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CHECK report for DEComplexDisease on tokay1

This page was generated on 2019-04-13 11:28:49 -0400 (Sat, 13 Apr 2019).

Package 378/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEComplexDisease 1.2.0
Guofeng Meng
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/DEComplexDisease
Branch: RELEASE_3_8
Last Commit: 9785cef
Last Changed Date: 2018-10-30 11:42:07 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DEComplexDisease
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEComplexDisease.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DEComplexDisease_1.2.0.tar.gz
StartedAt: 2019-04-13 01:40:06 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:46:11 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 364.7 seconds
RetCode: 0
Status:  OK  
CheckDir: DEComplexDisease.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEComplexDisease.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DEComplexDisease_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DEComplexDisease.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DEComplexDisease/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DEComplexDisease' version '1.2.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/DEComplexDisease/libs/i386/DEComplexDisease.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
bi.deg 36.06   1.29   37.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
bi.deg 26.1    0.5    26.6
* 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/DEComplexDisease.Rcheck/00check.log'
for details.



Installation output

DEComplexDisease.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DEComplexDisease_1.2.0.tar.gz && rm -rf DEComplexDisease.buildbin-libdir && mkdir DEComplexDisease.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEComplexDisease.buildbin-libdir DEComplexDisease_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DEComplexDisease_1.2.0.zip && rm DEComplexDisease_1.2.0.tar.gz DEComplexDisease_1.2.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1144k  100 1144k    0     0  6790k      0 --:--:-- --:--:-- --:--:-- 6934k

install for i386

* installing *source* package 'DEComplexDisease' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c sig.cpp -o sig.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o DEComplexDisease.dll tmp.def RcppExports.o sig.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/DEComplexDisease.buildbin-libdir/DEComplexDisease/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DEComplexDisease'
    finding HTML links ... done
    Plot.cluster.module                     html  
    Plot.deg                                html  
    Plot.deg.specific                       html  
    Plot.deg.specific.test                  html  
    Plot.seed.module                        html  
    ann.er                                  html  
    bi.deg                                  html  
    cl                                      html  
    cluster.mod                             html  
    cluster.module                          html  
    deg                                     html  
    deg.spc                                 html  
    deg.specific                            html  
    exp                                     html  
    module.compare                          html  
    module.curve                            html  
    module.exact                            html  
    module.modeling                         html  
    module.overlap                          html  
    module.screen                           html  
    res.mod1                                html  
    res.mod2                                html  
    seed.mod                                html  
    seed.module                             html  
    summarize.cluster.module                html  
    summarize.deg.specific                  html  
    summarize.seed.module                   html  
** building package indices
** installing vignettes
   'decd.Rmd' 
   'vignettes.Rmd' 
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DEComplexDisease' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c sig.cpp -o sig.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o DEComplexDisease.dll tmp.def RcppExports.o sig.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/DEComplexDisease.buildbin-libdir/DEComplexDisease/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEComplexDisease' as DEComplexDisease_1.2.0.zip
* DONE (DEComplexDisease)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DEComplexDisease' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

DEComplexDisease.Rcheck/examples_i386/DEComplexDisease-Ex.timings

nameusersystemelapsed
Plot.cluster.module2.220.002.22
Plot.deg1.840.021.86
Plot.deg.specific1.640.011.66
Plot.deg.specific.test1.250.001.25
Plot.seed.module1.080.041.11
bi.deg36.06 1.2937.36
cluster.module1.100.001.09
deg.specific1.290.001.30
module.compare0.360.000.36
module.curve0.020.000.01
module.exact000
module.modeling0.050.000.05
module.overlap0.820.000.83
module.screen0.070.000.06
seed.module1.620.001.62
summarize.cluster.module000
summarize.deg.specific000
summarize.seed.module0.020.000.02

DEComplexDisease.Rcheck/examples_x64/DEComplexDisease-Ex.timings

nameusersystemelapsed
Plot.cluster.module2.970.073.03
Plot.deg1.460.001.45
Plot.deg.specific1.390.011.41
Plot.deg.specific.test1.450.001.45
Plot.seed.module1.170.001.17
bi.deg26.1 0.526.6
cluster.module0.430.000.54
deg.specific0.880.000.88
module.compare0.340.000.34
module.curve0.020.000.02
module.exact000
module.modeling0.060.000.06
module.overlap0.810.000.81
module.screen0.030.000.03
seed.module1.610.001.61
summarize.cluster.module000
summarize.deg.specific0.020.000.02
summarize.seed.module000