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CHECK report for Streamer on tokay1

This page was generated on 2018-04-12 13:21:03 -0400 (Thu, 12 Apr 2018).

Package 1362/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Streamer 1.24.0
Martin Morgan
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/Streamer
Branch: RELEASE_3_6
Last Commit: ccb4a10
Last Changed Date: 2017-10-30 12:39:35 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Streamer
Version: 1.24.0
Command: rm -rf Streamer.buildbin-libdir Streamer.Rcheck && mkdir Streamer.buildbin-libdir Streamer.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Streamer.buildbin-libdir Streamer_1.24.0.tar.gz >Streamer.Rcheck\00install.out 2>&1 && cp Streamer.Rcheck\00install.out Streamer-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Streamer.buildbin-libdir --install="check:Streamer-install.out" --force-multiarch --no-vignettes --timings Streamer_1.24.0.tar.gz
StartedAt: 2018-04-12 03:28:37 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:29:36 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 59.6 seconds
RetCode: 0
Status:  OK  
CheckDir: Streamer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Streamer.buildbin-libdir Streamer.Rcheck && mkdir Streamer.buildbin-libdir Streamer.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Streamer.buildbin-libdir Streamer_1.24.0.tar.gz >Streamer.Rcheck\00install.out 2>&1 && cp Streamer.Rcheck\00install.out Streamer-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Streamer.buildbin-libdir --install="check:Streamer-install.out" --force-multiarch --no-vignettes --timings Streamer_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Streamer.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Streamer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Streamer' version '1.24.0'
* 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 whether package 'Streamer' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Missing objects imported by ':::' calls:
  'parallel:::mckill' 'parallel:::sendMaster'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot.DAGTeam: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
* 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Streamer.buildbin-libdir/Streamer/libs/i386/Streamer.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'unit_tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/Streamer.Rcheck/00check.log'
for details.



Installation output

Streamer.Rcheck/00install.out


install for i386

* installing *source* package 'Streamer' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_Streamer.c -o R_init_Streamer.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c raw_input.c -o raw_input.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Streamer.dll tmp.def R_init_Streamer.o raw_input.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/Streamer.buildbin-libdir/Streamer/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'Streamer'
    finding HTML links ... done
    ConnectionProducer-classes              html  
    Consumer-class                          html  
    DAGTeam-class                           html  
    finding level-2 HTML links ... done

    Downsample-class                        html  
    FunctionProducerConsumer-classes        html  
    ParallelParam-classes                   html  
    Producer-class                          html  
    RawInput-class                          html  
    Reducer-class                           html  
    Seq-class                               html  
    Stream-class                            html  
    Streamer-package                        html  
    Team-class                              html  
    Utility-classes                         html  
    reset                                   html  
    status                                  html  
    yield                                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Streamer' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_Streamer.c -o R_init_Streamer.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c raw_input.c -o raw_input.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Streamer.dll tmp.def R_init_Streamer.o raw_input.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/Streamer.buildbin-libdir/Streamer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Streamer' as Streamer_1.24.0.zip
* DONE (Streamer)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Streamer.Rcheck/tests_i386/unit_tests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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("Streamer")
Timing stopped at: 0 0 0
Error in DEACTIVATED("should error with only a consumer (?)") : 
  should error with only a consumer (?)
In addition: Warning messages:
1: In .Internal(gc(verbose, reset)) :
  closing unused connection 4 (C:/Users/biocbuild/bbs-3.6-bioc/meat/Streamer.buildbin-libdir/Streamer/extdata/s_1_sequence.txt)
2: In .Internal(gc(verbose, reset)) :
  closing unused connection 3 (C:/Users/biocbuild/bbs-3.6-bioc/meat/Streamer.buildbin-libdir/Streamer/extdata/s_1_sequence.txt)
3: In .Internal(gc(verbose, reset)) :
  closing unused connection 3 (C:/Users/biocbuild/bbs-3.6-bioc/meat/Streamer.buildbin-libdir/Streamer/extdata/s_1_sequence.txt)


RUNIT TEST PROTOCOL -- Thu Apr 12 03:29:26 2018 
*********************************************** 
Number of test functions: 14 
Number of deactivated test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Streamer RUnit Tests - 14 test functions, 0 errors, 0 failures
Number of test functions: 14 
Number of deactivated test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.87    0.03    1.90 

Streamer.Rcheck/tests_x64/unit_tests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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("Streamer")
Timing stopped at: 0 0 0
Error in DEACTIVATED("should error with only a consumer (?)") : 
  should error with only a consumer (?)
In addition: Warning messages:
1: In .Internal(gc(verbose, reset)) :
  closing unused connection 4 (C:/Users/biocbuild/bbs-3.6-bioc/meat/Streamer.buildbin-libdir/Streamer/extdata/s_1_sequence.txt)
2: In .Internal(gc(verbose, reset)) :
  closing unused connection 3 (C:/Users/biocbuild/bbs-3.6-bioc/meat/Streamer.buildbin-libdir/Streamer/extdata/s_1_sequence.txt)
3: In .Internal(gc(verbose, reset)) :
  closing unused connection 3 (C:/Users/biocbuild/bbs-3.6-bioc/meat/Streamer.buildbin-libdir/Streamer/extdata/s_1_sequence.txt)


RUNIT TEST PROTOCOL -- Thu Apr 12 03:29:31 2018 
*********************************************** 
Number of test functions: 14 
Number of deactivated test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Streamer RUnit Tests - 14 test functions, 0 errors, 0 failures
Number of test functions: 14 
Number of deactivated test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   2.48    0.01    2.48 

Example timings

Streamer.Rcheck/examples_i386/Streamer-Ex.timings

nameusersystemelapsed
ConnectionProducer-classes0.300.000.53
Consumer-class000
DAGTeam-class0.350.000.34
Downsample-class000
FunctionProducerConsumer-classes0.450.000.45
ParallelParam-classes000
Producer-class0.010.000.01
RawInput-class000
Reducer-class0.030.000.04
Seq-class000
Stream-class0.050.000.05
Streamer-package0.050.000.05
Team-class000
Utility-classes000
reset000
status000
yield000

Streamer.Rcheck/examples_x64/Streamer-Ex.timings

nameusersystemelapsed
ConnectionProducer-classes0.30.00.3
Consumer-class000
DAGTeam-class0.390.000.39
Downsample-class000
FunctionProducerConsumer-classes0.630.000.62
ParallelParam-classes000
Producer-class0.010.000.02
RawInput-class0.020.000.02
Reducer-class0.050.000.04
Seq-class000
Stream-class0.040.000.05
Streamer-package0.050.000.05
Team-class000
Utility-classes000
reset000
status000
yield000