| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:24 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the srnadiff package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/srnadiff.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1842/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| srnadiff 1.12.2 (landing page) Zytnicki Matthias
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | TIMEOUT | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: srnadiff |
| Version: 1.12.2 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:srnadiff.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings srnadiff_1.12.2.tar.gz |
| StartedAt: 2021-10-15 06:11:20 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 06:51:20 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 2400.1 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: srnadiff.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:srnadiff.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings srnadiff_1.12.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/srnadiff.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.12.2'
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'BiocManager' 'BiocStyle'
A package should be listed in only one of these fields.
* 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 ... NOTE
useEdgeR: no visible global function definition for 'model.matrix'
useEdgeR: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
model.matrix p.adjust
Consider adding
importFrom("stats", "model.matrix", "p.adjust")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: parameters.Rd:38-40: Dropping empty section \details
* 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-3.13-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-3.13-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 (user + system) or elapsed time > 5s
user system elapsed
plotRegions 18.03 0.38 55.00
parameters 17.79 0.23 101.38
countMatrix 12.07 1.08 50.83
regions 10.97 0.01 49.39
srnadiffDefaultParameters 8.72 0.03 47.48
srnadiff 8.55 0.05 46.72
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
parameters 19.70 0.11 102.28
plotRegions 17.22 0.05 57.75
countMatrix 14.37 0.09 54.95
srnadiff 11.28 0.04 54.89
srnadiffDefaultParameters 10.20 0.03 54.61
regions 9.89 0.06 51.59
* 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:
Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component "padj": Numeric: lengths (24, 26) differ > >
Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component "log2FC": Numeric: lengths (24, 26) differ > >
Attributes: < Component "elementMetadata": Attributes: < Component "nrows": Mean relative difference: 0.08333333 > >
Attributes: < Component "ranges": Lengths: 24, 26 >
Attributes: < Component "ranges": Names: Lengths (24, 26) differ (string compare on first 24) >
Attributes: < Component "ranges": Names: 19 string mismatches >
...
-- Failure (test_srnadiff.R:64:5): Running main function -----------------------
length(regions(exp)) not equal to 26.
1/1 mismatches
[1] 24 - 26 == -2
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 32 ]
Error: Test failures
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 http://155.52.207.165/BBS/3.13/bioc/src/contrib/srnadiff_1.12.2.tar.gz && rm -rf srnadiff.buildbin-libdir && mkdir srnadiff.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=srnadiff.buildbin-libdir srnadiff_1.12.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL srnadiff_1.12.2.zip && rm srnadiff_1.12.2.tar.gz srnadiff_1.12.2.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
58 2010k 58 1173k 0 0 1574k 0 0:00:01 --:--:-- 0:00:01 1574k
100 2010k 100 2010k 0 0 1836k 0 0:00:01 0:00:01 --:--:-- 1838k
install for i386
* installing *source* package 'srnadiff' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_hmm.cpp -o rcpp_hmm.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_ir.cpp -o rcpp_ir.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_main.cpp -o rcpp_main.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_utils.cpp -o rcpp_utils.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c srnadiff_init.c -o srnadiff_init.o
C:/rtools40/mingw32/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-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-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
chromosomeSizes html
countMatrix html
coverages html
normFactors html
parameters html
plotRegions html
finding level-2 HTML links ... done
readAnnotation html
regions html
sampleInfo html
srnadiff html
srnadiffDefaultParameters html
srnadiffExample html
srnadiffExp 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 'srnadiff' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_hmm.cpp -o rcpp_hmm.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_ir.cpp -o rcpp_ir.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_main.cpp -o rcpp_main.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_utils.cpp -o rcpp_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c srnadiff_init.c -o srnadiff_init.o
C:/rtools40/mingw64/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-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/srnadiff.buildbin-libdir/srnadiff/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'srnadiff' as srnadiff_1.12.2.zip
* DONE (srnadiff)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'srnadiff' successfully unpacked and MD5 sums checked
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srnadiff.Rcheck/tests_i386/testthat.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
......== Failed tests ================================================================
-- Failure (test_srnadiff.R:10:5): Testing regions method ----------------------
length(regions(exp)) not equal to 26.
1/1 mismatches
[1] 24 - 26 == -2
-- Failure (test_srnadiff.R:60:5): Running several threads ---------------------
regions(exp) not equal to regions(exp2).
Lengths: 24, 26
Names: Lengths (24, 26) differ (string compare on first 24)
Names: 19 string mismatches
Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component "padj": Numeric: lengths (24, 26) differ > >
Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component "log2FC": Numeric: lengths (24, 26) differ > >
Attributes: < Component "elementMetadata": Attributes: < Component "nrows": Mean relative difference: 0.08333333 > >
Attributes: < Component "ranges": Lengths: 24, 26 >
Attributes: < Component "ranges": Names: Lengths (24, 26) differ (string compare on first 24) >
Attributes: < Component "ranges": Names: 19 string mismatches >
...
-- Failure (test_srnadiff.R:64:5): Running main function -----------------------
length(regions(exp)) not equal to 26.
1/1 mismatches
[1] 24 - 26 == -2
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 32 ]
Error: Test failures
Execution halted
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srnadiff.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
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srnadiff.Rcheck/examples_i386/srnadiff-Ex.timings
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srnadiff.Rcheck/examples_x64/srnadiff-Ex.timings
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