BioC 3.1: CHECK report for cosmiq on zin2

Package: cosmiq

Version: 1.2.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings cosmiq_1.2.0.tar.gz

StartedAt: 2015-10-09 00:04:20 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:05:41 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 81.0 seconds

RetCode: 0

Status:  OK

CheckDir: cosmiq.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings cosmiq_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/cosmiq.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 ‘cosmiq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cosmiq’ version ‘1.2.0’
* 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 ‘cosmiq’ can be installed ... [4s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 ... 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 compilation flags in Makevars ... OK
* checking for GNU extensions 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 files in ‘vignettes’ ... OK
* checking examples ... [9s/13s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
combine_spectra 3.754  0.051   5.111
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [2s/3s]
 [2s/3s] 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: OK

* installing *source* package ‘cosmiq’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c util.c -o util.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o cosmiq.so util.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/cosmiq.Rcheck/cosmiq/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 (cosmiq)

name	user	system	elapsed
combine_spectra	3.754	0.051	5.111
cosmiq	0.001	0.000	0.001
create_datamatrix	0.002	0.000	0.002
eicmatrix	0.000	0.000	0.001
peakdetection	3.460	0.023	4.910
quantify_combined	0.000	0.000	0.001
retention_time	0	0	0