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This page was generated on 2015-08-20 13:23:01 -0700 (Thu, 20 Aug 2015).
| Package 600/1069 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| metagene 2.1.1 Charles Joly Beauparlant
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | ERROR | ||||||
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | ||||||
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | ERROR | OK | ||||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK |
| Package: metagene |
| Version: 2.1.1 |
| Command: rm -rf metagene.buildbin-libdir metagene.Rcheck && mkdir metagene.buildbin-libdir metagene.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metagene.buildbin-libdir metagene_2.1.1.tar.gz >metagene.Rcheck\00install.out 2>&1 && cp metagene.Rcheck\00install.out metagene-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=metagene.buildbin-libdir --install="check:metagene-install.out" --force-multiarch --no-vignettes --timings metagene_2.1.1.tar.gz |
| StartedAt: 2015-08-20 06:54:15 -0700 (Thu, 20 Aug 2015) |
| EndedAt: 2015-08-20 07:04:54 -0700 (Thu, 20 Aug 2015) |
| EllapsedTime: 639.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: metagene.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### rm -rf metagene.buildbin-libdir metagene.Rcheck && mkdir metagene.buildbin-libdir metagene.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metagene.buildbin-libdir metagene_2.1.1.tar.gz >metagene.Rcheck\00install.out 2>&1 && cp metagene.Rcheck\00install.out metagene-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=metagene.buildbin-libdir --install="check:metagene-install.out" --force-multiarch --no-vignettes --timings metagene_2.1.1.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/metagene.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metagene/DESCRIPTION' ... OK
* this is package 'metagene' version '2.1.1'
* 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 'metagene' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
intoNbins: no visible global function definition for 'IRanges'
* 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [13s] OK
** running examples for arch 'x64' ... [12s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [158s]
Warning message:
running command '"D:/biocbld/BBS-3˜1.2-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:
1: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
2: In BiocParallel::MulticoreParam(workers = 2) :
MulticoreParam not supported on Windows. Use SnowParam instead.
3: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
4: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
5: In BiocParallel::MulticoreParam(workers = 2) :
MulticoreParam not supported on Windows. Use SnowParam instead.
6: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
Execution halted
** running tests for arch 'x64' ...
Running 'runTests.R' [177s]
Warning message:
running command '"D:/biocbld/BBS-3˜1.2-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:
1: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
2: In BiocParallel::MulticoreParam(workers = 2) :
MulticoreParam not supported on Windows. Use SnowParam instead.
3: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
4: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
5: In BiocParallel::MulticoreParam(workers = 2) :
MulticoreParam not supported on Windows. Use SnowParam instead.
6: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
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, 1 NOTE
See
'D:/biocbld/bbs-3.2-bioc/meat/metagene.Rcheck/00check.log'
for details.
metagene.Rcheck/tests_i386/runTests.Rout.fail:
R version 3.2.2 (2015-08-14) -- "Fire Safety"
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.
> ## Run all tests in the metagene package
> BiocGenerics:::testPackage("metagene")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rep.int, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
Timing stopped at: 82.82 21.74 104.58
Error in checkTrue(!all(sapply(sane, function(x) all(as.numeric(x) >= :
Test not TRUE
Bam_Handler get_normalized_coverage - Negative coverage did not pass sanity test
In addition: Warning messages:
1: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
2: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
Warning messages:
1: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
2: In BiocParallel::MulticoreParam(workers = 2) :
MulticoreParam not supported on Windows. Use SnowParam instead.
3: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
Timing stopped at: 0.39 0 0.39
Error in checkIdentical(obs, exp, msg) :
FALSE metagene heatmap - Invalid all extra seqnames did not generate the expected error with force_seqlevels = TRUE.
Timing stopped at: 0.36 0 0.36
Error in checkIdentical(obs, exp, msg) :
FALSE metagene heatmap - Invalid regions seqnames did not give the expected error message.
RUNIT TEST PROTOCOL -- Thu Aug 20 07:01:53 2015
***********************************************
Number of test functions: 105
Number of errors: 0
Number of failures: 3
1 Test Suite :
metagene RUnit Tests - 105 test functions, 0 errors, 3 failures
FAILURE in test.bam_handler_get_normalized_coverage_negative_coverage: Error in checkTrue(!all(sapply(sane, function(x) all(as.numeric(x) >= :
Test not TRUE
Bam_Handler get_normalized_coverage - Negative coverage did not pass sanity test
FAILURE in test.metagene_initialize_all_extra_seqnames_force_seqlevels: Error in checkIdentical(obs, exp, msg) :
FALSE metagene heatmap - Invalid all extra seqnames did not generate the expected error with force_seqlevels = TRUE.
