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BioC 3.0: CHECK report for CNAnorm on perceval

This page was generated on 2015-04-10 09:56:18 -0700 (Fri, 10 Apr 2015).

Package 173/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNAnorm 1.12.0
Stefano Berri
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/CNAnorm
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: CNAnorm
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CNAnorm_1.12.0.tar.gz
StartedAt: 2015-04-10 00:04:23 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:06:28 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 125.1 seconds
RetCode: 0
Status:  OK 
CheckDir: CNAnorm.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CNAnorm_1.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/CNAnorm.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.12.0’
* 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/26s] 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 ... [35s/37s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
peakPloidy 27.433  0.225  27.738
* 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

CNAnorm.Rcheck/00install.out:

* 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
Warning: Nonconforming tab character in column 1 of line 14
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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-3.0-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)

CNAnorm.Rcheck/CNAnorm-Ex.timings:

nameusersystemelapsed
CNAnorm-class0.0290.0040.073
DerivData-class0.0060.0010.008
InData-class0.0090.0020.010
Params-class0.0060.0000.006
addDNACopy-methods1.1570.0041.348
addSmooth-methods0.7910.0030.797
chrsAndpos-methods0.0780.0030.093
dataFrame2object0.0070.0000.008
discreteNorm-methods0.0160.0010.017
exportTable-method0.0660.0040.099
gcNorm-methods0.7310.0040.752
peakPloidy27.433 0.22527.738
plotGenome-methods1.3190.0091.342
plotPeaks-methods0.0430.0040.169
ratio-methods0.6640.0070.672
suggValid-methods0.0160.0030.039
validation-methods0.0110.0010.013
workflowWrapper1.2590.0271.298