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CHECK report for Streamer on malbec2

This page was generated on 2019-10-16 12:00:09 -0400 (Wed, 16 Oct 2019).

Package 1600/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Streamer 1.30.0
Martin Morgan
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/Streamer
Branch: RELEASE_3_9
Last Commit: 68c2fc5
Last Changed Date: 2019-05-02 11:53:27 -0400 (Thu, 02 May 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

Summary

Package: Streamer
Version: 1.30.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Streamer.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Streamer_1.30.0.tar.gz
StartedAt: 2019-10-16 05:18:29 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:19:08 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 38.3 seconds
RetCode: 0
Status:  OK 
CheckDir: Streamer.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Streamer.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Streamer_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Streamer.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.30.0’
* 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 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-3.9-bioc/meat/Streamer.Rcheck/00check.log’
for details.



Installation output

Streamer.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Streamer
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘Streamer’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/lib -L/usr/local/lib -o Streamer.so R_init_Streamer.o raw_input.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
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 -- Wed Oct 16 05:19:04 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 (i in 2:nargs) { :
  closing unused connection 5 (/home/biocbuild/bbs-3.9-bioc/R/library/Streamer/extdata/s_1_sequence.txt)
2: In for (i in 2:nargs) { :
  closing unused connection 4 (/home/biocbuild/bbs-3.9-bioc/R/library/Streamer/extdata/s_1_sequence.txt)
3: In for (i in 2:nargs) { :
  closing unused connection 3 (/home/biocbuild/bbs-3.9-bioc/R/library/Streamer/extdata/s_1_sequence.txt)
> 
> proc.time()
   user  system elapsed 
  1.543   0.341   1.744 

Example timings

Streamer.Rcheck/Streamer-Ex.timings

nameusersystemelapsed
ConnectionProducer-classes0.2830.0080.291
Consumer-class0.0010.0000.002
DAGTeam-class0.3300.0080.338
Downsample-class0.0000.0010.001
FunctionProducerConsumer-classes0.6790.0030.682
ParallelParam-classes0.0050.0000.004
Producer-class0.0250.0000.025
RawInput-class0.0090.0010.017
Reducer-class1.1740.1111.233
Seq-class0.0090.0080.006
Stream-class0.0410.0000.041
Streamer-package0.0500.0000.051
Team-class2.0640.1292.146
Utility-classes0.0010.0000.001
reset000
status000
yield000