FAILURE in test.metagene_initialize_invalid_extra_seqnames: Error in checkIdentical(obs, exp, msg) :
FALSE metagene heatmap - Invalid regions seqnames did not give the expected error message.
Test files with failing tests
test_bam_handler.R
test.bam_handler_get_normalized_coverage_negative_coverage
test_metagene.R
test.metagene_initialize_all_extra_seqnames_force_seqlevels
test.metagene_initialize_invalid_extra_seqnames
Error in BiocGenerics:::testPackage("metagene") :
unit tests failed for package metagene
In addition: Warning messages:
1: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
2: In BiocParallel::MulticoreParam(workers = 2) :
MulticoreParam not supported on Windows. Use SnowParam instead.
3: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
4: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
5: In BiocParallel::MulticoreParam(workers = 2) :
MulticoreParam not supported on Windows. Use SnowParam instead.
6: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
Execution halted
metagene.Rcheck/tests_x64/runTests.Rout.fail:
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 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.
> ## Run all tests in the metagene package
> BiocGenerics:::testPackage("metagene")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rep.int, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
Warning messages:
1: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
2: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
3: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
4: In BiocParallel::MulticoreParam(workers = 2) :
MulticoreParam not supported on Windows. Use SnowParam instead.
5: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
Timing stopped at: 0.59 0 0.6
Error in checkIdentical(obs, exp, msg) :
FALSE metagene heatmap - Invalid all extra seqnames did not generate the expected error with force_seqlevels = TRUE.
Timing stopped at: 0.52 0 0.51
Error in checkIdentical(obs, exp, msg) :
FALSE metagene heatmap - Invalid regions seqnames did not give the expected error message.
RUNIT TEST PROTOCOL -- Thu Aug 20 07:04:50 2015
***********************************************
Number of test functions: 105
Number of errors: 0
Number of failures: 2
1 Test Suite :
metagene RUnit Tests - 105 test functions, 0 errors, 2 failures
FAILURE in test.metagene_initialize_all_extra_seqnames_force_seqlevels: Error in checkIdentical(obs, exp, msg) :
FALSE metagene heatmap - Invalid all extra seqnames did not generate the expected error with force_seqlevels = TRUE.
FAILURE in test.metagene_initialize_invalid_extra_seqnames: Error in checkIdentical(obs, exp, msg) :
FALSE metagene heatmap - Invalid regions seqnames did not give the expected error message.
Test files with failing tests
test_metagene.R
test.metagene_initialize_all_extra_seqnames_force_seqlevels
test.metagene_initialize_invalid_extra_seqnames
Error in BiocGenerics:::testPackage("metagene") :
unit tests failed for package metagene
In addition: Warning messages:
1: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
2: In BiocParallel::MulticoreParam(workers = 2) :
MulticoreParam not supported on Windows. Use SnowParam instead.
3: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
4: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
5: In BiocParallel::MulticoreParam(workers = 2) :
MulticoreParam not supported on Windows. Use SnowParam instead.
6: In MulticoreParam(workers = cores) :
MulticoreParam not supported on Windows. Use SnowParam instead.
Execution halted
metagene.Rcheck/00install.out:
install for i386 * installing *source* package 'metagene' ... ** 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 'metagene' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'metagene' as metagene_2.1.1.zip * DONE (metagene)
metagene.Rcheck/examples_i386/metagene-Ex.timings:
| name | user | system | elapsed | |
| Bam_Handler | 0.40 | 0.02 | 0.42 | |
| getGenes | 0 | 0 | 0 | |
| getGenesBiomart | 0.00 | 0.01 | 0.01 | |
| get_demo_bam_files | 0 | 0 | 0 | |
| get_demo_regions | 0 | 0 | 0 | |
| metagene | 1.74 | 0.05 | 1.79 | |
metagene.Rcheck/examples_x64/metagene-Ex.timings:
| name | user | system | elapsed | |
| Bam_Handler | 0.40 | 0.02 | 0.43 | |
| getGenes | 0 | 0 | 0 | |
| getGenesBiomart | 0 | 0 | 0 | |
| get_demo_bam_files | 0 | 0 | 0 | |
| get_demo_regions | 0 | 0 | 0 | |
| metagene | 1.84 | 0.00 | 1.84 | |