Long tests report for BioC 3.8 - CHECK report for BiocParallel on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no BiocParallel_1.16.6.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc-longtests/meat/BiocParallel.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘BiocParallel/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiocParallel’ version ‘1.16.6’
* 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'
 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 ‘BiocParallel’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... NOTE
--------------------------------------------------------------------------
[[28684,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:

Module: OpenFabrics (openib)
  Host: malbec1

Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
Unexported objects imported by ':::' calls:
  ‘BatchJobs:::checkDir’ ‘parallel:::closeNode’ ‘parallel:::recvData’
  ‘parallel:::recvOneData’ ‘parallel:::sendData’
  See the note in ?`:::` about the use of this operator.
* 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 ... SKIPPED
* 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 ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
 WARNING
directory ‘longtests’ not found
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc-longtests/meat/BiocParallel.Rcheck/00check.log’
for details.

* installing *source* package ‘BiocParallel’ ...
checking for gcc... gcc
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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for shm_open in -lrt... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c ipcmutex.cpp -o ipcmutex.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/seed_impl.hpp:26,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/mersenne_twister.hpp:30,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o BiocParallel.so ipcmutex.o -lrt -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc-longtests/meat/BiocParallel.Rcheck/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
* DONE (BiocParallel)

CHECK report for BiocParallel on malbec1

Summary

Tests output

'R CMD check' output

Installation output