Back to Long tests report for BioC 3.7

CHECK report for BiocParallel on malbec2

This page was generated on 2018-10-16 13:43:37 -0400 (Tue, 16 Oct 2018).

Package 1/3HostnameOS / ArchCHECK
BiocParallel 1.14.2
Bioconductor Package Maintainer
Snapshot Date: 2018-10-13 07:35:05 -0400 (Sat, 13 Oct 2018)
URL: https://git.bioconductor.org/packages/BiocParallel
Branch: RELEASE_3_7
Last Commit: 1d5a449
Last Changed Date: 2018-07-08 06:50:57 -0400 (Sun, 08 Jul 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64 [ WARNINGS ]
merida2 OS X 10.11.6 El Capitan / x86_64  WARNINGS 

Summary

Package: BiocParallel
Version: 1.14.2
Command: /home/biocbuild/bbs-3.7-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_1.14.2.tar.gz
StartedAt: 2018-10-13 07:56:35 -0400 (Sat, 13 Oct 2018)
EndedAt: 2018-10-13 07:57:31 -0400 (Sat, 13 Oct 2018)
EllapsedTime: 56.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BiocParallel.Rcheck
Warnings: 1

Tests output

'R CMD check' output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-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_1.14.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc-longtests/meat/BiocParallel.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.14.2’
* 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 ‘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
--------------------------------------------------------------------------
[[55871,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:

Module: OpenFabrics (openib)
  Host: malbec2

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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘BiocParallel/libs/BiocParallel.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ipcmutex.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
 WARNING
directory ‘longtests’ not found
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc-longtests/meat/BiocParallel.Rcheck/00check.log’
for details.

Installation output

BiocParallel.Rcheck/00install.out

* installing *source* package ‘BiocParallel’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2 -c ipcmutex.cpp -o ipcmutex.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o BiocParallel.so ipcmutex.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-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)