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CHECK report for Streamer on celaya2

This page was generated on 2019-04-09 13:01:33 -0400 (Tue, 09 Apr 2019).

Package 1568/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Streamer 1.29.1
Martin Morgan
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/Streamer
Branch: master
Last Commit: b917775
Last Changed Date: 2019-03-06 09:51:10 -0400 (Wed, 06 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

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

Command output

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###
### Running 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
###
##############################################################################
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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.



Installation output

Streamer.Rcheck/00install.out

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###
### Running command:
###
###   /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)

Tests output

Streamer.Rcheck/tests/unit_tests.Rout


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 

Example timings

Streamer.Rcheck/Streamer-Ex.timings

nameusersystemelapsed
ConnectionProducer-classes0.3290.0300.361
Consumer-class0.0020.0000.003
DAGTeam-class0.4170.0300.447
Downsample-class0.0010.0010.002
FunctionProducerConsumer-classes0.9030.0120.915
ParallelParam-classes0.0070.0010.008
Producer-class0.0430.0030.046
RawInput-class0.0160.0030.022
Reducer-class1.1160.3031.286
Seq-class0.0100.0040.015
Stream-class0.0920.0130.105
Streamer-package0.1120.0080.120
Team-class1.9570.5022.309
Utility-classes0.0020.0010.004
reset0.0000.0000.001
status0.0010.0010.001
yield0.0000.0000.001