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BioC 3.2: CHECK report for DNAcopy on oaxaca

This page was generated on 2016-04-23 10:22:53 -0700 (Sat, 23 Apr 2016).

Package 285/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DNAcopy 1.44.0
Venkatraman E. Seshan
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/DNAcopy
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DNAcopy
Version: 1.44.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DNAcopy_1.44.0.tar.gz
StartedAt: 2016-04-22 23:39:25 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:39:51 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 26.6 seconds
RetCode: 0
Status:  OK 
CheckDir: DNAcopy.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 DNAcopy_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/DNAcopy.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DNAcopy/DESCRIPTION’ ... OK
* this is package ‘DNAcopy’ version ‘1.44.0’
* 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 ... [4s/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 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 ... [5s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘redundancy,20090610,segment.R’ [1s/1s]
 [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
* DONE

Status: OK

DNAcopy.Rcheck/00install.out:

* installing *source* package ‘DNAcopy’ ...
** libs
gfortran-4.8   -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 [-Wmaybe-uninitialized]
       iseg(2) = tmaxj
 ^
cbsWtstats.f:282:0: warning: ‘tmaxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       iseg(1) = tmaxi
 ^
gfortran-4.8   -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 [-Wmaybe-uninitialized]
                      tmaxj = sxmxi + i2j
 ^
gfortran-4.8   -fPIC  -g -O2 -Wall  -c changepoints-wtd.f -o changepoints-wtd.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c changepoints.f -o changepoints.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c esegment.f -o esegment.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c flchoose.c -o flchoose.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c fphyper.c -o fphyper.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c fpnorm.c -o fpnorm.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c getbdry.f -o getbdry.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c prune.f -o prune.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c rshared.c -o rshared.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c segmentp.f -o segmentp.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c smoothCNA.f -o smoothCNA.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c tailprobs.f -o tailprobs.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 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 -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-3.2-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
CNA0.0260.0030.030
exon.segment0.0960.0010.097
plot.DNAcopy1.0160.0151.035
plotSample0.8450.0040.851
segment1.7580.0081.769
segments.p0.0920.0010.093
segments.summary0.0950.0010.095
smooth.CNA0.0140.0000.015
subset.CNA0.0070.0000.008
zoomIntoRegion0.7660.0030.769