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BioC 3.1: CHECK report for CNAnorm on morelia

This page was generated on 2015-10-09 09:40:00 -0700 (Fri, 09 Oct 2015).

Package 184/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNAnorm 1.14.0
Stefano Berri
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/CNAnorm
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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: 2015-10-09 00:26:23 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 00:27:14 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 51.1 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 CNAnorm_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/CNAnorm.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [3s/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 ... [20s/21s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
peakPloidy 15.087  0.478  15.582
* 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

CNAnorm.Rcheck/00install.out:

* installing *source* package ‘CNAnorm’ ...
** libs
gfortran-4.8   -fPIC  -g -O2 -Wall  -c daxpy.f -o daxpy.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c ddot.f -o ddot.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c dgbfa.f -o dgbfa.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c dgbsl.f -o dgbsl.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c dscal.f -o dscal.o
gfortran-4.8   -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 [-Wmaybe-uninitialized]
  function amed3(a,b,c)
 ^
gfortran-4.8   -fPIC  -g -O2 -Wall  -c idamax.f -o idamax.o
clang -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 -o CNAnorm.so daxpy.o ddot.o dgbfa.o dgbsl.o dscal.o dsmooth.o idamax.o -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -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)

CNAnorm.Rcheck/CNAnorm-Ex.timings:

nameusersystemelapsed
CNAnorm-class0.0500.0030.052
DerivData-class0.0040.0000.003
InData-class0.0040.0010.004
Params-class0.0030.0010.004
addDNACopy-methods0.8190.0030.833
addSmooth-methods0.4130.0020.415
chrsAndpos-methods0.0500.0020.051
dataFrame2object0.0030.0000.004
discreteNorm-methods0.0150.0010.015
exportTable-method0.0590.0020.061
gcNorm-methods0.3740.0010.374
peakPloidy15.087 0.47815.582
plotGenome-methods1.0420.0221.117
plotPeaks-methods0.0310.0010.035
ratio-methods0.3920.0100.401
suggValid-methods0.0130.0050.019
validation-methods0.0100.0000.011
workflowWrapper0.9760.0070.983