Package: Streamer

Version: 1.29.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Streamer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Streamer_1.29.1.tar.gz

StartedAt: 2019-04-09 05:49:54 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:50:55 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 61.9 seconds

RetCode: 0

Status:  OK

CheckDir: Streamer.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Streamer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Streamer_1.29.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Streamer.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Streamer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Streamer’ version ‘1.29.1’
* 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 ‘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
* 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
Unexported objects imported by ':::' calls:
  ‘parallel:::mckill’ ‘parallel:::sendMaster’
  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 ... 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/Streamer.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Streamer
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Streamer’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c R_init_Streamer.c -o R_init_Streamer.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c raw_input.c -o raw_input.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Streamer.so R_init_Streamer.o raw_input.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Streamer/00new/Streamer/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 (Streamer)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 for (a in as.list(elist)) if (!missing(a) && !checkSkipLoopCntxt(a,  :
  closing unused connection 4 (/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Streamer/extdata/s_1_sequence.txt)
2: In for (a in as.list(elist)) if (!missing(a) && !checkSkipLoopCntxt(a,  :
  closing unused connection 3 (/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Streamer/extdata/s_1_sequence.txt)


RUNIT TEST PROTOCOL -- Tue Apr  9 05:50:48 2019 
*********************************************** 
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 
Warning message:
In for (what in en) { :
  closing unused connection 3 (/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Streamer/extdata/s_1_sequence.txt)
> 
> proc.time()
   user  system elapsed 
  2.207   0.752   2.601 

name	user	system	elapsed
ConnectionProducer-classes	0.329	0.030	0.361
Consumer-class	0.002	0.000	0.003
DAGTeam-class	0.417	0.030	0.447
Downsample-class	0.001	0.001	0.002
FunctionProducerConsumer-classes	0.903	0.012	0.915
ParallelParam-classes	0.007	0.001	0.008
Producer-class	0.043	0.003	0.046
RawInput-class	0.016	0.003	0.022
Reducer-class	1.116	0.303	1.286
Seq-class	0.010	0.004	0.015
Stream-class	0.092	0.013	0.105
Streamer-package	0.112	0.008	0.120
Team-class	1.957	0.502	2.309
Utility-classes	0.002	0.001	0.004
reset	0.000	0.000	0.001
status	0.001	0.001	0.001
yield	0.000	0.000	0.001