BioC 3.3: CHECK report for CNAnorm on linux2.bioconductor.org

Package: CNAnorm

Version: 1.17.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings CNAnorm_1.17.0.tar.gz

StartedAt: 2015-10-27 02:43:22 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:44:05 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 42.5 seconds

RetCode: 0

Status:  OK

CheckDir: CNAnorm.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings CNAnorm_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/CNAnorm.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNAnorm/DESCRIPTION’ ... OK
* this is package ‘CNAnorm’ version ‘1.17.0’
* 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 ‘CNAnorm’ can be installed ... [2s/2s] 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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
peakPloidy 14.81  0.024   14.85
* 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 ‘CNAnorm’ ...
** libs
gfortran   -fpic  -g -O2  -c daxpy.f -o daxpy.o
gfortran   -fpic  -g -O2  -c ddot.f -o ddot.o
gfortran   -fpic  -g -O2  -c dgbfa.f -o dgbfa.o
gfortran   -fpic  -g -O2  -c dgbsl.f -o dgbsl.o
gfortran   -fpic  -g -O2  -c dscal.f -o dscal.o
gfortran   -fpic  -g -O2  -c dsmooth.f -o dsmooth.o
gfortran   -fpic  -g -O2  -c idamax.f -o idamax.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o CNAnorm.so daxpy.o ddot.o dgbfa.o dgbsl.o dscal.o dsmooth.o idamax.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/CNAnorm.Rcheck/CNAnorm/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 (CNAnorm)

name	user	system	elapsed
CNAnorm-class	0.021	0.003	0.026
DerivData-class	0.039	0.000	0.039
InData-class	0.002	0.004	0.005
Params-class	0.006	0.000	0.005
addDNACopy-methods	1.074	0.000	1.075
addSmooth-methods	0.596	0.004	0.600
chrsAndpos-methods	0.042	0.000	0.043
dataFrame2object	0.006	0.000	0.005
discreteNorm-methods	0.015	0.000	0.014
exportTable-method	0.112	0.004	0.116
gcNorm-methods	0.419	0.000	0.419
peakPloidy	14.810	0.024	14.850
plotGenome-methods	0.84	0.00	0.84
plotPeaks-methods	0.026	0.000	0.026
ratio-methods	0.426	0.000	0.426
suggValid-methods	0.01	0.00	0.01
validation-methods	0.007	0.000	0.007
workflowWrapper	0.825	0.000	0.824