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This page was generated on 2021-10-23 14:06:57 -0400 (Sat, 23 Oct 2021).

CHECK results for DEComplexDisease on merida1

To the developers/maintainers of the DEComplexDisease package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DEComplexDisease.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 463/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEComplexDisease 1.13.0  (landing page)
Guofeng Meng
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/DEComplexDisease
git_branch: master
git_last_commit: 4e90466
git_last_commit_date: 2021-05-19 12:33:11 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DEComplexDisease
Version: 1.13.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DEComplexDisease.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DEComplexDisease_1.13.0.tar.gz
StartedAt: 2021-10-23 02:45:22 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 02:50:34 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 312.3 seconds
RetCode: 0
Status:   OK  
CheckDir: DEComplexDisease.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DEComplexDisease.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DEComplexDisease_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/DEComplexDisease.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.13.0’
* 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 LazyData ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
bi.deg              22.957  0.815  23.799
Plot.cluster.module  6.409  0.203   6.619
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/DEComplexDisease.Rcheck/00check.log’
for details.



Installation output

DEComplexDisease.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DEComplexDisease
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘DEComplexDisease’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sig.cpp -o sig.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 DEComplexDisease.so RcppExports.o sig.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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.module6.4090.2036.619
Plot.deg1.0600.0051.068
Plot.deg.specific0.7670.0060.775
Plot.deg.specific.test0.7290.0050.737
Plot.seed.module0.5510.0050.559
bi.deg22.957 0.81523.799
cluster.module2.1040.0082.114
deg.specific1.5310.0061.538
module.compare0.2210.0010.223
module.curve0.0270.0000.028
module.exact0.0020.0010.002
module.modeling1.5730.0041.578
module.overlap0.5120.0020.515
module.screen0.4750.0030.481
seed.module4.0440.0104.058
summarize.cluster.module0.0070.0000.007
summarize.deg.specific0.0080.0000.009
summarize.seed.module0.010.000.01