| Back to the "Multiple platform build/check report" | A B C D E F G H I J K L M N O P Q [R] S T U V W X Y Z |
This page was generated on 2017-10-18 14:21:55 -0400 (Wed, 18 Oct 2017).
| Package 1104/1381 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RGalaxy 1.20.1 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ ERROR ] | OK | |||||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | ERROR | OK |
| Package: RGalaxy |
| Version: 1.20.1 |
| Command: rm -rf RGalaxy.buildbin-libdir RGalaxy.Rcheck && mkdir RGalaxy.buildbin-libdir RGalaxy.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RGalaxy.buildbin-libdir RGalaxy_1.20.1.tar.gz >RGalaxy.Rcheck\00install.out 2>&1 && cp RGalaxy.Rcheck\00install.out RGalaxy-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=RGalaxy.buildbin-libdir --install="check:RGalaxy-install.out" --force-multiarch --no-vignettes --timings RGalaxy_1.20.1.tar.gz |
| StartedAt: 2017-10-18 02:30:52 -0400 (Wed, 18 Oct 2017) |
| EndedAt: 2017-10-18 02:32:28 -0400 (Wed, 18 Oct 2017) |
| EllapsedTime: 95.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: RGalaxy.Rcheck |
| Warnings: NA |
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### Running command:
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### rm -rf RGalaxy.buildbin-libdir RGalaxy.Rcheck && mkdir RGalaxy.buildbin-libdir RGalaxy.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RGalaxy.buildbin-libdir RGalaxy_1.20.1.tar.gz >RGalaxy.Rcheck\00install.out 2>&1 && cp RGalaxy.Rcheck\00install.out RGalaxy-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=RGalaxy.buildbin-libdir --install="check:RGalaxy-install.out" --force-multiarch --no-vignettes --timings RGalaxy_1.20.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RGalaxy/DESCRIPTION' ... OK
* this is package 'RGalaxy' version '1.20.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'RSclient'
* 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 'RGalaxy' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'RSclient' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
'digest' 'optparse'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
'tools:::.Rd_get_argument_table' 'tools:::.Rd_get_metadata'
'tools:::fetchRdDB'
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 installed files from 'inst/doc' ... OK
* 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 'runTests.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386/R" CMD BATCH --vanilla "runTests.R" "runTests.Rout"' had status 1
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
FAILURE in test_missing_param: Error in checkEquals(expected, output) : 1 string mismatch
Test files with failing tests
test_galaxy.R
test_missing_param
Error in BiocGenerics:::testPackage("RGalaxy") :
unit tests failed for package RGalaxy
In addition: Warning messages:
1: Not enough information to create a functional test.
2: Not enough information to create a functional test.
Execution halted
** running tests for arch 'x64' ...
Running 'runTests.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64/R" CMD BATCH --vanilla "runTests.R" "runTests.Rout"' had status 1
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
FAILURE in test_missing_param: Error in checkEquals(expected, output) : 1 string mismatch
Test files with failing tests
test_galaxy.R
test_missing_param
Error in BiocGenerics:::testPackage("RGalaxy") :
unit tests failed for package RGalaxy
In addition: Warning messages:
1: Not enough information to create a functional test.
2: Not enough information to create a functional test.
Execution halted
* 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 ERRORs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00check.log'
for details.
runTests.Rout.fail:
R version 3.4.2 Patched (2017-10-07 r73498) -- "Short Summer"
Copyright (C) 2017 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("RGalaxy")
Attaching package: 'tools'
The following object is masked from 'package:XML':
toHTML
null device
1
Timing stopped at: 0.16 0 1.57
Error in checkEquals(expected, output) : 1 string mismatch
In addition: Warning messages:
1: Not enough information to create a functional test.
2: Not enough information to create a functional test.
3: Not enough information to create a functional test.
4: Not enough information to create a functional test.
Note: Did not find section 'Details' in man page.
