BioC 2.12: CHECK report for CNAnorm on george2

Package: CNAnorm

Version: 1.6.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings CNAnorm_1.6.0.tar.gz

StartedAt: 2013-10-09 01:03:39 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:05:26 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 107.0 seconds

RetCode: 0

Status:  OK

CheckDir: CNAnorm.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/CNAnorm.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNAnorm/DESCRIPTION’ ... OK
* this is package ‘CNAnorm’ version ‘1.6.0’
* 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 ... [4s/5s] OK
* checking installed package size ... OK
* checking package 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 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [51s/54s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
peakPloidy 43.411  0.152  46.265
* 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

* installing *source* package ‘CNAnorm’ ...
** libs
gfortran   -fpic  -g -O2  -Wall -c daxpy.f -o daxpy.o
gfortran   -fpic  -g -O2  -Wall -c ddot.f -o ddot.o
gfortran   -fpic  -g -O2  -Wall -c dgbfa.f -o dgbfa.o
gfortran   -fpic  -g -O2  -Wall -c dgbsl.f -o dgbsl.o
gfortran   -fpic  -g -O2  -Wall -c dscal.f -o dscal.o
gfortran   -fpic  -g -O2  -Wall -c dsmooth.f -o dsmooth.o
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dsmooth.f:62.20:

      do 10 i=1,n-1                                                     
                    1
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dsmooth.f:70.7:

     &       diff(i-1)*diff(i+1) .lt. 0.) isplit(i)=1                   
       1
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dsmooth.f: In function ‘amed3’:
dsmooth.f:50:0: warning: ‘__result_amed3’ may be used uninitialized in this function [-Wuninitialized]
gfortran   -fpic  -g -O2  -Wall -c idamax.f -o idamax.o
gcc -std=gnu99 -shared -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-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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	0.072	0.004	0.077
DerivData-class	0.028	0.000	0.027
InData-class	0.028	0.000	0.030
Params-class	0.032	0.000	0.033
addDNACopy-methods	1.548	0.008	1.563
addSmooth-methods	1.028	0.008	1.200
chrsAndpos-methods	0.184	0.008	0.200
dataFrame2object	0.044	0.000	0.062
discreteNorm-methods	0.148	0.000	0.164
exportTable-method	0.104	0.004	0.125
gcNorm-methods	0.788	0.000	0.847
peakPloidy	43.411	0.152	46.265
plotGenome-methods	1.628	0.004	1.637
plotPeaks-methods	0.056	0.000	0.054
ratio-methods	0.684	0.000	0.707
suggValid-methods	0.028	0.000	0.029
validation-methods	0.040	0.000	0.039