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CHECK report for DEComplexDisease on malbec2

This page was generated on 2019-10-16 12:13:12 -0400 (Wed, 16 Oct 2019).

Package 399/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEComplexDisease 1.4.0
Guofeng Meng
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/DEComplexDisease
Branch: RELEASE_3_9
Last Commit: a295f72
Last Changed Date: 2019-05-02 11:54:10 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DEComplexDisease
Version: 1.4.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DEComplexDisease.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DEComplexDisease_1.4.0.tar.gz
StartedAt: 2019-10-16 00:59:57 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:04:07 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 249.7 seconds
RetCode: 0
Status:  OK 
CheckDir: DEComplexDisease.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DEComplexDisease.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DEComplexDisease_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/DEComplexDisease.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEComplexDisease/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DEComplexDisease’ version ‘1.4.0’
* 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 ‘DEComplexDisease’ 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 ... NOTE
prepare_Rd: Plot.cluster.module.Rd:53-55: Dropping empty section \references
prepare_Rd: Plot.deg.specific.test.Rd:43-45: Dropping empty section \references
prepare_Rd: module.curve.Rd:27-29: Dropping empty section \references
prepare_Rd: summarize.cluster.module.Rd:30-32: Dropping empty section \references
prepare_Rd: summarize.seed.module.Rd:31-33: Dropping empty section \references
* 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 ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
bi.deg 28.121  0.088  28.333
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/DEComplexDisease.Rcheck/00check.log’
for details.



Installation output

DEComplexDisease.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DEComplexDisease
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘DEComplexDisease’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c sig.cpp -o sig.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o DEComplexDisease.so RcppExports.o sig.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-DEComplexDisease/00new/DEComplexDisease/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘decd.Rmd’ 
   ‘vignettes.Rmd’ 
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DEComplexDisease)

Tests output


Example timings

DEComplexDisease.Rcheck/DEComplexDisease-Ex.timings

nameusersystemelapsed
Plot.cluster.module4.7280.0884.815
Plot.deg0.6290.0000.628
Plot.deg.specific0.4530.0000.453
Plot.deg.specific.test0.6540.0000.657
Plot.seed.module0.5950.0000.595
bi.deg28.121 0.08828.333
cluster.module0.6960.0040.700
deg.specific1.7780.0001.778
module.compare0.1500.0000.149
module.curve0.0220.0000.022
module.exact0.0020.0000.001
module.modeling0.0460.0000.046
module.overlap0.4280.0040.432
module.screen0.0410.0000.041
seed.module2.2720.0042.286
summarize.cluster.module0.0060.0000.007
summarize.deg.specific0.0190.0000.019
summarize.seed.module0.0080.0000.008