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CHECK report for derfinder on tokay2

This page was generated on 2019-04-09 12:21:25 -0400 (Tue, 09 Apr 2019).

Package 412/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
derfinder 1.17.1
Leonardo Collado-Torres
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/derfinder
Branch: master
Last Commit: efb0859
Last Changed Date: 2018-12-03 16:40:56 -0400 (Mon, 03 Dec 2018)
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 

Summary

Package: derfinder
Version: 1.17.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:derfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings derfinder_1.17.1.tar.gz
StartedAt: 2019-04-09 02:14:15 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:28:00 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 824.2 seconds
RetCode: 1
Status:  ERROR  
CheckDir: derfinder.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:derfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings derfinder_1.17.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/derfinder.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 '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 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
* 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
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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 ERROR
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
    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: 114 SKIPPED: 0 FAILED: 1
  1. Failure: calculatePvalues (@test_Fstats.R#76) 
  
  Error: testthat unit tests failed
  Execution halted
** running tests for arch 'x64' ...
  Running 'test-all.R'
 ERROR
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
    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: 114 SKIPPED: 0 FAILED: 1
  1. Failure: calculatePvalues (@test_Fstats.R#76) 
  
  Error: testthat unit tests failed
  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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/derfinder.Rcheck/00check.log'
for details.

Installation output

derfinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/derfinder_1.17.1.tar.gz && rm -rf derfinder.buildbin-libdir && mkdir derfinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=derfinder.buildbin-libdir derfinder_1.17.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL derfinder_1.17.1.zip && rm derfinder_1.17.1.tar.gz derfinder_1.17.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 50  254k   50  128k    0     0   589k      0 --:--:-- --:--:-- --:--:--  606k
100  254k  100  254k    0     0  1140k      0 --:--:-- --:--:-- --:--:-- 1168k

install for i386

* installing *source* package 'derfinder' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'derfinder'
    finding HTML links ... done
    analyzeChr                              html  
    annotateRegions                         html  
    calculatePvalues                        html  
    calculateStats                          html  
    coerceGR                                html  
    collapseFullCoverage                    html  
    coverageToExon                          html  
    createBw                                html  
    createBwSample                          html  
    define_cluster                          html  
    derfinder-deprecated                    html  
    derfinder-package                       html  
    extendedMapSeqlevels                    html  
    filterData                              html  
    findRegions                             html  
    fullCoverage                            html  
    genomeData                              html  
    genomeDataRaw                           html  
    genomeFstats                            html  
    genomeInfo                              html  
    genomeRegions                           html  
    genomicState                            html  
    getRegionCoverage                       html  
    getTotalMapped                          html  
    loadCoverage                            html  
    makeGenomicState                        html  
    makeModels                              html  
    mergeResults                            html  
    preprocessCoverage                      html  
    railMatrix                              html  
    rawFiles                                html  
    regionMatrix                            html  
    sampleDepth                             html  
** 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

install for x64

* installing *source* package 'derfinder' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'derfinder' as derfinder_1.17.1.zip
* DONE (derfinder)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'derfinder' successfully unpacked and MD5 sums checked

Tests output

derfinder.Rcheck/tests_i386/test-all.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.

> ## 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
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: 114 SKIPPED: 0 FAILED: 1
1. Failure: calculatePvalues (@test_Fstats.R#76) 

Error: testthat unit tests failed
Execution halted

derfinder.Rcheck/tests_x64/test-all.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.

> ## 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
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: 114 SKIPPED: 0 FAILED: 1
1. Failure: calculatePvalues (@test_Fstats.R#76) 

Error: testthat unit tests failed
Execution halted

Example timings

derfinder.Rcheck/examples_i386/derfinder-Ex.timings

nameusersystemelapsed
analyzeChr1.220.471.68
annotateRegions0.280.000.28
calculatePvalues0.710.000.70
calculateStats0.450.010.47
coerceGR0.050.000.05
collapseFullCoverage0.010.000.01
coverageToExon3.860.354.21
createBw0.130.000.12
createBwSample0.030.000.03
define_cluster000
derfinder-deprecated000
extendedMapSeqlevels0.060.010.08
filterData0.130.000.13
findRegions0.530.000.53
fullCoverage0.280.020.33
getRegionCoverage0.230.050.28
getTotalMapped0.020.000.04
loadCoverage0.230.000.24
makeGenomicState2.990.033.01
makeModels0.010.000.02
mergeResults0.270.010.28
preprocessCoverage0.440.000.44
railMatrix000
rawFiles0.010.000.01
regionMatrix0.670.080.75
sampleDepth000

derfinder.Rcheck/examples_x64/derfinder-Ex.timings

nameusersystemelapsed
analyzeChr2.120.042.17
annotateRegions0.290.050.33
calculatePvalues0.880.000.88
calculateStats0.790.000.79
coerceGR0.080.000.08
collapseFullCoverage000
coverageToExon4.420.194.61
createBw0.210.000.20
createBwSample0.060.000.07
define_cluster000
derfinder-deprecated000
extendedMapSeqlevels0.140.010.15
filterData0.120.000.12
findRegions0.620.000.62
fullCoverage0.190.040.22
getRegionCoverage0.190.010.21
getTotalMapped000
loadCoverage0.120.000.12
makeGenomicState2.990.043.03
makeModels0.020.000.02
mergeResults0.280.020.30
preprocessCoverage0.50.00.5
railMatrix000
rawFiles000
regionMatrix0.780.000.78
sampleDepth0.010.000.02