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CHECK report for icetea on tokay2

This page was generated on 2019-04-09 12:40:19 -0400 (Tue, 09 Apr 2019).

Package 774/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
icetea 1.1.1
Vivek Bhardwaj
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/icetea
Branch: master
Last Commit: e7839c0
Last Changed Date: 2019-03-23 09:13:23 -0400 (Sat, 23 Mar 2019)
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  ERROR  OK 

Summary

Package: icetea
Version: 1.1.1
Command: set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:icetea.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings icetea_1.1.1.tar.gz
StartedAt: 2019-04-09 03:34:28 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:46:42 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 734.4 seconds
RetCode: 1
Status:  ERROR  
CheckDir: icetea.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:icetea.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings icetea_1.1.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/icetea.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 'icetea/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'icetea' version '1.1.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'Rsubread'
* 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 'icetea' 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
detectTSS        14.98   2.75   31.23
annotateTSS       9.92   0.31   10.31
demultiplexFASTQ  1.79   0.20    7.06
getNormFactors    1.11   0.04   33.52
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
detectTSS      12.38   2.83   36.00
annotateTSS    10.78   0.25   11.96
getNormFactors  0.64   0.04   81.83
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(icetea)
  > 
  > test_check("icetea")
  -- 1. Failure: TSS annotation produces correct table (@test_annotateTSS.R#14)  -
  annot$value not equal to `expected_vals`.
  2/7 mismatches (average diff: 5)
  [2]  7 - 12 == -5
  [3] 56 - 51 ==  5
  
  == testthat results  ===========================================================
  OK: 20 SKIPPED: 0 FAILED: 1
  1. Failure: TSS annotation produces correct table (@test_annotateTSS.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(icetea)
  > 
  > test_check("icetea")
  -- 1. Failure: TSS annotation produces correct table (@test_annotateTSS.R#14)  -
  annot$value not equal to `expected_vals`.
  2/7 mismatches (average diff: 5)
  [2]  7 - 12 == -5
  [3] 56 - 51 ==  5
  
  == testthat results  ===========================================================
  OK: 20 SKIPPED: 0 FAILED: 1
  1. Failure: TSS annotation produces correct table (@test_annotateTSS.R#14) 
  
  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/icetea.Rcheck/00check.log'
for details.

Installation output

icetea.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/icetea_1.1.1.tar.gz && rm -rf icetea.buildbin-libdir && mkdir icetea.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=icetea.buildbin-libdir icetea_1.1.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL icetea_1.1.1.zip && rm icetea_1.1.1.tar.gz icetea_1.1.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1337k  100 1337k    0     0  18.4M      0 --:--:-- --:--:-- --:--:-- 20.4M

install for i386

* installing *source* package 'icetea' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'icetea'
    finding HTML links ... done
    ResizeReads                             html  
    activeChrs                              html  
    annotateTSS                             html  
    check_capSet                            html  
    demultiplexFASTQ                        html  
    detectDiffTSS                           html  
    finding level-2 HTML links ... done

    detectTSS                               html  
    exampleCSobject                         html  
    exportTSS                               html  
    filterDuplicates                        html  
    filterDups                              html  
    fitDiffTSS                              html  
    getBamFlags                             html  
    getChromBins                            html  
    getChromWindows                         html  
    getGeneCounts                           html  
    getMCparams                             html  
    getNormFactors                          html  
    get_newfastq                            html  
    getranks                                html  
    mapCaps                                 html  
    newCapSet                               html  
    numReadsInBed                           html  
    plotPrecision                           html  
    plotReadStats                           html  
    plotTSSprecision                        html  
    sampleInfo                              html  
    splitBAM_byIndex                        html  
    splitBAM_byRepindex                     html  
    split_fastq                             html  
    splitranks                              html  
    strandBinCounts                         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 'icetea' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'icetea' as icetea_1.1.1.zip
* DONE (icetea)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'icetea' successfully unpacked and MD5 sums checked

Tests output

icetea.Rcheck/tests_i386/testthat.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.

> library(testthat)
> library(icetea)
> 
> test_check("icetea")
-- 1. Failure: TSS annotation produces correct table (@test_annotateTSS.R#14)  -
annot$value not equal to `expected_vals`.
2/7 mismatches (average diff: 5)
[2]  7 - 12 == -5
[3] 56 - 51 ==  5

== testthat results  ===========================================================
OK: 20 SKIPPED: 0 FAILED: 1
1. Failure: TSS annotation produces correct table (@test_annotateTSS.R#14) 

Error: testthat unit tests failed
Execution halted

icetea.Rcheck/tests_x64/testthat.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.

> library(testthat)
> library(icetea)
> 
> test_check("icetea")
-- 1. Failure: TSS annotation produces correct table (@test_annotateTSS.R#14)  -
annot$value not equal to `expected_vals`.
2/7 mismatches (average diff: 5)
[2]  7 - 12 == -5
[3] 56 - 51 ==  5

== testthat results  ===========================================================
OK: 20 SKIPPED: 0 FAILED: 1
1. Failure: TSS annotation produces correct table (@test_annotateTSS.R#14) 

Error: testthat unit tests failed
Execution halted

Example timings

icetea.Rcheck/examples_i386/icetea-Ex.timings

nameusersystemelapsed
annotateTSS 9.92 0.3110.31
demultiplexFASTQ1.790.207.06
detectDiffTSS000
detectTSS14.98 2.7531.23
exampleCSobject0.140.000.14
exportTSS0.270.000.27
filterDuplicates1.310.642.11
fitDiffTSS000
getGeneCounts1.370.181.55
getNormFactors 1.11 0.0433.52
mapCaps000
newCapSet0.090.000.09
plotReadStats0.580.021.05
plotTSSprecision2.690.152.84
sampleInfo0.110.000.11
splitBAM_byIndex0.250.130.37
splitBAM_byRepindex0.240.060.54

icetea.Rcheck/examples_x64/icetea-Ex.timings

nameusersystemelapsed
annotateTSS10.78 0.2511.96
demultiplexFASTQ1.810.112.88
detectDiffTSS000
detectTSS12.38 2.8336.00
exampleCSobject0.120.010.14
exportTSS0.240.000.24
filterDuplicates1.230.162.01
fitDiffTSS000
getGeneCounts1.360.021.38
getNormFactors 0.64 0.0481.83
mapCaps000
newCapSet0.100.020.11
plotReadStats0.620.000.62
plotTSSprecision2.140.152.30
sampleInfo0.110.000.11
splitBAM_byIndex0.270.140.40
splitBAM_byRepindex0.170.180.36