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This page was generated on 2016-06-17 11:32:54 -0700 (Fri, 17 Jun 2016).
| Package 1186/1211 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| Uniquorn 1.0.7 'Raik Otto'
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | ERROR | ||||||
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | ||||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK |
| Package: Uniquorn |
| Version: 1.0.7 |
| Command: rm -rf Uniquorn.buildbin-libdir Uniquorn.Rcheck && mkdir Uniquorn.buildbin-libdir Uniquorn.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Uniquorn.buildbin-libdir Uniquorn_1.0.7.tar.gz >Uniquorn.Rcheck\00install.out 2>&1 && cp Uniquorn.Rcheck\00install.out Uniquorn-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=Uniquorn.buildbin-libdir --install="check:Uniquorn-install.out" --force-multiarch --no-vignettes --timings Uniquorn_1.0.7.tar.gz |
| StartedAt: 2016-06-16 20:59:00 -0700 (Thu, 16 Jun 2016) |
| EndedAt: 2016-06-16 21:02:27 -0700 (Thu, 16 Jun 2016) |
| EllapsedTime: 206.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: Uniquorn.Rcheck |
| Warnings: NA |
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### Running command:
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### rm -rf Uniquorn.buildbin-libdir Uniquorn.Rcheck && mkdir Uniquorn.buildbin-libdir Uniquorn.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Uniquorn.buildbin-libdir Uniquorn_1.0.7.tar.gz >Uniquorn.Rcheck\00install.out 2>&1 && cp Uniquorn.Rcheck\00install.out Uniquorn-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=Uniquorn.buildbin-libdir --install="check:Uniquorn-install.out" --force-multiarch --no-vignettes --timings Uniquorn_1.0.7.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/Uniquorn.Rcheck'
* using R version 3.3.0 (2016-05-03)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Uniquorn/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Uniquorn' version '1.0.7'
* 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 'Uniquorn' 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 ... 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
Examples with CPU or elapsed time > 5s
user system elapsed
add_custom_vcf_to_database 25.15 1.14 27.99
identify_vcf_file 20.33 1.00 22.59
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
add_custom_vcf_to_database 23.15 0.99 26.16
identify_vcf_file 20.80 0.97 22.12
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
Warning message:
running command '"E:/biocbld/BBS-3˜1.3-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_identification: Error in checkTrue((as.logical(ident_result$Conf_score_sig[2:60]) == (rep(FALSE, :
Test not TRUE
Test files with failing tests
test_identification.R
test_identification
Error in BiocGenerics:::testPackage("Uniquorn") :
unit tests failed for package Uniquorn
Execution halted
** running tests for arch 'x64' ...
Running 'runTests.R'
Warning message:
running command '"E:/biocbld/BBS-3˜1.3-B/R/bin/x64/R" CMD BATCH --vanilla "runTests.R" "runTests.Rout"' had status 1
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
FAILURE in test_identification: Error in checkTrue((as.logical(ident_result$Conf_score_sig[2:60]) == (rep(FALSE, :
Test not TRUE
Test files with failing tests
test_identification.R
test_identification
Error in BiocGenerics:::testPackage("Uniquorn") :
unit tests failed for package Uniquorn
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
See
'E:/biocbld/bbs-3.3-bioc/meat/Uniquorn.Rcheck/00check.log'
for details.
runTests.Rout.fail:
R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
Copyright (C) 2016 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("Uniquorn")
[1] "Assuming reference genome GRCH37"
[1] "Reading VCF file: E:/biocbld/bbs-3.3-bioc/meat/Uniquorn.buildbin-libdir/Uniquorn/extdata/HT29.vcf.gz"
[1] "Finished reading the VCF file, loading database"
[1] "Found 60 many CLs for reference genome GRCH37"
[1] "Finished reading database, identifying CL"
[1] "Adjusted mutational inclusion weight, \n only using mutations that are have a weight higher than 1"
[1] "Found 53314 many mutations with mutational weight of at least 1"
[1] "Candidate(s): HT29,KM12"
[1] "Storing information in table: E:/biocbld/bbs-3.3-bioc/meat/Uniquorn.buildbin-libdir/Uniquorn/extdata/HT29.vcf.gz_uniquorn_ident.tab"
Timing stopped at: 19.62 1.27 21.98
Error in checkTrue((as.logical(ident_result$Conf_score_sig[2:60]) == (rep(FALSE, :
Test not TRUE
In addition: Warning message:
In identify_vcf_file(HT29_vcf_file, ref_gen = "GRCH37", verbose = TRUE) :
CCLE & CoSMIC CLP cancer cell line fingerprint NOT
found, defaulting to 60 CellMiner cancer cell lines!
