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This page was generated on 2024-11-20 12:05 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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

Package 190/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocParallel 1.40.0  (landing page)
Martin Morgan
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/BiocParallel
git_branch: RELEASE_3_20
git_last_commit: a57b788
git_last_commit_date: 2024-10-29 09:43:33 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for BiocParallel on lconway

To the developers/maintainers of the BiocParallel package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocParallel.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BiocParallel
Version: 1.40.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocParallel_1.40.0.tar.gz
StartedAt: 2024-11-19 19:52:48 -0500 (Tue, 19 Nov 2024)
EndedAt: 2024-11-19 20:05:21 -0500 (Tue, 19 Nov 2024)
EllapsedTime: 752.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocParallel.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocParallel_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiocParallel.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocParallel/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiocParallel’ version ‘1.40.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 NOTE
Package which this enhances but not available for checking: ‘Rmpi’
* 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 ‘BiocParallel’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 code 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 ... NOTE
':::' calls which should be '::':
  ‘parallel:::closeNode’ ‘parallel:::recvData’ ‘parallel:::recvOneData’
  ‘parallel:::sendData’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.workerLapply_impl’
* 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 shell scripts ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
BatchtoolsParam-class 2.260  1.454  13.355
bpvalidate            2.963  0.259   5.376
MulticoreParam-class  1.046  0.689   5.386
SnowParam-class       1.021  0.110  21.070
bpok                  0.594  0.073  13.439
bpoptions             0.022  0.002   5.762
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiocParallel.Rcheck/00check.log’
for details.


Installation output

BiocParallel.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocParallel
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘BiocParallel’ ...
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether clang++ -arch x86_64 -std=gnu++17 accepts -g... yes
checking for clang++ -arch x86_64 -std=gnu++17 option to enable C++11 features... none needed
checking for library containing shm_open... none required
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for sys/mman.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cpp11.cpp -o cpp11.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ipcmutex.cpp -o ipcmutex.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o BiocParallel.so cpp11.o ipcmutex.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-BiocParallel/00new/BiocParallel/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
** 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 (BiocParallel)

Tests output

BiocParallel.Rcheck/tests/test.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> BiocGenerics:::testPackage("BiocParallel")
Testing BatchtoolsParam
Submitting 5 jobs in 4 chunks using cluster functions 'Multicore' ...
Submitting 5 jobs in 4 chunks using cluster functions 'Socket' ...
Submitting 5 jobs in 4 chunks using cluster functions 'Socket' ...
> > > > > > > > Submitting 5 jobs in 4 chunks using cluster functions 'Multicore' ...
> > > > > > > > Testing BiocParallelParam
Testing DoparParam
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
Testing MulticoreParam
Testing SerialParam
Testing SnowParam
Timing stopped at: 0 0 0.001
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
Timing stopped at: 0.001 0 0
Error in DEACTIVATED("'snow' and/or 'Rmpi' package did not load") : 
  'snow' and/or 'Rmpi' package did not load
Timing stopped at: 0.001 0 0
Error in DEACTIVATED("'snow' and/or 'Rmpi' package did not load") : 
  'snow' and/or 'Rmpi' package did not load
Testing bpaggregate
Testing bpexportglobals
Testing bpiterate
Testing bplapply
Testing bploop
Testing bpmapply
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
Testing bpoptions
Testing bpvalidate
Testing bpvec
Testing bpvectorize
Testing errorhandling
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
Testing internal_rng_stream
Testing ipcmutex
Testing logging
Testing refclass
Testing rng
Testing utilities
Testing worker-number


RUNIT TEST PROTOCOL -- Tue Nov 19 20:05:11 2024 
*********************************************** 
Number of test functions: 109 
Number of deactivated test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocParallel RUnit Tests - 109 test functions, 0 errors, 0 failures
Number of test functions: 109 
Number of deactivated test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 49.681  20.674 314.714 

Example timings

BiocParallel.Rcheck/BiocParallel-Ex.timings

nameusersystemelapsed
BatchtoolsParam-class 2.260 1.45413.355
BiocParallelParam-class0.0020.0030.034
DeveloperInterface0.0000.0000.001
DoparParam-class0.0000.0000.001
MulticoreParam-class1.0460.6895.386
SerialParam-class0.0230.0040.027
SnowParam-class 1.021 0.11021.070
bpaggregate0.0010.0010.001
bpiterate0.5300.5051.713
bplapply0.1040.2070.747
bploop000
bpmapply0.3530.1720.823
bpok 0.594 0.07313.439
bpoptions0.0220.0025.762
bpschedule0.3610.0790.804
bptry0.0720.1970.231
bpvalidate2.9630.2595.376
bpvec0.3450.1320.568
bpvectorize0.0640.2130.193
ipcmutex0.4420.2591.325
register0.7510.2900.937
worker-number1.2980.0911.406