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CHECK report for sRACIPE on malbec2

This page was generated on 2019-10-16 12:17:59 -0400 (Wed, 16 Oct 2019).

Package 1579/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sRACIPE 1.0.0
Vivek Kohar
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/sRACIPE
Branch: RELEASE_3_9
Last Commit: 318a47d
Last Changed Date: 2019-05-02 11:54:15 -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: sRACIPE
Version: 1.0.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:sRACIPE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings sRACIPE_1.0.0.tar.gz
StartedAt: 2019-10-16 05:13:57 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:16:55 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 178.1 seconds
RetCode: 0
Status:  OK 
CheckDir: sRACIPE.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:sRACIPE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings sRACIPE_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/sRACIPE.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 ‘sRACIPE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sRACIPE’ version ‘1.0.0’
* 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 ... OK
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
sracipeSimulate 10.085  0.006  10.093
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/sRACIPE.Rcheck/00check.log’
for details.



Installation output

sRACIPE.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL sRACIPE
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘sRACIPE’ ...
** 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 generateThresholds.cpp -o generateThresholds.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 header.cpp -o header.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 simulateGRC.cpp -o simulateGRC.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 steppers.cpp -o steppers.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o sRACIPE.so RcppExports.o generateThresholds.o header.o simulateGRC.o steppers.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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
RacipeSE0.1120.0280.140
annotation-RacipeSE-method0.9350.0961.031
annotation-set-RacipeSE-ANY-method0.6090.0200.629
sracipeCircuit-set0.0340.0040.038
sracipeCircuit0.0340.0000.034
sracipeConfig-set0.0100.0000.009
sracipeConfig0.0320.0000.032
sracipeGenParamNames0.0350.0000.035
sracipeIC-set0.1410.0000.142
sracipeIC0.0520.0080.059
sracipeKnockDown0.0020.0000.001
sracipeNormalize0.0580.0000.058
sracipeOverExp0.0000.0010.002
sracipeParams-set0.0530.0060.060
sracipeParams0.0530.0000.052
sracipePlotCircuit0.0000.0010.001
sracipePlotData0.0000.0010.001
sracipePlotParamBifur0.0000.0020.001
sracipeSimulate10.085 0.00610.093