Package: Streamer

Version: 1.28.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Streamer.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Streamer_1.28.1.tar.gz

StartedAt: 2019-04-16 03:18:47 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:19:22 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 35.3 seconds

RetCode: 0

Status:  OK

CheckDir: Streamer.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Streamer.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Streamer_1.28.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/Streamer.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 option ‘--no-vignettes’
* checking for file ‘Streamer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Streamer’ version ‘1.28.1’
* 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 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/Streamer.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL Streamer
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘Streamer’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_Streamer.c -o R_init_Streamer.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c raw_input.c -o raw_input.o
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o Streamer.so R_init_Streamer.o raw_input.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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
* DONE (Streamer)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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("Streamer")
Timing stopped at: 0 0 0.001
Error in DEACTIVATED("should error with only a consumer (?)") : 
  should error with only a consumer (?)


RUNIT TEST PROTOCOL -- Tue Apr 16 03:19:19 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 messages:
1: In for (field in elNames) envRefSetField(.Object, field, classDef,  :
  closing unused connection 5 (/home/biocbuild/bbs-3.8-bioc/R/library/Streamer/extdata/s_1_sequence.txt)
2: In for (field in elNames) envRefSetField(.Object, field, classDef,  :
  closing unused connection 4 (/home/biocbuild/bbs-3.8-bioc/R/library/Streamer/extdata/s_1_sequence.txt)
3: In for (field in elNames) envRefSetField(.Object, field, classDef,  :
  closing unused connection 3 (/home/biocbuild/bbs-3.8-bioc/R/library/Streamer/extdata/s_1_sequence.txt)
> 
> proc.time()
   user  system elapsed 
  1.488   0.172   1.692 

name	user	system	elapsed
ConnectionProducer-classes	0.264	0.008	0.273
Consumer-class	0.000	0.000	0.002
DAGTeam-class	0.288	0.004	0.293
Downsample-class	0.000	0.000	0.001
FunctionProducerConsumer-classes	0.704	0.000	0.702
ParallelParam-classes	0.004	0.000	0.005
Producer-class	0.032	0.000	0.031
RawInput-class	0.016	0.000	0.027
Reducer-class	1.152	0.092	1.244
Seq-class	0.008	0.000	0.006
Stream-class	0.060	0.004	0.064
Streamer-package	0.072	0.004	0.074
Team-class	2.008	0.160	2.175
Utility-classes	0.004	0.000	0.001
reset	0	0	0
status	0.000	0.000	0.001
yield	0	0	0