BioC 3.1: CHECK report for CNAnorm on petty

Package: CNAnorm

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CNAnorm_1.14.0.tar.gz

StartedAt: 2015-10-08 22:11:15 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:12:38 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 83.6 seconds

RetCode: 0

Status:  OK

CheckDir: CNAnorm.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CNAnorm_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/CNAnorm.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNAnorm/DESCRIPTION’ ... OK
* this is package ‘CNAnorm’ 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 ‘CNAnorm’ can be installed ... [4s/4s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [36s/36s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
peakPloidy 26.314  0.171  26.514
* 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-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c daxpy.f -o daxpy.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c ddot.f -o ddot.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c dgbfa.f -o dgbfa.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c dgbsl.f -o dgbsl.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c dscal.f -o dscal.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c dsmooth.f -o dsmooth.o
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dsmooth.f:62.21:

       do 10 i=1,n-1                                                    
                    1
Warning: Nonconforming tab character at (1)
dsmooth.f: In function ‘amed3’:
dsmooth.f:50: warning: ‘__result_amed3’ may be used uninitialized in this function
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c idamax.f -o idamax.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o CNAnorm.so daxpy.o ddot.o dgbfa.o dgbsl.o dscal.o dsmooth.o idamax.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-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	0.003	0.076
DerivData-class	0.006	0.001	0.007
InData-class	0.006	0.002	0.007
Params-class	0.006	0.001	0.006
addDNACopy-methods	1.674	0.007	1.697
addSmooth-methods	0.998	0.003	1.002
chrsAndpos-methods	0.107	0.002	0.109
dataFrame2object	0.007	0.001	0.008
discreteNorm-methods	0.025	0.001	0.027
exportTable-method	0.106	0.004	0.111
gcNorm-methods	0.962	0.003	0.965
peakPloidy	26.314	0.171	26.514
plotGenome-methods	1.588	0.021	1.610
plotPeaks-methods	0.051	0.003	0.055
ratio-methods	0.956	0.003	0.960
suggValid-methods	0.022	0.002	0.025
validation-methods	0.012	0.001	0.012
workflowWrapper	1.610	0.010	1.623