RUNIT TEST PROTOCOL -- Wed Oct 18 02:32:12 2017
***********************************************
Number of test functions: 9
Number of errors: 0
Number of failures: 1
1 Test Suite :
RGalaxy RUnit Tests - 9 test functions, 0 errors, 1 failure
FAILURE in test_missing_param: Error in checkEquals(expected, output) : 1 string mismatch
Test files with failing tests
test_galaxy.R
test_missing_param
Error in BiocGenerics:::testPackage("RGalaxy") :
unit tests failed for package RGalaxy
In addition: Warning messages:
1: Not enough information to create a functional test.
2: Not enough information to create a functional test.
Execution halted
runTests.Rout.fail:
R version 3.4.2 Patched (2017-10-07 r73498) -- "Short Summer"
Copyright (C) 2017 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("RGalaxy")
Attaching package: 'tools'
The following object is masked from 'package:XML':
toHTML
null device
1
Timing stopped at: 0.14 0 1.59
Error in checkEquals(expected, output) : 1 string mismatch
In addition: Warning messages:
1: Not enough information to create a functional test.
2: Not enough information to create a functional test.
3: Not enough information to create a functional test.
4: Not enough information to create a functional test.
Note: Did not find section 'Details' in man page.
RUNIT TEST PROTOCOL -- Wed Oct 18 02:32:23 2017
***********************************************
Number of test functions: 9
Number of errors: 0
Number of failures: 1
1 Test Suite :
RGalaxy RUnit Tests - 9 test functions, 0 errors, 1 failure
FAILURE in test_missing_param: Error in checkEquals(expected, output) : 1 string mismatch
Test files with failing tests
test_galaxy.R
test_missing_param
Error in BiocGenerics:::testPackage("RGalaxy") :
unit tests failed for package RGalaxy
In addition: Warning messages:
1: Not enough information to create a functional test.
2: Not enough information to create a functional test.
Execution halted
RGalaxy.Rcheck/00install.out:
install for i386 * installing *source* package 'RGalaxy' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded install for x64 * installing *source* package 'RGalaxy' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'RGalaxy' as RGalaxy_1.20.1.zip * DONE (RGalaxy)
RGalaxy.Rcheck/examples_i386/RGalaxy-Ex.timings:
| name | user | system | elapsed | |
| GalaxyClasses | 0.04 | 0.00 | 0.05 | |
| GalaxyConfig-class | 0 | 0 | 0 | |
| GalaxyInputFile-class | 0.02 | 0.00 | 0.01 | |
| GalaxyOutput-class | 0.02 | 0.00 | 0.02 | |
| RserveConnection-class | 0 | 0 | 0 | |
| addTwoNumbers | 0 | 0 | 0 | |
| addTwoNumbersWithTest | 0.04 | 0.02 | 0.06 | |
| anotherTestFunction | 0.06 | 0.00 | 0.06 | |
| functionToGalaxify | 0.04 | 0.02 | 0.05 | |
| galaxy | 0 | 0 | 0 | |
| getFriendlyName | 0 | 0 | 0 | |
| probeLookup | 2.79 | 0.14 | 3.05 | |
| utilities | 0 | 0 | 0 | |
RGalaxy.Rcheck/examples_x64/RGalaxy-Ex.timings:
| name | user | system | elapsed | |
| GalaxyClasses | 0.08 | 0.00 | 0.08 | |
| GalaxyConfig-class | 0.02 | 0.00 | 0.01 | |
| GalaxyInputFile-class | 0.00 | 0.02 | 0.02 | |
| GalaxyOutput-class | 0.01 | 0.00 | 0.01 | |
| RserveConnection-class | 0 | 0 | 0 | |
| addTwoNumbers | 0.02 | 0.00 | 0.02 | |
| addTwoNumbersWithTest | 0.06 | 0.00 | 0.06 | |
| anotherTestFunction | 0.06 | 0.00 | 0.06 | |
| functionToGalaxify | 0.04 | 0.00 | 0.04 | |
| galaxy | 0 | 0 | 0 | |
| getFriendlyName | 0 | 0 | 0 | |
| probeLookup | 2.83 | 0.01 | 2.85 | |
| utilities | 0 | 0 | 0 | |