Package: sRACIPE

Version: 1.2.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:sRACIPE.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings sRACIPE_1.2.0.tar.gz

StartedAt: 2020-04-15 06:27:47 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:30:49 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 182.6 seconds

RetCode: 0

Status:  OK

CheckDir: sRACIPE.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:sRACIPE.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings sRACIPE_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/sRACIPE.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.2.0’
* 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 ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    GeneEx   3.1Mb
    libs     2.4Mb
* 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 11.664  0.004  11.743
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/sRACIPE.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL sRACIPE
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘sRACIPE’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/lib -L/usr/local/lib -o sRACIPE.so RcppExports.o generateThresholds.o header.o simulateGRC.o steppers.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-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)

name	user	system	elapsed
RacipeSE	0.06	0.00	0.06
annotation-RacipeSE-method	1.316	0.044	1.367
annotation-set-RacipeSE-ANY-method	0.636	0.020	0.659
sracipeCircuit-set	0.036	0.004	0.043
sracipeCircuit	0.040	0.000	0.038
sracipeConfig-set	0.016	0.000	0.013
sracipeConfig	0.040	0.000	0.039
sracipeGenParamNames	0.024	0.004	0.026
sracipeGetTS	0.072	0.000	0.073
sracipeIC-set	0.112	0.000	0.114
sracipeIC	0.064	0.000	0.065
sracipeKnockDown	0.000	0.004	0.001
sracipeNormalize	0.092	0.000	0.094
sracipeOverExp	0.004	0.000	0.001
sracipeParams-set	0.12	0.00	0.12
sracipeParams	0.092	0.000	0.097
sracipePlotCircuit	0.000	0.000	0.002
sracipePlotData	0.000	0.000	0.002
sracipePlotParamBifur	0.004	0.000	0.002
sracipeSimulate	11.664	0.004	11.743