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CHECK report for sRACIPE on tokay1

This page was generated on 2021-05-06 12:33:46 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the sRACIPE package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1783/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sRACIPE 1.6.0  (landing page)
Vivek Kohar
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/sRACIPE
Branch: RELEASE_3_12
Last Commit: 15f5583
Last Changed Date: 2020-10-27 11:44:53 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: sRACIPE
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sRACIPE.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings sRACIPE_1.6.0.tar.gz
StartedAt: 2021-05-06 07:15:03 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 07:19:11 -0400 (Thu, 06 May 2021)
EllapsedTime: 248.7 seconds
RetCode: 0
Status:   OK   
CheckDir: sRACIPE.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sRACIPE.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings sRACIPE_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/sRACIPE.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sRACIPE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sRACIPE' version '1.6.0'
* package encoding: UTF-8
* 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 whether package 'sRACIPE' 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 ... NOTE
sracipeSimulate: no visible global function definition for
  'registerDoFuture'
sracipeSimulate: no visible global function definition for 'plan'
sracipeSimulate: no visible global function definition for '%dopar%'
sracipeSimulate: no visible global function definition for 'foreach'
sracipeSimulate: no visible binding for global variable
  'configurationTmp'
sracipeSimulate: no visible binding for global variable 'outFileGETmp'
sracipeSimulate: no visible binding for global variable
  'outFileParamsTmp'
sracipeSimulate: no visible binding for global variable 'outFileICTmp'
Undefined global functions or variables:
  %dopar% configurationTmp foreach outFileGETmp outFileICTmp
  outFileParamsTmp plan registerDoFuture
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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-3.12-bioc/R/library/sRACIPE/libs/i386/sRACIPE.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/sRACIPE/libs/x64/sRACIPE.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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
sracipeSimulate 7.72   0.05    7.77
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
sracipeSimulate 6.14   0.02    6.16
* 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-3.12-bioc/meat/sRACIPE.Rcheck/00check.log'
for details.



Installation output

sRACIPE.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/sRACIPE_1.6.0.tar.gz && rm -rf sRACIPE.buildbin-libdir && mkdir sRACIPE.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sRACIPE.buildbin-libdir sRACIPE_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL sRACIPE_1.6.0.zip && rm sRACIPE_1.6.0.tar.gz sRACIPE_1.6.0.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 1279k  100 1279k    0     0  29.8M      0 --:--:-- --:--:-- --:--:-- 31.2M

install for i386

* installing *source* package 'sRACIPE' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c generateThresholds.cpp -o generateThresholds.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c header.cpp -o header.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c simulateGRC.cpp -o simulateGRC.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c steppers.cpp -o steppers.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o sRACIPE.dll tmp.def RcppExports.o generateThresholds.o header.o simulateGRC.o steppers.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/sRACIPE.buildbin-libdir/00LOCK-sRACIPE/00new/sRACIPE/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sRACIPE'
    finding HTML links ... done
    CoupledToggleSwitchSA                   html  
    EMT1                                    html  
    EMT2                                    html  
    RacipeSE-class                          html  
    finding level-2 HTML links ... done

    RacipeSE                                html  
    annotation-RacipeSE-method              html  
    annotation-set-RacipeSE-ANY-method      html  
    configData                              html  
    demoCircuit                             html  
    densityPlot                             html  
    dot-ModelPvalue                         html  
    dot-NthMin                              html  
    dot-PermutedVar                         html  
    dot-SimulatedPValueAbs                  html  
    dot-SimulatedVarPValue                  html  
    dot-loadNetworkFile                     html  
    sRACIPE                                 html  
    sracipeCircuit-set                      html  
    sracipeCircuit                          html  
    sracipeConfig-set                       html  
    sracipeConfig                           html  
    sracipeGenParamNames                    html  
    sracipeGetTS                            html  
    sracipeHeatmapSimilarity                html  
    sracipeIC-set                           html  
    sracipeIC                               html  
    sracipeKnockDown                        html  
    sracipeNormalize                        html  
    sracipeOverExp                          html  
    sracipeParams-set                       html  
    sracipeParams                           html  
    sracipePlotCircuit                      html  
    sracipePlotData                         html  
    sracipePlotParamBifur                   html  
    sracipeSimulate                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'sRACIPE' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c generateThresholds.cpp -o generateThresholds.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c header.cpp -o header.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c simulateGRC.cpp -o simulateGRC.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c steppers.cpp -o steppers.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o sRACIPE.dll tmp.def RcppExports.o generateThresholds.o header.o simulateGRC.o steppers.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/sRACIPE.buildbin-libdir/sRACIPE/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sRACIPE' as sRACIPE_1.6.0.zip
* DONE (sRACIPE)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'sRACIPE' successfully unpacked and MD5 sums checked

Tests output


Example timings

sRACIPE.Rcheck/examples_i386/sRACIPE-Ex.timings

nameusersystemelapsed
RacipeSE0.030.010.04
annotation-RacipeSE-method0.420.110.55
annotation-set-RacipeSE-ANY-method0.470.000.47
sracipeCircuit-set0.070.020.08
sracipeCircuit0.040.010.06
sracipeConfig-set0.010.000.01
sracipeConfig0.050.020.07
sracipeGenParamNames0.080.000.07
sracipeGetTS0.090.020.11
sracipeIC-set0.140.010.16
sracipeIC0.080.000.08
sracipeKnockDown0.020.000.01
sracipeNormalize0.090.000.10
sracipeOverExp000
sracipeParams-set0.080.020.09
sracipeParams0.060.030.09
sracipePlotCircuit000
sracipePlotData0.020.000.02
sracipePlotParamBifur000
sracipeSimulate7.720.057.77

sRACIPE.Rcheck/examples_x64/sRACIPE-Ex.timings

nameusersystemelapsed
RacipeSE0.050.000.05
annotation-RacipeSE-method0.930.041.10
annotation-set-RacipeSE-ANY-method0.350.010.36
sracipeCircuit-set0.030.000.04
sracipeCircuit0.030.020.04
sracipeConfig-set000
sracipeConfig0.050.000.05
sracipeGenParamNames0.010.010.03
sracipeGetTS0.080.020.09
sracipeIC-set0.140.000.14
sracipeIC0.080.010.10
sracipeKnockDown000
sracipeNormalize0.060.020.08
sracipeOverExp0.000.020.01
sracipeParams-set0.10.00.1
sracipeParams0.070.000.07
sracipePlotCircuit000
sracipePlotData000
sracipePlotParamBifur000
sracipeSimulate6.140.026.16