BioC 3.2: CHECK report for iBBiG on linux1.bioconductor.org

Package: iBBiG

Version: 1.14.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings iBBiG_1.14.0.tar.gz

StartedAt: 2015-10-27 04:44:09 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:46:02 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 113.4 seconds

RetCode: 0

Status:  OK

CheckDir: iBBiG.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings iBBiG_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/iBBiG.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 ‘iBBiG/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iBBiG’ version ‘1.14.0’
* 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 ‘iBBiG’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' call to ‘biclust’ which was already attached by Depends.
  Please remove these calls from your code.
* 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 compiled code ... NOTE
File ‘iBBiG/libs/iBBiG.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘iBBiG.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘iBBiG.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [90s/90s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
iBBiG-package 32.087  0.028  32.139
iBBiG         30.097  0.028  30.198
iBBiG-class   26.364  0.032  26.449
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/iBBiG.Rcheck/00check.log’
for details.

* installing *source* package ‘iBBiG’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_iBBiG.c -o R_init_iBBiG.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c iBBiG.c -o iBBiG.o
iBBiG.c: In function ‘clusterCovsC’:
iBBiG.c:300:6: warning: implicit declaration of function ‘time’ [-Wimplicit-function-declaration]
      srand((unsigned)time(NULL));     
      ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o iBBiG.so R_init_iBBiG.o iBBiG.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/iBBiG.Rcheck/iBBiG/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 (iBBiG)

name	user	system	elapsed
iBBiG-class	26.364	0.032	26.449
iBBiG-package	32.087	0.028	32.139
iBBiG	30.097	0.028	30.198
makeArtificial	0.447	0.004	0.451