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CHECK report for sRACIPE on machv2

This page was generated on 2020-10-17 11:59:42 -0400 (Sat, 17 Oct 2020).

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 1726/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sRACIPE 1.4.0
Vivek Kohar
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/sRACIPE
Branch: RELEASE_3_11
Last Commit: c11b212
Last Changed Date: 2020-04-27 15:25:42 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: sRACIPE
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sRACIPE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sRACIPE_1.4.0.tar.gz
StartedAt: 2020-10-17 05:36:45 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:40:34 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 229.1 seconds
RetCode: 0
Status:  OK 
CheckDir: sRACIPE.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 --install=check:sRACIPE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sRACIPE_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/sRACIPE.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sRACIPE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sRACIPE’ version ‘1.4.0’
* 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 for sufficient/correct file permissions ... 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
sracipeSimulate 11.193  0.095   11.38
* 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-3.11-bioc/meat/sRACIPE.Rcheck/00check.log’
for details.



Installation output

sRACIPE.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sRACIPE
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘sRACIPE’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c generateThresholds.cpp -o generateThresholds.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c header.cpp -o header.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c simulateGRC.cpp -o simulateGRC.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c steppers.cpp -o steppers.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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 sRACIPE.so RcppExports.o generateThresholds.o header.o simulateGRC.o steppers.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-sRACIPE/00new/sRACIPE/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (sRACIPE)

Tests output


Example timings

sRACIPE.Rcheck/sRACIPE-Ex.timings

nameusersystemelapsed
RacipeSE0.0630.0080.070
annotation-RacipeSE-method0.8110.0590.871
annotation-set-RacipeSE-ANY-method0.7000.0310.732
sracipeCircuit-set0.0460.0040.050
sracipeCircuit0.0460.0070.054
sracipeConfig-set0.0110.0020.014
sracipeConfig0.0420.0070.049
sracipeGenParamNames0.0440.0060.050
sracipeGetTS0.1180.0110.129
sracipeIC-set0.2050.0100.216
sracipeIC0.1380.0070.145
sracipeKnockDown0.0020.0030.005
sracipeNormalize0.1000.0060.107
sracipeOverExp0.0010.0020.004
sracipeParams-set0.1290.0070.135
sracipeParams0.1020.0060.108
sracipePlotCircuit0.0020.0030.005
sracipePlotData0.0010.0030.005
sracipePlotParamBifur0.0020.0040.005
sracipeSimulate11.193 0.09511.380