| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:12:30 -0400 (Tue, 09 Apr 2019).
| Package 412/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| derfinder 1.17.1 Leonardo Collado-Torres
| 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: derfinder |
| Version: 1.17.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:derfinder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings derfinder_1.17.1.tar.gz |
| StartedAt: 2019-04-09 01:18:08 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:31:59 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 830.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: derfinder.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:derfinder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings derfinder_1.17.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/derfinder.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘derfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘derfinder’ version ‘1.17.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘derfinder’ 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
* 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
Unexported objects imported by ':::' calls:
‘GenomeInfoDb:::.guessSpeciesStyle’
‘GenomeInfoDb:::.supportedSeqnameMappings’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.smootherFstats’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
railMatrix 14.036 2.408 16.515
coverageToExon 5.536 1.040 6.577
makeGenomicState 6.425 0.074 6.503
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’
ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
class: SerialParam
bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
bpexportglobals: TRUE
bplogdir: NA
bpresultdir: NA
══ testthat results ═══════════════════════════════════════════════════════════
OK: 136 SKIPPED: 0 FAILED: 1
1. Failure: calculatePvalues (@test_Fstats.R#76)
Error: testthat unit tests failed
In addition: Warning message:
call dbDisconnect() when finished working with a connection
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: 1 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/derfinder.Rcheck/00check.log’
for details.
derfinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL derfinder ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘derfinder’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (derfinder)
derfinder.Rcheck/tests/test-all.Rout.fail
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.
> ## Disable the tests if the system variable 'R_DISABLE_TESTS' is set to TRUE
>
> flag <- as.logical(Sys.getenv('R_DISABLE_TESTS'))
> if(is.na(flag) | flag == FALSE) {
+ library('testthat')
+ test_check('derfinder')
+ }
Loading required package: derfinder
── 1. Failure: calculatePvalues (@test_Fstats.R#76) ───────────────────────────
`x` not equivalent to `expected`.
Component "nullStats": Lengths: 528, 540
Component "nullWidths": Lengths: 528, 540
Component "nullPermutation": Lengths: 528, 540
class: SerialParam
bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
bpexportglobals: TRUE
bplogdir: NA
bpresultdir: NA
Error in x$.self$finalize() : attempt to apply non-function
class: SerialParam
bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
bpexportglobals: TRUE
bplogdir: NA
bpresultdir: NA
class: SerialParam
bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
bpexportglobals: TRUE
bplogdir: NA
bpresultdir: NA
class: SerialParam
bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
bpexportglobals: TRUE
bplogdir: NA
bpresultdir: NA
class: SerialParam
bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
bpexportglobals: TRUE
bplogdir: NA
bpresultdir: NA
class: SerialParam
bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
bpexportglobals: TRUE
bplogdir: NA
bpresultdir: NA
class: SerialParam
bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
bpexportglobals: TRUE
bplogdir: NA
bpresultdir: NA
class: SerialParam
bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
bpexportglobals: TRUE
bplogdir: NA
bpresultdir: NA
══ testthat results ═══════════════════════════════════════════════════════════
OK: 136 SKIPPED: 0 FAILED: 1
1. Failure: calculatePvalues (@test_Fstats.R#76)
Error: testthat unit tests failed
In addition: Warning message:
call dbDisconnect() when finished working with a connection
Execution halted
derfinder.Rcheck/derfinder-Ex.timings
| name | user | system | elapsed | |
| analyzeChr | 2.150 | 0.197 | 2.397 | |
| annotateRegions | 0.562 | 0.025 | 0.588 | |
| calculatePvalues | 1.691 | 0.017 | 1.708 | |
| calculateStats | 0.874 | 0.003 | 0.877 | |
| coerceGR | 0.109 | 0.003 | 0.112 | |
| collapseFullCoverage | 0.017 | 0.006 | 0.022 | |
| coverageToExon | 5.536 | 1.040 | 6.577 | |
| createBw | 0.282 | 0.004 | 0.287 | |
| createBwSample | 0.086 | 0.002 | 0.089 | |
| define_cluster | 0.011 | 0.001 | 0.012 | |
| derfinder-deprecated | 0.004 | 0.000 | 0.005 | |
| extendedMapSeqlevels | 0.118 | 0.015 | 0.133 | |
| filterData | 0.232 | 0.007 | 0.239 | |
| findRegions | 1.079 | 0.057 | 1.136 | |
| fullCoverage | 0.441 | 0.017 | 0.460 | |
| getRegionCoverage | 0.408 | 0.021 | 0.429 | |
| getTotalMapped | 0.017 | 0.001 | 0.020 | |
| loadCoverage | 0.265 | 0.006 | 0.271 | |
| makeGenomicState | 6.425 | 0.074 | 6.503 | |
| makeModels | 0.025 | 0.002 | 0.028 | |
| mergeResults | 0.598 | 0.041 | 0.642 | |
| preprocessCoverage | 0.821 | 0.011 | 0.832 | |
| railMatrix | 14.036 | 2.408 | 16.515 | |
| rawFiles | 0.004 | 0.001 | 0.005 | |
| regionMatrix | 1.356 | 0.065 | 1.422 | |
| sampleDepth | 0.029 | 0.002 | 0.030 | |