Ken Shun Hang Yip
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Linnorm |
| Branch: RELEASE_3_8 |
| Last Commit: af8fd00 |
| Last Changed Date: 2019-01-04 13:36:56 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:52:00 -0400 (Tue, 16 Apr 2019).
| Package 836/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Linnorm 2.6.1 Ken Shun Hang Yip
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Linnorm |
| Version: 2.6.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Linnorm.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Linnorm_2.6.1.tar.gz |
| StartedAt: 2019-04-16 01:00:46 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:07:35 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 409.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Linnorm.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Linnorm.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Linnorm_2.6.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/Linnorm.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Linnorm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Linnorm’ version ‘2.6.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Linnorm’ 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
* 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
Linnorm.HClust: no visible binding for global variable ‘x’
Linnorm.HClust: no visible binding for global variable ‘y’
Linnorm.HClust: no visible binding for global variable ‘xend’
Linnorm.HClust: no visible binding for global variable ‘yend’
Linnorm.HClust: no visible binding for global variable ‘cluster’
Linnorm.HClust: no visible binding for global variable ‘X1’
Linnorm.HClust: no visible binding for global variable ‘X2’
Linnorm.HVar: no visible binding for global variable ‘SD’
Linnorm.HVar: no visible binding for global variable ‘group’
Undefined global functions or variables:
SD X1 X2 cluster group x xend y yend
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
RnaXSim 92.728 0.012 92.858
Linnorm.Cor 63.244 0.116 63.609
Linnorm 41.252 0.008 41.378
Linnorm.limma 41.100 0.004 41.157
Linnorm.Norm 40.128 0.008 40.233
Linnorm.tSNE 6.292 0.040 6.335
Linnorm.PCA 5.692 0.044 5.768
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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 NOTEs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/Linnorm.Rcheck/00check.log’
for details.
Linnorm.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL Linnorm
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘Linnorm’ ...
** libs
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c Misc.cpp -o Misc.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from Misc.cpp:18:
/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:514:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
#pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
^
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o Linnorm.so Misc.o -std=c++11 -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -DARMA_64BIT_WORD=1 -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/Linnorm/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Linnorm)
Linnorm.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(Linnorm)
>
> test_check("Linnorm")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 26 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
27.756 0.184 28.032
Linnorm.Rcheck/Linnorm-Ex.timings
| name | user | system | elapsed | |
| LinearRegression | 0.004 | 0.000 | 0.002 | |
| LinearRegressionFP | 0.000 | 0.000 | 0.001 | |
| Linnorm.Cor | 63.244 | 0.116 | 63.609 | |
| Linnorm.DataImput | 2.924 | 0.088 | 3.031 | |
| Linnorm.HClust | 3.856 | 0.032 | 3.469 | |
| Linnorm.HVar | 1.552 | 0.016 | 1.571 | |
| Linnorm.Norm | 40.128 | 0.008 | 40.233 | |
| Linnorm.PCA | 5.692 | 0.044 | 5.768 | |
| Linnorm | 41.252 | 0.008 | 41.378 | |
| Linnorm.SGenes | 0.392 | 0.044 | 0.439 | |
| Linnorm.limma | 41.100 | 0.004 | 41.157 | |
| Linnorm.tSNE | 6.292 | 0.040 | 6.335 | |
| RnaXSim | 92.728 | 0.012 | 92.858 | |