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This page was generated on 2023-04-12 11:05:06 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for gpuMagic on nebbiolo2


To the developers/maintainers of the gpuMagic package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gpuMagic.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 851/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gpuMagic 1.14.0  (landing page)
Jiefei Wang
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/gpuMagic
git_branch: RELEASE_3_16
git_last_commit: 22d30da
git_last_commit_date: 2022-11-01 11:19:49 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: gpuMagic
Version: 1.14.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:gpuMagic.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings gpuMagic_1.14.0.tar.gz
StartedAt: 2023-04-10 21:05:59 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:07:18 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 79.7 seconds
RetCode: 0
Status:   OK  
CheckDir: gpuMagic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:gpuMagic.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings gpuMagic_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/gpuMagic.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘gpuMagic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gpuMagic’ version ‘1.14.0’
* 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 loading without being on the library search path ... 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 ...
  ‘Customized-openCL-code.Rmd’ using ‘UTF-8’... OK
  ‘Quick_start_guide.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/gpuMagic.Rcheck/00check.log’
for details.



Installation output

gpuMagic.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL gpuMagic
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘gpuMagic’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.16-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-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c C_Interface.cpp -o C_Interface.o
C_Interface.cpp: In function ‘SEXPREC* download(SEXP)’:
C_Interface.cpp:142:12: warning: ‘res’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  142 |  return(res);
      |            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.16-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-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.16-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-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.16-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-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.16-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-3.16-bioc/R/site-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-3.16-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-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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")
[ FAIL 0 | WARN 0 | SKIP 7 | PASS 0 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• gpuMagic:::getTotalDeviceNum() == 0 is TRUE (7)

[ FAIL 0 | WARN 0 | SKIP 7 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  2.176   0.181   2.362 

Example timings

gpuMagic.Rcheck/gpuMagic-Ex.timings

nameusersystemelapsed
DeviceInfo0.0010.0000.001
Matrix0.0000.0000.001
Scalar000
compileGPUCode0.3560.0000.356
dot-kernel0.0030.0000.004
gpuMagic.getAvailableType000
gpuMagic.getMemUsage0.0010.0000.001
gpuMagic.getOptions0.0010.0000.002
gpuMagic.setOptions0.0010.0000.001
gpuMatrix0.0000.0000.001
gpuSapply0.010.000.01
gpuSapply.getOption0.0010.0000.002
internalFunctions000
kernel.getOption0.0020.0000.001
ncol-gpuMatrix-method0.0010.0000.000
no_copy_method000
printFunctions0.0020.0000.001
subRef0.0000.0000.001