It is strongly advised to add ˜1900 CCLE & CoSMIC CLs, see readme.
RUNIT TEST PROTOCOL -- Thu Jun 16 21:02:21 2016
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 1
1 Test Suite :
Uniquorn RUnit Tests - 1 test function, 0 errors, 1 failure
FAILURE in test_identification: Error in checkTrue((as.logical(ident_result$Conf_score_sig[2:60]) == (rep(FALSE, :
Test not TRUE
Test files with failing tests
test_identification.R
test_identification
Error in BiocGenerics:::testPackage("Uniquorn") :
unit tests failed for package Uniquorn
Execution halted
runTests.Rout.fail:
R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
Copyright (C) 2016 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("Uniquorn")
[1] "Assuming reference genome GRCH37"
[1] "Reading VCF file: E:/biocbld/bbs-3.3-bioc/meat/Uniquorn.buildbin-libdir/Uniquorn/extdata/HT29.vcf.gz"
[1] "Finished reading the VCF file, loading database"
[1] "Found 60 many CLs for reference genome GRCH37"
[1] "Finished reading database, identifying CL"
[1] "Adjusted mutational inclusion weight, \n only using mutations that are have a weight higher than 1"
[1] "Found 53314 many mutations with mutational weight of at least 1"
[1] "Candidate(s): HT29,KM12"
[1] "Storing information in table: E:/biocbld/bbs-3.3-bioc/meat/Uniquorn.buildbin-libdir/Uniquorn/extdata/HT29.vcf.gz_uniquorn_ident.tab"
Timing stopped at: 19.97 1 23.66
Error in checkTrue((as.logical(ident_result$Conf_score_sig[2:60]) == (rep(FALSE, :
Test not TRUE
In addition: Warning message:
In identify_vcf_file(HT29_vcf_file, ref_gen = "GRCH37", verbose = TRUE) :
CCLE & CoSMIC CLP cancer cell line fingerprint NOT
found, defaulting to 60 CellMiner cancer cell lines!
It is strongly advised to add ˜1900 CCLE & CoSMIC CLs, see readme.
RUNIT TEST PROTOCOL -- Thu Jun 16 21:01:58 2016
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 1
1 Test Suite :
Uniquorn RUnit Tests - 1 test function, 0 errors, 1 failure
FAILURE in test_identification: Error in checkTrue((as.logical(ident_result$Conf_score_sig[2:60]) == (rep(FALSE, :
Test not TRUE
Test files with failing tests
test_identification.R
test_identification
Error in BiocGenerics:::testPackage("Uniquorn") :
unit tests failed for package Uniquorn
Execution halted
Uniquorn.Rcheck/00install.out:
install for i386 * installing *source* package 'Uniquorn' ... ** 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 'Uniquorn' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'Uniquorn' as Uniquorn_1.0.7.zip * DONE (Uniquorn)
Uniquorn.Rcheck/examples_i386/Uniquorn-Ex.timings:
| name | user | system | elapsed | |
| add_custom_vcf_to_database | 25.15 | 1.14 | 27.99 | |
| identify_vcf_file | 20.33 | 1.00 | 22.59 | |
| initiate_canonical_databases | 0.14 | 0.00 | 0.14 | |
| remove_custom_vcf_from_database | 1.53 | 0.03 | 1.56 | |
| show_contained_cls | 0 | 0 | 0 | |
| show_contained_mutations | 0.11 | 0.01 | 0.12 | |
| show_contained_mutations_for_cl | 0.17 | 0.00 | 0.17 | |
| show_which_cls_contain_mutation | 0.16 | 0.00 | 0.16 | |
Uniquorn.Rcheck/examples_x64/Uniquorn-Ex.timings:
| name | user | system | elapsed | |
| add_custom_vcf_to_database | 23.15 | 0.99 | 26.16 | |
| identify_vcf_file | 20.80 | 0.97 | 22.12 | |
| initiate_canonical_databases | 0.09 | 0.02 | 0.11 | |
| remove_custom_vcf_from_database | 1.17 | 0.04 | 1.21 | |
| show_contained_cls | 0 | 0 | 0 | |
| show_contained_mutations | 0.13 | 0.00 | 0.13 | |
| show_contained_mutations_for_cl | 0.2 | 0.0 | 0.2 | |
| show_which_cls_contain_mutation | 0.14 | 0.00 | 0.14 | |