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BioC 3.5: CHECK report for DNAcopy on malbec2

This page was generated on 2017-08-16 13:12:18 -0400 (Wed, 16 Aug 2017).

Package 360/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DNAcopy 1.50.1
Venkatraman E. Seshan
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/DNAcopy
Last Changed Rev: 129423 / Revision: 131943
Last Changed Date: 2017-05-05 15:32:27 -0400 (Fri, 05 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DNAcopy
Version: 1.50.1
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DNAcopy_1.50.1.tar.gz
StartedAt: 2017-08-15 22:37:25 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:37:48 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 22.6 seconds
RetCode: 0
Status:  OK 
CheckDir: DNAcopy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DNAcopy_1.50.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/DNAcopy.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.50.1’
* 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 ... 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-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c flchoose.c -o flchoose.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fphyper.c -o fphyper.o
gcc -I/home/biocbuild/bbs-3.5-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-3.5-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-3.5-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-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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
CNA0.0240.0000.024
exon.segment0.2120.0000.210
plot.DNAcopy1.0000.0041.002
plotSample0.6400.0040.646
segment1.0840.0041.089
segments.p0.0520.0000.051
segments.summary0.0480.0000.050
smooth.CNA0.0040.0000.008
subset.CNA0.0040.0000.004
zoomIntoRegion0.660.000.66