Jakob Theorell
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/DepecheR |
| Branch: RELEASE_3_9 |
| Last Commit: 5174d68 |
| Last Changed Date: 2019-06-28 07:05:57 -0400 (Fri, 28 Jun 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:43:41 -0400 (Wed, 16 Oct 2019).
| Package 417/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DepecheR 1.0.3 Jakob Theorell
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DepecheR |
| Version: 1.0.3 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DepecheR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DepecheR_1.0.3.tar.gz |
| StartedAt: 2019-10-16 03:10:10 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:14:04 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 234.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: DepecheR.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DepecheR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DepecheR_1.0.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DepecheR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DepecheR/DESCRIPTION' ... OK
* this is package 'DepecheR' version '1.0.3'
* 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 'DepecheR' 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
Namespace in Imports field not imported from: 'BiocParallel'
All declared Imports should be used.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/DepecheR/libs/i386/DepecheR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'rand', possibly from 'rand' (C)
Found 'srand', possibly from 'srand' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/DepecheR/libs/x64/DepecheR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'rand', possibly from 'rand' (C)
Found 'srand', possibly from 'srand' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
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-- 1. Error: (unknown) (@test_sPLSDA.R#28) ------------------------------------
'newdata' must include all the variables of 'object$X'
1: dSplsda(xYData = xYData, idsVector = idsVector, groupVector = groupVector, clusterVector = clusterVector,
testSampleRows = subsetVector, createOutput = FALSE) at testthat/test_sPLSDA.R:28
2: predict(object = sPLSDAObject, newdata = t(dSplsdaInDataTest[[1]]), multilevel = dSplsdaInDataTest[[4]])
3: predict.mixo_spls(object = sPLSDAObject, newdata = t(dSplsdaInDataTest[[1]]), multilevel = dSplsdaInDataTest[[4]])
4: stop("'newdata' must include all the variables of 'object$X'")
== testthat results ===========================================================
[ OK: 23 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
1. Error: (unknown) (@test_sPLSDA.R#28)
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: 1 ERROR, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/DepecheR.Rcheck/00check.log'
for details.
DepecheR.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/DepecheR_1.0.3.tar.gz && rm -rf DepecheR.buildbin-libdir && mkdir DepecheR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DepecheR.buildbin-libdir DepecheR_1.0.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DepecheR_1.0.3.zip && rm DepecheR_1.0.3.tar.gz DepecheR_1.0.3.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
13 1068k 13 144k 0 0 340k 0 0:00:03 --:--:-- 0:00:03 345k
100 1068k 100 1068k 0 0 2181k 0 --:--:-- --:--:-- --:--:-- 2208k
install for i386
* installing *source* package 'DepecheR' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I../inst/include -pthread -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Clusterer.cpp -o Clusterer.o
Clusterer.cpp: In member function 'double Clusterer::cluster_norm(const RowMatrixXd&, const RowMatrixXd&, Eigen::VectorXi, double)':
Clusterer.cpp:204:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i = 0; i
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DepecheR.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(DepecheR)
>
> test_check("DepecheR")
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== testthat results ===========================================================
[ OK: 23 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
7.64 0.84 82.32
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DepecheR.Rcheck/tests_x64/testthat.Rout.fail
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(DepecheR)
>
> test_check("DepecheR")
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-- 1. Error: (unknown) (@test_sPLSDA.R#28) ------------------------------------
'newdata' must include all the variables of 'object$X'
1: dSplsda(xYData = xYData, idsVector = idsVector, groupVector = groupVector, clusterVector = clusterVector,
testSampleRows = subsetVector, createOutput = FALSE) at testthat/test_sPLSDA.R:28
2: predict(object = sPLSDAObject, newdata = t(dSplsdaInDataTest[[1]]), multilevel = dSplsdaInDataTest[[4]])
3: predict.mixo_spls(object = sPLSDAObject, newdata = t(dSplsdaInDataTest[[1]]), multilevel = dSplsdaInDataTest[[4]])
4: stop("'newdata' must include all the variables of 'object$X'")
== testthat results ===========================================================
[ OK: 23 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
1. Error: (unknown) (@test_sPLSDA.R#28)
Error: testthat unit tests failed
Execution halted
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DepecheR.Rcheck/examples_i386/DepecheR-Ex.timings
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DepecheR.Rcheck/examples_x64/DepecheR-Ex.timings
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