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BioC 2.14: CHECK report for CNAnorm on zin2

This page was generated on 2014-10-08 08:49:17 -0700 (Wed, 08 Oct 2014).

Package 166/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNAnorm 1.10.1
Stefano Berri
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/CNAnorm
Last Changed Rev: 90176 / Revision: 95116
Last Changed Date: 2014-05-09 15:54:26 -0700 (Fri, 09 May 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: CNAnorm
Version: 1.10.1
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings CNAnorm_1.10.1.tar.gz
StartedAt: 2014-10-07 22:44:31 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:45:19 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 48.0 seconds
RetCode: 0
Status:  OK 
CheckDir: CNAnorm.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings CNAnorm_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/CNAnorm.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.10.1’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... [23s/24s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
peakPloidy 18.261  0.016  18.351
* 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

CNAnorm.Rcheck/00install.out:

* 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
Warning: Nonconforming tab character in column 1 of line 14
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dsmooth.f:62.20:

      do 10 i=1,n-1                                                     
                    1
Warning: Nonconforming tab character at (1)
dsmooth.f:70.7:

     &       diff(i-1)*diff(i+1) .lt. 0.) isplit(i)=1                   
       1
Warning: Nonconforming tab character at (1)
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-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-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-class0.0200.0000.022
DerivData-class0.0080.0000.006
InData-class0.0080.0000.008
Params-class0.0080.0000.006
addDNACopy-methods0.8840.0000.884
addSmooth-methods0.5720.0040.577
chrsAndpos-methods0.080.000.08
dataFrame2object0.0040.0000.006
discreteNorm-methods0.0160.0000.015
exportTable-method0.0640.0000.066
gcNorm-methods0.4880.0040.493
peakPloidy18.261 0.01618.351
plotGenome-methods1.0440.0081.054
plotPeaks-methods0.0320.0040.038
ratio-methods0.4640.0000.464
suggValid-methods0.0120.0000.013
validation-methods0.0080.0000.010
workflowWrapper0.9960.0000.997