BioC 3.1: CHECK report for SamSPECTRAL on zin2

Package: SamSPECTRAL

Version: 1.22.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings SamSPECTRAL_1.22.0.tar.gz

StartedAt: 2015-10-09 05:19:00 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:19:13 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 13.4 seconds

RetCode: 0

Status:  OK

CheckDir: SamSPECTRAL.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings SamSPECTRAL_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/SamSPECTRAL.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SamSPECTRAL/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SamSPECTRAL’ version ‘1.22.0’
* 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 ‘SamSPECTRAL’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 loading without being on the library search path ... OK
* checking 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 ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

.First.lib: no visible global function definition for ‘provide’
* 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 compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/SamSPECTRAL.Rcheck/00check.log’
for details.

* installing *source* package ‘SamSPECTRAL’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c conductance_computation.c -o conductance_computation.o
conductance_computation.c: In function ‘conductance_computation’:
conductance_computation.c:155:17: warning: variable ‘repres_ind’ set but not used [-Wunused-but-set-variable]
  int *density, *repres_ind;
                 ^
conductance_computation.c:155:7: warning: variable ‘density’ set but not used [-Wunused-but-set-variable]
  int *density, *repres_ind;
       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c maximum_of_rows.c -o maximum_of_rows.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o SamSPECTRAL.so Rinit.o conductance_computation.o maximum_of_rows.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/SamSPECTRAL.Rcheck/SamSPECTRAL/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SamSPECTRAL)

name	user	system	elapsed
Building_Communities	0.000	0.000	0.001
Civilized_Spectral_Clustering	0.001	0.000	0.002
Conductance_Calculation	0.001	0.000	0.001
Connecting	0.001	0.000	0.002
SamSPECTRAL-package	0.000	0.000	0.001
SamSPECTRAL	0.001	0.000	0.000
eigen.values.10	0.021	0.000	0.021
eigen.values.1000	0.008	0.000	0.009
kneepointDetection	0.062	0.000	0.062
small	0.020	0.003	0.023
stmFSC	0.185	0.005	0.189