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BioC 3.4: CHECK report for DNAcopy on malbec1

This page was generated on 2017-04-15 16:08:53 -0400 (Sat, 15 Apr 2017).

Package 338/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DNAcopy 1.48.0
Venkatraman E. Seshan
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/DNAcopy
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DNAcopy
Version: 1.48.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DNAcopy_1.48.0.tar.gz
StartedAt: 2017-04-14 22:09:22 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:09:45 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 23.2 seconds
RetCode: 0
Status:  OK 
CheckDir: DNAcopy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DNAcopy_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/DNAcopy.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DNAcopy/DESCRIPTION’ ... OK
* this is package ‘DNAcopy’ version ‘1.48.0’
* 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 ‘DNAcopy’ can be installed ... 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘redundancy,20090610,segment.R’
 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
* DONE

Status: OK

DNAcopy.Rcheck/00install.out:

* installing *source* package ‘DNAcopy’ ...
** libs
f95   -fpic  -g -O2  -Wall -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f:283:0:

       iseg(2) = tmaxj
 ^
Warning: ‘tmaxj’ may be used uninitialized in this function [-Wmaybe-uninitialized]
cbsWtstats.f:282:0:

       iseg(1) = tmaxi
 ^
Warning: ‘tmaxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
f95   -fpic  -g -O2  -Wall -c cbststats.f -o cbststats.o
cbststats.f:258:0:

                      tmaxj = sxmxi + i2j
 ^
Warning: ‘sxmxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
f95   -fpic  -g -O2  -Wall -c changepoints-wtd.f -o changepoints-wtd.o
f95   -fpic  -g -O2  -Wall -c changepoints.f -o changepoints.o
f95   -fpic  -g -O2  -Wall -c esegment.f -o esegment.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c flchoose.c -o flchoose.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fphyper.c -o fphyper.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fpnorm.c -o fpnorm.o
f95   -fpic  -g -O2  -Wall -c getbdry.f -o getbdry.o
f95   -fpic  -g -O2  -Wall -c prune.f -o prune.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rshared.c -o rshared.o
f95   -fpic  -g -O2  -Wall -c segmentp.f -o segmentp.o
f95   -fpic  -g -O2  -Wall -c smoothCNA.f -o smoothCNA.o
f95   -fpic  -g -O2  -Wall -c tailprobs.f -o tailprobs.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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
CNA0.020.000.02
exon.segment0.2720.0000.272
plot.DNAcopy0.6200.0000.618
plotSample0.5280.0000.529
segment1.0520.0001.050
segments.p0.0560.0000.054
segments.summary0.0520.0000.052
smooth.CNA0.0080.0000.009
subset.CNA0.0040.0000.005
zoomIntoRegion0.5160.0000.516