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Package 530/609HostnameOS / ArchBUILDCHECKBUILD BIN
SamSPECTRAL 1.12.0
Habil Zare
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/SamSPECTRAL
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  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 

Summary

Package: SamSPECTRAL
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SamSPECTRAL_1.12.0.tar.gz
StartedAt: 2013-03-25 01:14:51 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:15:14 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 23.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: SamSPECTRAL.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/SamSPECTRAL.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'SamSPECTRAL/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SamSPECTRAL' version '1.12.0'
* 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 'SamSPECTRAL' can be installed ... WARNING
Found the following significant warnings:
  /Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning is a GCC extension
  /Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0"
See '/Users/biocbuild/bbs-2.11-bioc/meat/SamSPECTRAL.Rcheck/00install.out' for details.
* 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 ... NOTE
Non-standard license specification:
  GPL version 2 or newer
Standardizable: TRUE
Standardized license specification:
  GPL (>= 2)
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/SamSPECTRAL.Rcheck/00check.log'
for details.

SamSPECTRAL.Rcheck/00install.out:

* installing *source* package 'SamSPECTRAL' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c Rinit.c -o Rinit.o
In file included from Rinit.c:7:
/Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning is a GCC extension
/Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0"
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c conductance_computation.c -o conductance_computation.o
conductance_computation.c: In function 'conductance_computation':
conductance_computation.c:153: warning: unused variable 'dj'
conductance_computation.c:153: warning: unused variable 'di'
conductance_computation.c:152: warning: unused variable 'memberLen'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c maximum_of_rows.c -o maximum_of_rows.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o SamSPECTRAL.so Rinit.o conductance_computation.o maximum_of_rows.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/SamSPECTRAL.Rcheck/SamSPECTRAL/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'Clustering_by_SamSPECTRAL.Rnw' 
** testing if installed package can be loaded

* DONE (SamSPECTRAL)

SamSPECTRAL.Rcheck/SamSPECTRAL-Ex.timings:

nameusersystemelapsed
Building_Communities000
Civilized_Spectral_Clustering000
Conductance_Calculation0.0000.0000.001
Connecting0.0000.0000.001
SamSPECTRAL-package0.0000.0010.001
SamSPECTRAL0.0000.0000.001
eigen.values.100.0340.0080.045
eigen.values.10000.0100.0030.014
small0.0270.0040.032
stmFSC0.2090.0260.236