| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 12:01:39 -0400 (Tue, 09 Apr 2019).
| Package 279/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| clipper 1.23.0 Paolo Martini
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: clipper |
| Version: 1.23.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clipper.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings clipper_1.23.0.tar.gz |
| StartedAt: 2019-04-09 01:48:26 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:10:37 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 1330.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: clipper.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clipper.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings clipper_1.23.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/clipper.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clipper/DESCRIPTION' ... OK
* this is package 'clipper' version '1.23.0'
* 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 'clipper' 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
clipper 52.53 18.53 71.10
clipperAllRoots 54.65 1.08 55.73
getJunctionTreePaths 47.25 0.13 47.40
pathwayTest 46.17 0.36 46.53
easyClip 44.10 1.01 45.14
deleteEdge 39.40 4.58 44.03
cliqueMeanTest 43.00 0.10 43.11
getGraphEntryGenes 41.96 0.47 42.46
cliqueVarianceTest 40.29 1.70 41.98
cliqueMixedTest 39.61 0.07 39.70
cliquePairedTest 38.59 0.18 38.77
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
clipper 50.61 0.74 51.39
getJunctionTreePaths 50.55 0.06 50.99
pathwayTest 49.33 0.13 49.45
cliqueVarianceTest 47.88 0.12 48.00
deleteEdge 46.97 0.16 48.10
easyClip 45.23 0.19 46.32
cliqueMixedTest 42.33 0.16 42.50
clipperAllRoots 41.61 0.10 41.72
getGraphEntryGenes 40.13 0.09 41.03
cliquePairedTest 36.17 0.09 36.27
cliqueMeanTest 30.97 0.13 31.09
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
1 Test Suite :
clipper RUnit Tests - 10 test functions, 0 errors, 1 failure
FAILURE in test_clipper: Error in checkEqualsNumeric(-log(0.001) * 2, as.numeric(clipped[1, 5])) :
Mean relative difference: 0.2461869
Test files with failing tests
test_clipper.R
test_clipper
Error in BiocGenerics:::testPackage("clipper") :
unit tests failed for package clipper
Execution halted
** running tests for arch 'x64' ...
Running 'runTests.R'
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
1 Test Suite :
clipper RUnit Tests - 10 test functions, 0 errors, 1 failure
FAILURE in test_clipper: Error in checkEqualsNumeric(-log(0.001) * 2, as.numeric(clipped[1, 5])) :
Mean relative difference: 0.2461869
Test files with failing tests
test_clipper.R
test_clipper
Error in BiocGenerics:::testPackage("clipper") :
unit tests failed for package clipper
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
'C:/Users/biocbuild/bbs-3.9-bioc/meat/clipper.Rcheck/00check.log'
for details.
clipper.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/clipper_1.23.0.tar.gz && rm -rf clipper.buildbin-libdir && mkdir clipper.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clipper.buildbin-libdir clipper_1.23.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL clipper_1.23.0.zip && rm clipper_1.23.0.tar.gz clipper_1.23.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 418k 100 418k 0 0 1647k 0 --:--:-- --:--:-- --:--:-- 1685k
install for i386
* installing *source* package 'clipper' ...
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
** help
*** installing help indices
converting help for package 'clipper'
finding HTML links ... done
clipper html
clipperAllRoots html
cliqueMeanTest html
cliqueMixedTest html
cliquePairedTest html
cliqueVarianceTest html
deleteEdge html
easyClip html
easyLook html
getGraphEntryGenes html
getJunctionTreePaths html
nameCliques html
pathwayTest html
plotInCytoscape html
prunePaths html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
** testing if installed package can be loaded from final location
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'clipper' ...
** testing if installed package can be loaded
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
* MD5 sums
packaged installation of 'clipper' as clipper_1.23.0.zip
* DONE (clipper)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'clipper' successfully unpacked and MD5 sums checked
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clipper.Rcheck/tests_i386/runTests.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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("clipper")
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:Matrix':
colMeans, colSums, rowMeans, rowSums, which
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, 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, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
Timing stopped at: 0.31 0 0.31
Error in checkEqualsNumeric(-log(0.001) * 2, as.numeric(clipped[1, 5])) :
Mean relative difference: 0.2461869
RUNIT TEST PROTOCOL -- Tue Apr 09 02:10:17 2019
***********************************************
Number of test functions: 10
Number of errors: 0
Number of failures: 1
1 Test Suite :
clipper RUnit Tests - 10 test functions, 0 errors, 1 failure
FAILURE in test_clipper: Error in checkEqualsNumeric(-log(0.001) * 2, as.numeric(clipped[1, 5])) :
Mean relative difference: 0.2461869
Test files with failing tests
test_clipper.R
test_clipper
Error in BiocGenerics:::testPackage("clipper") :
unit tests failed for package clipper
Execution halted
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clipper.Rcheck/tests_x64/runTests.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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("clipper")
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:Matrix':
colMeans, colSums, rowMeans, rowSums, which
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, 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, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
Timing stopped at: 0.25 0.01 0.27
Error in checkEqualsNumeric(-log(0.001) * 2, as.numeric(clipped[1, 5])) :
Mean relative difference: 0.2461869
RUNIT TEST PROTOCOL -- Tue Apr 09 02:10:30 2019
***********************************************
Number of test functions: 10
Number of errors: 0
Number of failures: 1
1 Test Suite :
clipper RUnit Tests - 10 test functions, 0 errors, 1 failure
FAILURE in test_clipper: Error in checkEqualsNumeric(-log(0.001) * 2, as.numeric(clipped[1, 5])) :
Mean relative difference: 0.2461869
Test files with failing tests
test_clipper.R
test_clipper
Error in BiocGenerics:::testPackage("clipper") :
unit tests failed for package clipper
Execution halted
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clipper.Rcheck/examples_i386/clipper-Ex.timings
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clipper.Rcheck/examples_x64/clipper-Ex.timings
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