| Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-13 11:29:25 -0400 (Sat, 13 Apr 2019).
| Package 750/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| icetea 1.0.1 Vivek Bhardwaj
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: icetea |
| Version: 1.0.1 |
| Command: set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:icetea.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings icetea_1.0.1.tar.gz |
| StartedAt: 2019-04-13 03:06:54 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:17:18 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 624.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: icetea.Rcheck |
| Warnings: NA |
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### Running command:
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### set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:icetea.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings icetea_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/icetea.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.0.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 13.44 2.08 27.42
annotateTSS 9.52 0.56 10.12
getNormFactors 0.71 0.03 30.72
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
detectTSS 11.82 1.71 24.97
annotateTSS 9.60 0.20 9.79
getNormFactors 0.69 0.03 28.00
* 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-3.8-bioc/meat/icetea.Rcheck/00check.log'
for details.
icetea.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/icetea_1.0.1.tar.gz && rm -rf icetea.buildbin-libdir && mkdir icetea.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=icetea.buildbin-libdir icetea_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL icetea_1.0.1.zip && rm icetea_1.0.1.tar.gz icetea_1.0.1.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 1378k 100 1378k 0 0 26.2M 0 --:--:-- --:--:-- --:--:-- 28.6M
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
In R CMD INSTALL
install for x64
* installing *source* package 'icetea' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'icetea' as icetea_1.0.1.zip
* DONE (icetea)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'icetea' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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icetea.Rcheck/tests_i386/testthat.Rout.fail
R version 3.5.3 (2019-03-11) -- "Great Truth"
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$value not equal to `expected_vals`.
2/7 mismatches (average diff: 5)
[2] 7 - 12 == -5
[3] 56 - 51 == 5
== testthat results ===========================================================
OK: 20 SKIPPED: 0 FAILED: 1
1. Failure: TSS annotation produces correct table (@test_annotateTSS.R#14)
Error: testthat unit tests failed
Execution halted
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icetea.Rcheck/tests_x64/testthat.Rout.fail
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(icetea)
>
> test_check("icetea")
-- 1. Failure: TSS annotation produces correct table (@test_annotateTSS.R#14) -
annot$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
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icetea.Rcheck/examples_i386/icetea-Ex.timings
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icetea.Rcheck/examples_x64/icetea-Ex.timings
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