Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

CHECK report for synergyfinder on malbec2

This page was generated on 2020-10-17 11:55:53 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE synergyfinder PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1772/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
synergyfinder 2.2.4
Shuyu Zheng
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/synergyfinder
Branch: RELEASE_3_11
Last Commit: d110362
Last Changed Date: 2020-07-06 03:47:36 -0400 (Mon, 06 Jul 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: synergyfinder
Version: 2.2.4
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:synergyfinder.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings synergyfinder_2.2.4.tar.gz
StartedAt: 2020-10-17 05:57:48 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:58:32 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 44.3 seconds
RetCode: 0
Status:  OK 
CheckDir: synergyfinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:synergyfinder.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings synergyfinder_2.2.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/synergyfinder.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘synergyfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘synergyfinder’ version ‘2.2.4’
* 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 ‘synergyfinder’ 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
PlotDoseResponse: no visible binding for global variable ‘conc_c’
PlotDoseResponse: no visible binding for global variable ‘conc_r’
PlotDoseResponse: no visible binding for global variable ‘Inhibition’
Undefined global functions or variables:
  Inhibition conc_c conc_r
* 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
* 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-3.11-bioc/meat/synergyfinder.Rcheck/00check.log’
for details.



Installation output

synergyfinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL synergyfinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘synergyfinder’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c covariance.c -o covariance.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c kriging.c -o kriging.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c synergyfinder_init.c -o synergyfinder_init.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o synergyfinder.so covariance.o kriging.o synergyfinder_init.o utils.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-synergyfinder/00new/synergyfinder/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 (synergyfinder)

Tests output


Example timings

synergyfinder.Rcheck/synergyfinder-Ex.timings

nameusersystemelapsed
AddNoise0.1630.0080.172
Bliss0.0060.0000.006
CalculateSynergy1.7060.0561.762
CorrectBaseLine0.1050.0000.104
ExtractSingleDrug0.0030.0040.006
FindModelType0.0160.0000.016
FitDoseResponse0.0160.0000.016
HSA0.0060.0000.006
ImputeNA0.0070.0000.006
Loewe0.1250.0000.125
PlotDoseResponse0.5250.0040.530
PlotSynergy0.9410.0160.958
ReshapeData0.0050.0000.006
ZIP0.7230.0000.724