BioC 3.3: CHECK report for edge on morelia
This page was generated on 2015-10-22 17:54:58 -0400 (Thu, 22 Oct 2015).
edge 2.3.0 John D. Storey , Andrew J. Bass
Snapshot Date: 2015-10-21 20:20:05 -0400 (Wed, 21 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge | Last Changed Rev: 109592 / Revision: 109826 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK |  |
Summary
Package: edge |
Version: 2.3.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edge_2.3.0.tar.gz |
StartedAt: 2015-10-22 05:38:51 -0400 (Thu, 22 Oct 2015) |
EndedAt: 2015-10-22 05:41:25 -0400 (Thu, 22 Oct 2015) |
EllapsedTime: 154.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: edge.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 edge_2.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/edge.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘edge’ version ‘2.3.0’
* 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 ‘edge’ can be installed ... [11s/11s] 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 loading without being on the library search path ... 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 ... [40s/40s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
apply_snm 12.48 1.033 13.649
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [8s/8s]
[8s/8s] 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
edge.Rcheck/00install.out:
* installing *source* package ‘edge’ ...
** libs
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 edge-init.c -o edge-init.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 edgeKLODP.c -o edgeKLODP.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 edge.so edge-init.o edgeKLODP.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-bioc/meat/edge.Rcheck/edge/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (edge)
edge.Rcheck/edge-Ex.timings:
name | user | system | elapsed
|
apply_jackstraw | 2.132 | 0.045 | 2.181 |
|
apply_qvalue | 0.820 | 0.026 | 0.848 |
|
apply_snm | 12.480 | 1.033 | 13.649 |
|
apply_sva | 2.595 | 0.163 | 2.846 |
|
betaCoef | 0.501 | 0.015 | 0.515 |
|
build_models | 0.351 | 0.002 | 0.353 |
|
build_study | 0.457 | 0.001 | 0.457 |
|
deSet | 0.714 | 0.002 | 0.717 |
|
edge | 0 | 0 | 0 |
|
endotoxin | 0.977 | 0.057 | 1.034 |
|
fitFull | 0.347 | 0.004 | 0.351 |
|
fitNull | 0.350 | 0.002 | 0.353 |
|
fit_models | 0.394 | 0.024 | 0.418 |
|
fullMatrix | 0.351 | 0.005 | 0.356 |
|
fullModel | 0.556 | 0.004 | 0.560 |
|
gibson | 0.779 | 0.041 | 0.820 |
|
individual | 0.361 | 0.006 | 0.367 |
|
kidney | 0.871 | 0.061 | 0.932 |
|
kl_clust | 0.444 | 0.014 | 0.459 |
|
lrt | 1.077 | 0.079 | 1.157 |
|
nullMatrix | 0.378 | 0.005 | 0.383 |
|
nullModel | 0.792 | 0.008 | 0.799 |
|
odp | 1.339 | 0.163 | 1.502 |
|
qvalueObj | 0.836 | 0.059 | 0.894 |
|
resFull | 0.326 | 0.006 | 0.332 |
|
resNull | 0.356 | 0.014 | 0.369 |
|
sType | 0.346 | 0.009 | 0.355 |
|
show | 0.833 | 0.063 | 0.898 |
|
summary | 0.776 | 0.057 | 0.833 |
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