Multiple platform build/check report for BioC 3.10 - CHECK report for Streamer on tokay1

Package: Streamer

Version: 1.32.1

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Streamer.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Streamer_1.32.1.tar.gz

StartedAt: 2020-04-15 06:57:19 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:58:07 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 47.6 seconds

RetCode: 0

Status: OK

CheckDir: Streamer.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Streamer.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Streamer_1.32.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Streamer.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.32.1'
* 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 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 ... 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/Streamer/libs/i386/Streamer.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/Streamer/libs/x64/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 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/Streamer.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/Streamer_1.32.1.tar.gz && rm -rf Streamer.buildbin-libdir && mkdir Streamer.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Streamer.buildbin-libdir Streamer_1.32.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL Streamer_1.32.1.zip && rm Streamer_1.32.1.tar.gz Streamer_1.32.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 43919  100 43919    0     0  1021k      0 --:--:-- --:--:-- --:--:-- 1128k

install for i386

* installing *source* package 'Streamer' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_Streamer.c -o R_init_Streamer.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c raw_input.c -o raw_input.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o Streamer.dll tmp.def R_init_Streamer.o raw_input.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/Streamer.buildbin-libdir/00LOCK-Streamer/00new/Streamer/libs/i386
** R
** inst
** byte-compile and prepare 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'Streamer' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_Streamer.c -o R_init_Streamer.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c raw_input.c -o raw_input.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Streamer.dll tmp.def R_init_Streamer.o raw_input.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/Streamer.buildbin-libdir/Streamer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Streamer' as Streamer_1.32.1.zip
* DONE (Streamer)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'Streamer' successfully unpacked and MD5 sums checked


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 for (i in seq_along(cenv$extra)) { :
  closing unused connection 4 (C:/Users/biocbuild/bbs-3.10-bioc/R/library/Streamer/extdata/s_1_sequence.txt)
2: In for (i in seq_along(cenv$extra)) { :
  closing unused connection 3 (C:/Users/biocbuild/bbs-3.10-bioc/R/library/Streamer/extdata/s_1_sequence.txt)


RUNIT TEST PROTOCOL -- Wed Apr 15 06:58:00 2020 
*********************************************** 
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 lapply(findLocals1(e, shadowed, cntxt, vars), function(x) if (typeof(x) ==  :
  closing unused connection 3 (C:/Users/biocbuild/bbs-3.10-bioc/R/library/Streamer/extdata/s_1_sequence.txt)
> 
> proc.time()
   user  system elapsed 
   1.28    0.06    1.50


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 for (i in seq_along(cenv$extra)) { :
  closing unused connection 4 (C:/Users/biocbuild/bbs-3.10-bioc/R/library/Streamer/extdata/s_1_sequence.txt)
2: In for (i in seq_along(cenv$extra)) { :
  closing unused connection 3 (C:/Users/biocbuild/bbs-3.10-bioc/R/library/Streamer/extdata/s_1_sequence.txt)


RUNIT TEST PROTOCOL -- Wed Apr 15 06:58:02 2020 
*********************************************** 
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:
closing unused connection 3 (C:/Users/biocbuild/bbs-3.10-bioc/R/library/Streamer/extdata/s_1_sequence.txt) 
> 
> proc.time()
   user  system elapsed 
   1.09    0.09    1.18

name	user	system	elapsed
ConnectionProducer-classes	0.30	0.02	0.31
Consumer-class	0.01	0.00	0.02
DAGTeam-class	0.28	0.00	0.28
Downsample-class	0	0	0
FunctionProducerConsumer-classes	0.6	0.0	0.6
ParallelParam-classes	0	0	0
Producer-class	0.03	0.00	0.03
RawInput-class	0.00	0.00	0.02
Reducer-class	0.04	0.00	0.05
Seq-class	0.02	0.00	0.02
Stream-class	0.06	0.00	0.06
Streamer-package	0.08	0.00	0.08
Team-class	0	0	0
Utility-classes	0	0	0
reset	0	0	0
status	0	0	0
yield	0	0	0

name	user	system	elapsed
ConnectionProducer-classes	0.24	0.00	0.24
Consumer-class	0	0	0
DAGTeam-class	0.21	0.02	0.23
Downsample-class	0	0	0
FunctionProducerConsumer-classes	0.49	0.00	0.49
ParallelParam-classes	0	0	0
Producer-class	0.03	0.00	0.03
RawInput-class	0	0	0
Reducer-class	0.05	0.00	0.04
Seq-class	0	0	0
Stream-class	0.04	0.00	0.05
Streamer-package	0.05	0.00	0.05
Team-class	0	0	0
Utility-classes	0	0	0
reset	0	0	0
status	0	0	0
yield	0	0	0

CHECK report for Streamer on tokay1

Summary

Command output

Installation output

Tests output

Example timings