Zytnicki Matthias
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/srnadiff |
| Branch: RELEASE_3_10 |
| Last Commit: 179be34 |
| Last Changed Date: 2019-10-29 13:10:57 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:29:47 -0400 (Wed, 15 Apr 2020).
| Package 1659/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| srnadiff 1.6.0 Zytnicki Matthias
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ TIMEOUT ] | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: srnadiff |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:srnadiff.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings srnadiff_1.6.0.tar.gz |
| StartedAt: 2020-04-15 06:52:53 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 07:32:53 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 2400.2 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: srnadiff.Rcheck |
| Warnings: NA |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:srnadiff.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings srnadiff_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/srnadiff.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'srnadiff/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'srnadiff' version '1.6.0'
* package encoding: UTF-8
* 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 'srnadiff' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/bamFiles.Rd:19: file link 'BamFileList' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/coverages.Rd:19: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/plotRegions.Rd:87: file link 'GenomeAxisTrack' in package 'Gviz' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/plotRegions.Rd:90: file link 'GeneRegionTrack' in package 'Gviz' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/plotRegions.Rd:93: file link 'AnnotationTrack' in package 'Gviz' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/plotRegions.Rd:96: file link 'DataTrack' in package 'Gviz' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/srnadiff.Rd:28: file link 'multicoreWorkers' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/srnadiffExp.Rd:59: file link 'BamFileList' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/srnadiffExp.Rd:70: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/srnadiff.Rcheck/00install.out' for details.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/srnadiff/libs/i386/srnadiff.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/srnadiff/libs/x64/srnadiff.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotRegions 12.70 0.28 82.58
parameters 10.19 0.08 142.40
countMatrix 7.39 0.92 75.09
srnadiff 6.44 0.03 78.94
srnadiffDefaultParameters 5.97 0.03 73.14
regions 5.78 0.06 77.95
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotRegions 18.60 0.05 118.24
parameters 13.65 0.07 163.82
regions 8.55 0.01 86.02
countMatrix 7.22 0.15 72.84
srnadiff 7.06 0.07 98.34
srnadiffDefaultParameters 6.31 0.03 81.10
* 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:
-- 5. Failure: Running main function (@test_srnadiff.R#64) --------------------
length(regions(exp)) not equal to 21.
1/1 mismatches
[1] 20 - 21 == -1
== testthat results ===========================================================
[ OK: 25 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 5 ]
1. Failure: Running IR method (@test_IR.R#11)
2. Failure: Testing regions method (@test_srnadiff.R#10)
3. Failure: Running with different sizes (@test_srnadiff.R#22)
4. Failure: Running with different minimum depth (@test_srnadiff.R#28)
5. Failure: Running main function (@test_srnadiff.R#64)
Error: testthat unit tests failed
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
srnadiff.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/srnadiff_1.6.0.tar.gz && rm -rf srnadiff.buildbin-libdir && mkdir srnadiff.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=srnadiff.buildbin-libdir srnadiff_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL srnadiff_1.6.0.zip && rm srnadiff_1.6.0.tar.gz srnadiff_1.6.0.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 1909k 100 1909k 0 0 5012k 0 --:--:-- --:--:-- --:--:-- 5050k
install for i386
* installing *source* package 'srnadiff' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c rcpp_hmm.cpp -o rcpp_hmm.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c rcpp_ir.cpp -o rcpp_ir.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c rcpp_main.cpp -o rcpp_main.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c rcpp_utils.cpp -o rcpp_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c srnadiff_init.c -o srnadiff_init.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o srnadiff.dll tmp.def RcppExports.o rcpp_hmm.o rcpp_ir.o rcpp_main.o rcpp_utils.o srnadiff_init.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/srnadiff.buildbin-libdir/00LOCK-srnadiff/00new/srnadiff/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'srnadiff'
finding HTML links ... done
annotReg html
bamFiles html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/bamFiles.Rd:19: file link 'BamFileList' in package 'Rsamtools' does not exist and so has been treated as a topic
chromosomeSizes html
countMatrix html
coverages html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/coverages.Rd:19: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
normFactors html
parameters html
plotRegions html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/plotRegions.Rd:87: file link 'GenomeAxisTrack' in package 'Gviz' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/plotRegions.Rd:90: file link 'GeneRegionTrack' in package 'Gviz' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/plotRegions.Rd:93: file link 'AnnotationTrack' in package 'Gviz' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/plotRegions.Rd:96: file link 'DataTrack' in package 'Gviz' does not exist and so has been treated as a topic
readAnnotation html
regions html
sampleInfo html
srnadiff html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/srnadiff.Rd:28: file link 'multicoreWorkers' in package 'BiocParallel' does not exist and so has been treated as a topic
srnadiffDefaultParameters html
srnadiffExample html
srnadiffExp html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/srnadiffExp.Rd:59: file link 'BamFileList' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpoD69WV/R.INSTALL73431473840/srnadiff/man/srnadiffExp.Rd:70: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
** 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 'srnadiff' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c rcpp_hmm.cpp -o rcpp_hmm.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c rcpp_ir.cpp -o rcpp_ir.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c rcpp_main.cpp -o rcpp_main.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c rcpp_utils.cpp -o rcpp_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c srnadiff_init.c -o srnadiff_init.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o srnadiff.dll tmp.def RcppExports.o rcpp_hmm.o rcpp_ir.o rcpp_main.o rcpp_utils.o srnadiff_init.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/srnadiff.buildbin-libdir/srnadiff/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'srnadiff' as srnadiff_1.6.0.zip
* DONE (srnadiff)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'srnadiff' successfully unpacked and MD5 sums checked
|
srnadiff.Rcheck/tests_i386/testthat.Rout.fail
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(srnadiff)
>
> test_check("srnadiff")
-- 1. Failure: Running IR method (@test_IR.R#11) ------------------------------
length(ranges) not equal to 8.
1/1 mismatches
[1] 3 - 8 == -5
-- 2. Failure: Testing regions method (@test_srnadiff.R#10) -------------------
length(regions(exp)) not equal to 21.
1/1 mismatches
[1] 20 - 21 == -1
-- 3. Failure: Running with different sizes (@test_srnadiff.R#22) -------------
length(regions(exp2)) not equal to 32.
1/1 mismatches
[1] 31 - 32 == -1
-- 4. Failure: Running with different minimum depth (@test_srnadiff.R#28) -----
length(regions(exp2)) not equal to 50.
1/1 mismatches
[1] 41 - 50 == -9
-- 5. Failure: Running main function (@test_srnadiff.R#64) --------------------
length(regions(exp)) not equal to 21.
1/1 mismatches
[1] 20 - 21 == -1
== testthat results ===========================================================
[ OK: 25 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 5 ]
1. Failure: Running IR method (@test_IR.R#11)
2. Failure: Testing regions method (@test_srnadiff.R#10)
3. Failure: Running with different sizes (@test_srnadiff.R#22)
4. Failure: Running with different minimum depth (@test_srnadiff.R#28)
5. Failure: Running main function (@test_srnadiff.R#64)
Error: testthat unit tests failed
Execution halted
|
srnadiff.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(srnadiff)
>
> test_check("srnadiff")
-- 1. Failure: Running IR method (@test_IR.R#11) ------------------------------
length(ranges) not equal to 8.
1/1 mismatches
[1] 3 - 8 == -5
|
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srnadiff.Rcheck/examples_i386/srnadiff-Ex.timings
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srnadiff.Rcheck/examples_x64/srnadiff-Ex.timings
|