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BioC 2.14: CHECK report for DNAcopy on zin2

This page was generated on 2014-10-08 08:47:41 -0700 (Wed, 08 Oct 2014).

Package 232/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DNAcopy 1.38.1
Venkatraman E. Seshan
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/DNAcopy
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  OK  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: DNAcopy
Version: 1.38.1
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings DNAcopy_1.38.1.tar.gz
StartedAt: 2014-10-07 23:12:42 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:13:01 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 19.0 seconds
RetCode: 0
Status:  OK 
CheckDir: DNAcopy.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 DNAcopy_1.38.1.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/DNAcopy.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 ‘DNAcopy/DESCRIPTION’ ... OK
* this is package ‘DNAcopy’ version ‘1.38.1’
* 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 ‘DNAcopy’ can be installed ... [3s/3s] 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 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 ... [4s/4s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘redundancy,20090610,segment.R’ [0s/0s]
 [1s/1s] OK
* 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

DNAcopy.Rcheck/00install.out:

* installing *source* package ‘DNAcopy’ ...
** libs
gfortran   -fpic  -g -O2  -Wall -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f: In function ‘wtmaxo’:
cbsWtstats.f:283:0: warning: ‘tmaxj’ may be used uninitialized in this function [-Wuninitialized]
cbsWtstats.f:282:0: warning: ‘tmaxi’ may be used uninitialized in this function [-Wuninitialized]
gfortran   -fpic  -g -O2  -Wall -c cbststats.f -o cbststats.o
cbststats.f: In function ‘tmaxo’:
cbststats.f:258:0: warning: ‘sxmxi’ may be used uninitialized in this function [-Wuninitialized]
gfortran   -fpic  -g -O2  -Wall -c changepoints-wtd.f -o changepoints-wtd.o
gfortran   -fpic  -g -O2  -Wall -c changepoints.f -o changepoints.o
gfortran   -fpic  -g -O2  -Wall -c esegment.f -o esegment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c flchoose.c -o flchoose.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fphyper.c -o fphyper.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fpnorm.c -o fpnorm.o
gfortran   -fpic  -g -O2  -Wall -c getbdry.f -o getbdry.o
gfortran   -fpic  -g -O2  -Wall -c prune.f -o prune.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rshared.c -o rshared.o
gfortran   -fpic  -g -O2  -Wall -c segmentp.f -o segmentp.o
gfortran   -fpic  -g -O2  -Wall -c smoothCNA.f -o smoothCNA.o
gfortran   -fpic  -g -O2  -Wall -c tailprobs.f -o tailprobs.o
gcc -std=gnu99 -shared -L/usr/local/lib -o DNAcopy.so cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/DNAcopy.Rcheck/DNAcopy/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DNAcopy)

DNAcopy.Rcheck/DNAcopy-Ex.timings:

nameusersystemelapsed
CNA0.0200.0040.026
exon.segment0.1440.0000.144
plot.DNAcopy0.7760.0000.803
plotSample0.6400.0040.643
segment1.2640.0001.267
segments.p0.0680.0000.069
segments.summary0.0640.0040.067
smooth.CNA0.0120.0000.011
subset.CNA0.0080.0000.008
zoomIntoRegion0.5800.0000.579