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CHECK report for gpuMagic on malbec2

This page was generated on 2020-10-17 11:54:53 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE gpuMagic PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 766/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gpuMagic 1.4.0
Jiefei Wang
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/gpuMagic
Branch: RELEASE_3_11
Last Commit: 336d502
Last Changed Date: 2020-04-27 15:26:33 -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  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gpuMagic
Version: 1.4.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:gpuMagic.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings gpuMagic_1.4.0.tar.gz
StartedAt: 2020-10-17 01:57:45 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:59:04 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 78.9 seconds
RetCode: 0
Status:  OK 
CheckDir: gpuMagic.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:gpuMagic.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings gpuMagic_1.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/gpuMagic.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 ‘gpuMagic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gpuMagic’ 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 ‘gpuMagic’ 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 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 include directives 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 ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/gpuMagic.Rcheck/00check.log’
for details.



Installation output

gpuMagic.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘gpuMagic’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.11-bioc/R/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS  -DCL_SILENCE_DEPRECATION -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c C_Interface.cpp -o C_Interface.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.11-bioc/R/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS  -DCL_SILENCE_DEPRECATION -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_functionRegistration.cpp -o R_functionRegistration.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.11-bioc/R/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS  -DCL_SILENCE_DEPRECATION -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Tools.cpp -o Tools.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.11-bioc/R/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS  -DCL_SILENCE_DEPRECATION -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c kernelManager.cpp -o kernelManager.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.11-bioc/R/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS  -DCL_SILENCE_DEPRECATION -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c openArray.cpp -o openArray.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o gpuMagic.so C_Interface.o R_functionRegistration.o Tools.o kernelManager.o openArray.o -lOpenCL -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-gpuMagic/00new/gpuMagic/libs
** R
** 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
No device has been found, please make sure the computer has a graphic card or the driver has been properly installed.
Hint:
For CPU, you can install the intel's / ATI's graphic driver for the intel's / AMD's CPU respectively.
For GPU, you need to download the graphic driver from your vendor's website.
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No device has been found, please make sure the computer has a graphic card or the driver has been properly installed.
Hint:
For CPU, you can install the intel's / ATI's graphic driver for the intel's / AMD's CPU respectively.
For GPU, you need to download the graphic driver from your vendor's website.
** testing if installed package keeps a record of temporary installation path
* DONE (gpuMagic)

Tests output

gpuMagic.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(gpuMagic)
No device has been found, please make sure the computer has a graphic card or the driver has been properly installed.
Hint:
For CPU, you can install the intel's / ATI's graphic driver for the intel's / AMD's CPU respectively.
For GPU, you need to download the graphic driver from your vendor's website.
> 
> test_check("gpuMagic")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  3.397   0.135   3.517 

Example timings

gpuMagic.Rcheck/gpuMagic-Ex.timings

nameusersystemelapsed
DeviceInfo0.0030.0000.003
Matrix000
Scalar000
compileGPUCode0.6570.0040.661
dot-kernel0.0070.0000.007
gpuMagic.getAvailableType0.0000.0000.001
gpuMagic.getMemUsage0.0010.0000.001
gpuMagic.getOptions0.0040.0000.003
gpuMagic.setOptions0.0020.0000.002
gpuMatrix0.0010.0000.001
gpuSapply0.020.000.02
gpuSapply.getOption0.0020.0000.003
internalFunctions0.0010.0000.001
kernel.getOption0.0040.0000.004
ncol-gpuMatrix-method0.0010.0000.000
no_copy_method0.0010.0000.001
printFunctions0.0030.0000.003
subRef000