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This page was generated on 2015-10-27 12:15:11 -0400 (Tue, 27 Oct 2015).
| Package 556/1104 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| KEGGREST 1.11.0 Bioconductor Package Maintainer
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK |  | |||||
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ ERROR ] | OK |
| Package: KEGGREST |
| Version: 1.11.0 |
| Command: rm -rf KEGGREST.buildbin-libdir KEGGREST.Rcheck && mkdir KEGGREST.buildbin-libdir KEGGREST.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGREST.buildbin-libdir KEGGREST_1.11.0.tar.gz >KEGGREST.Rcheck\00install.out 2>&1 && cp KEGGREST.Rcheck\00install.out KEGGREST-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=KEGGREST.buildbin-libdir --install="check:KEGGREST-install.out" --force-multiarch --no-vignettes --timings KEGGREST_1.11.0.tar.gz |
| StartedAt: 2015-10-27 03:32:23 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 03:44:40 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 736.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: KEGGREST.Rcheck |
| Warnings: NA |
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### Running command:
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### rm -rf KEGGREST.buildbin-libdir KEGGREST.Rcheck && mkdir KEGGREST.buildbin-libdir KEGGREST.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGREST.buildbin-libdir KEGGREST_1.11.0.tar.gz >KEGGREST.Rcheck\00install.out 2>&1 && cp KEGGREST.Rcheck\00install.out KEGGREST-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=KEGGREST.buildbin-libdir --install="check:KEGGREST-install.out" --force-multiarch --no-vignettes --timings KEGGREST_1.11.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/KEGGREST.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'KEGGREST/DESCRIPTION' ... OK
* this is package 'KEGGREST' version '1.11.0'
* 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 'KEGGREST' 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
Namespace in Imports field not imported from: 'methods'
All declared Imports should be used.
Unexported object imported by a ':::' call: 'BiocGenerics:::testPackage'
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' ... [166s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
keggList 7.16 1.16 29.94
listDatabases 6.81 0.98 29.39
keggLink 0.73 0.22 43.14
keggConv 0.13 0.03 22.35
mark.pathway.by.objects 0.16 0.00 8.17
keggFind 0.05 0.03 26.97
** running examples for arch 'x64' ... [175s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
keggList 6.11 1.08 33.66
listDatabases 5.40 0.89 33.53
keggLink 0.56 0.18 42.45
keggConv 0.14 0.02 22.28
mark.pathway.by.objects 0.16 0.00 8.14
keggFind 0.08 0.00 28.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'KEGGREST_unit_tests.R' [158s]
Warning message:
running command '"c:/biocbld/BBS-3˜1.3-B/R/bin/i386/R" CMD BATCH --vanilla "KEGGREST_unit_tests.R" "KEGGREST_unit_tests.Rout"' had status 1
ERROR
Running the tests in 'tests/KEGGREST_unit_tests.R' failed.
Last 13 lines of output:
Test files with failing tests
test_KEGGREST.R
test_keggLink
Error in BiocGenerics:::testPackage("KEGGREST") :
unit tests failed for package KEGGREST
In addition: Warning message:
In download.file(url, t, quiet = TRUE) :
downloaded length 265740 != reported length 200
Execution halted
** running tests for arch 'x64' ...
Running 'KEGGREST_unit_tests.R' [153s]
[153s] 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: 1 ERROR, 1 NOTE
See
'c:/biocbld/bbs-3.3-bioc/meat/KEGGREST.Rcheck/00check.log'
for details.
KEGGREST.Rcheck/tests_i386/KEGGREST_unit_tests.Rout.fail:
R Under development (unstable) (2015-09-22 r69418) -- "Unsuffered Consequences"
Copyright (C) 2015 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("KEGGREST")
Timing stopped at: 0.4 0 43.67
Error in FUN(X[[i]], ...) : subscript out of bounds
RUNIT TEST PROTOCOL -- Tue Oct 27 03:42:04 2015
***********************************************
Number of test functions: 10
Number of errors: 1
Number of failures: 0
1 Test Suite :
KEGGREST RUnit Tests - 10 test functions, 1 error, 0 failures
ERROR in test_keggLink: Error in FUN(X[[i]], ...) : subscript out of bounds
Test files with failing tests
test_KEGGREST.R
test_keggLink
Error in BiocGenerics:::testPackage("KEGGREST") :
unit tests failed for package KEGGREST
In addition: Warning message:
In download.file(url, t, quiet = TRUE) :
downloaded length 265740 != reported length 200
Execution halted
KEGGREST.Rcheck/00install.out:
install for i386 * installing *source* package 'KEGGREST' ... ** 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 'KEGGREST' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'KEGGREST' as KEGGREST_1.11.0.zip * DONE (KEGGREST)
KEGGREST.Rcheck/examples_i386/KEGGREST-Ex.timings:
| name | user | system | elapsed | |
| keggConv | 0.13 | 0.03 | 22.35 | |
| keggFind | 0.05 | 0.03 | 26.97 | |
| keggGet | 0.89 | 0.00 | 2.99 | |
| keggInfo | 0.03 | 0.00 | 1.07 | |
| keggLink | 0.73 | 0.22 | 43.14 | |
| keggList | 7.16 | 1.16 | 29.94 | |
| listDatabases | 6.81 | 0.98 | 29.39 | |
| mark.pathway.by.objects | 0.16 | 0.00 | 8.17 | |
KEGGREST.Rcheck/examples_x64/KEGGREST-Ex.timings:
| name | user | system | elapsed | |
| keggConv | 0.14 | 0.02 | 22.28 | |
| keggFind | 0.08 | 0.00 | 28.05 | |
| keggGet | 1.01 | 0.02 | 3.50 | |
| keggInfo | 0.05 | 0.00 | 1.13 | |
| keggLink | 0.56 | 0.18 | 42.45 | |
| keggList | 6.11 | 1.08 | 33.66 | |
| listDatabases | 5.40 | 0.89 | 33.53 | |
| mark.pathway.by.objects | 0.16 | 0.00 | 8.14 | |