| Back to First build/check report with an "external build node" |
This page was generated on 2023-06-01 18:17:19 -0400 (Thu, 01 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| xps15 | Linux (Ubuntu 23.04) | x86_64 | 4.3.0 Patched (2023-05-23 r84466) -- "Already Tomorrow" | 544 |
| 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 | ||||
|
To the developers/maintainers of the BiocParallel package: Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 17/91 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
| BiocParallel 1.35.2 (landing page) Martin Morgan
| xps15 | Linux (Ubuntu 23.04) / x86_64 | OK | OK | OK | ||||||||
| Package: BiocParallel |
| Version: 1.35.2 |
| Command: /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings BiocParallel_1.35.2.tar.gz |
| StartedAt: 2023-06-01 12:58:49 -0700 (Thu, 01 Jun 2023) |
| EndedAt: 2023-06-01 13:06:37 -0700 (Thu, 01 Jun 2023) |
| EllapsedTime: 467.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocParallel.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings BiocParallel_1.35.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/hpages/bbs-3.18-bioc-testing/meat/BiocParallel.Rcheck’
* using R version 4.3.0 Patched (2023-05-23 r84466)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0
GNU Fortran (Ubuntu 12.2.0-17ubuntu1) 12.2.0
* running under: Ubuntu 23.04
* using session charset: UTF-8
* checking for file ‘BiocParallel/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiocParallel’ version ‘1.35.2’
* checking package namespace information ... OK
* checking package dependencies ... 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: ‘g++ (Ubuntu 12.2.0-17ubuntu1) 12.2.0’
* 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 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 ... NOTE
Unexported objects imported by ':::' calls:
‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BatchtoolsParam-class 3.085 0.678 11.152
SnowParam-class 1.002 0.015 6.355
bpoptions 0.029 0.000 5.035
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘Introduction_To_BiocParallel.Rmd’ using ‘UTF-8’... OK
‘Random_Numbers.Rmd’ using ‘UTF-8’... OK
‘BiocParallel_BatchtoolsParam.Rnw’... OK
‘Errors_Logs_And_Debugging.Rnw’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/hpages/bbs-3.18-bioc-testing/meat/BiocParallel.Rcheck/00check.log’
for details.
BiocParallel.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/hpages/bbs-3.18-bioc/R/bin/R CMD INSTALL BiocParallel
###
##############################################################################
##############################################################################
* installing to library ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs’
* 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 g++ -std=gnu++17 accepts -g... yes
checking for g++ -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: ‘g++ (Ubuntu 12.2.0-17ubuntu1) 12.2.0’
using C++11
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc/R/site-library/BH/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/cpp11/include' -I/usr/local/include -fpic -g -O2 -Wall -c cpp11.cpp -o cpp11.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc/R/site-library/BH/include' -I'/home/hpages/bbs-3.18-bioc/R/site-library/cpp11/include' -I/usr/local/include -fpic -g -O2 -Wall -c ipcmutex.cpp -o ipcmutex.o
In file included from /home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/apply.hpp:24,
from /home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/aux_/fold_impl.hpp:19,
from /home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/fold.hpp:20,
from /home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/remove_if.hpp:18,
from /home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/remove.hpp:18,
from /home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/function_types/components.hpp:44,
from /home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/function_types/is_member_function_pointer.hpp:14,
from /home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/tti/detail/dmem_fun.hpp:10,
from /home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/tti/has_member_function.hpp:15,
from /home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/uuid/random_generator.hpp:20,
from /home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/uuid/uuid_generators.hpp:17,
from ipcmutex.cpp:3:
/home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
/home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
/home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
/home/hpages/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
g++ -std=gnu++11 -shared -L/usr/local/lib -o BiocParallel.so cpp11.o ipcmutex.o
installing to /home/hpages/bbs-3.18-bioc-testing/Rlibs/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)
BiocParallel.Rcheck/tests/test.Rout
R version 4.3.0 Patched (2023-05-23 r84466) -- "Already Tomorrow"
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.
> 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
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 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 -- Thu Jun 1 13:04:55 2023
***********************************************
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
64.640 20.743 289.323
BiocParallel.Rcheck/BiocParallel-Ex.timings
| name | user | system | elapsed | |
| BatchtoolsParam-class | 3.085 | 0.678 | 11.152 | |
| BiocParallelParam-class | 0.002 | 0.000 | 0.001 | |
| DeveloperInterface | 0 | 0 | 0 | |
| DoparParam-class | 0 | 0 | 0 | |
| MulticoreParam-class | 0.987 | 0.268 | 2.777 | |
| SerialParam-class | 0.032 | 0.009 | 0.029 | |
| SnowParam-class | 1.002 | 0.015 | 6.355 | |
| bpaggregate | 0.000 | 0.000 | 0.001 | |
| bpiterate | 0.363 | 0.109 | 0.385 | |
| bplapply | 0.037 | 0.071 | 0.049 | |
| bploop | 0 | 0 | 0 | |
| bpmapply | 0.180 | 0.082 | 0.223 | |
| bpok | 0.422 | 0.004 | 3.004 | |
| bpoptions | 0.029 | 0.000 | 5.035 | |
| bpschedule | 0.446 | 0.016 | 0.454 | |
| bptry | 0.051 | 0.076 | 0.059 | |
| bpvalidate | 3.378 | 0.159 | 3.539 | |
| bpvec | 0.353 | 0.134 | 0.387 | |
| bpvectorize | 0.022 | 0.052 | 0.073 | |
| ipcmutex | 0.393 | 0.207 | 0.924 | |
| register | 0.634 | 0.244 | 0.783 | |
| worker-number | 1.145 | 0.141 | 1.227 | |