BioC 3.5: CHECK report for DNAcopy on toluca2
This page was generated on 2017-04-23 14:33:14 -0400 (Sun, 23 Apr 2017).
DNAcopy 1.49.1 Venkatraman E. Seshan
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DNAcopy | Last Changed Rev: 124418 / Revision: 129046 | Last Changed Date: 2016-11-23 14:57:58 -0500 (Wed, 23 Nov 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
Summary
Package: DNAcopy |
Version: 1.49.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DNAcopy_1.49.1.tar.gz |
StartedAt: 2017-04-23 03:06:32 -0400 (Sun, 23 Apr 2017) |
EndedAt: 2017-04-23 03:07:05 -0400 (Sun, 23 Apr 2017) |
EllapsedTime: 32.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DNAcopy.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DNAcopy_1.49.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/DNAcopy.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.49.1’
* 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 sizes of PDF files under ‘inst/doc’ ... 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
gfortran-4.8 -fPIC -g -O2 -c cbsWtstats.f -o cbsWtstats.o
gfortran-4.8 -fPIC -g -O2 -c cbststats.f -o cbststats.o
gfortran-4.8 -fPIC -g -O2 -c changepoints-wtd.f -o changepoints-wtd.o
gfortran-4.8 -fPIC -g -O2 -c changepoints.f -o changepoints.o
gfortran-4.8 -fPIC -g -O2 -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 -c getbdry.f -o getbdry.o
gfortran-4.8 -fPIC -g -O2 -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 -c segmentp.f -o segmentp.o
gfortran-4.8 -fPIC -g -O2 -c smoothCNA.f -o smoothCNA.o
gfortran-4.8 -fPIC -g -O2 -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-3.5-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:
name | user | system | elapsed
|
CNA | 0.052 | 0.003 | 0.055 |
|
exon.segment | 0.118 | 0.003 | 0.122 |
|
plot.DNAcopy | 1.573 | 0.022 | 1.607 |
|
plotSample | 1.097 | 0.006 | 1.111 |
|
segment | 1.719 | 0.008 | 1.737 |
|
segments.p | 0.098 | 0.001 | 0.100 |
|
segments.summary | 0.096 | 0.001 | 0.098 |
|
smooth.CNA | 0.051 | 0.001 | 0.054 |
|
subset.CNA | 0.009 | 0.002 | 0.010 |
|
zoomIntoRegion | 0.790 | 0.003 | 0.797 |
|