Martin Morgan
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/Streamer |
| Branch: RELEASE_3_7 |
| Last Commit: 1b60d46 |
| Last Changed Date: 2018-04-30 10:35:20 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:35:34 -0400 (Wed, 17 Oct 2018).
| Package 1441/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Streamer 1.26.0 Martin Morgan
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Streamer |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Streamer.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Streamer_1.26.0.tar.gz |
| StartedAt: 2018-10-17 05:05:19 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 05:06:13 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 54.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Streamer.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Streamer.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Streamer_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Streamer.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.26.0'
* 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 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 ... NOTE
plot.DAGTeam: no visible global function definition for 'plot'
Undefined global functions or variables:
plot
Consider adding
importFrom("graphics", "plot")
to your NAMESPACE file.
* 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-3.7-bioc/R/library/Streamer/libs/i386/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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/Streamer.Rcheck/00check.log'
for details.
Streamer.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Streamer_1.26.0.tar.gz && rm -rf Streamer.buildbin-libdir && mkdir Streamer.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Streamer.buildbin-libdir Streamer_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Streamer_1.26.0.zip && rm Streamer_1.26.0.tar.gz Streamer_1.26.0.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 44102 100 44102 0 0 701k 0 --:--:-- --:--:-- --:--:-- 783k
install for i386
* installing *source* package 'Streamer' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_init_Streamer.c -o R_init_Streamer.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Streamer.buildbin-libdir/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
In R CMD INSTALL
install for x64
* installing *source* package 'Streamer' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_init_Streamer.c -o R_init_Streamer.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Streamer.buildbin-libdir/Streamer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Streamer' as Streamer_1.26.0.zip
* DONE (Streamer)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'Streamer' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
Streamer.Rcheck/tests_i386/unit_tests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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 cb :
closing unused connection 4 (C:/Users/biocbuild/bbs-3.7-bioc/R/library/Streamer/extdata/s_1_sequence.txt)
2: In cb :
closing unused connection 3 (C:/Users/biocbuild/bbs-3.7-bioc/R/library/Streamer/extdata/s_1_sequence.txt)
RUNIT TEST PROTOCOL -- Wed Oct 17 05:06:06 2018
***********************************************
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-3.7-bioc/R/library/Streamer/extdata/s_1_sequence.txt)
>
> proc.time()
user system elapsed
1.48 0.01 1.59
|
Streamer.Rcheck/tests_x64/unit_tests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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 getInlineHandler(name, info$package) :
closing unused connection 4 (C:/Users/biocbuild/bbs-3.7-bioc/R/library/Streamer/extdata/s_1_sequence.txt)
2: In getInlineHandler(name, info$package) :
closing unused connection 3 (C:/Users/biocbuild/bbs-3.7-bioc/R/library/Streamer/extdata/s_1_sequence.txt)
RUNIT TEST PROTOCOL -- Wed Oct 17 05:06:08 2018
***********************************************
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-3.7-bioc/R/library/Streamer/extdata/s_1_sequence.txt)
>
> proc.time()
user system elapsed
1.12 0.07 1.18
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Streamer.Rcheck/examples_i386/Streamer-Ex.timings
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Streamer.Rcheck/examples_x64/Streamer-Ex.timings
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