS0.0160.0010.017
SPADE.addDensityToFCS0.0110.0010.011
SPADE.annotateGraph0.0120.0010.013
SPADE.downsampleFCS0.0140.0000.014
SPADE.driver69.980 7.15747.364
SPADE.flattenAnnotations0.0120.0060.018
SPADE.installPlugin0.0020.0010.004
SPADE.layout.arch0.0130.0040.016
SPADE.markerMedians0.0120.0050.017
SPADE.plot.trees0.0120.0040.016
SPADE.read.FCS0.0850.0170.101
SPADE.write.graph0.0160.0020.018