Philipp Angerer
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/destiny |
| Branch: RELEASE_3_6 |
| Last Commit: 24459aa |
| Last Changed Date: 2018-02-27 11:41:49 -0400 (Tue, 27 Feb 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:13:54 -0400 (Thu, 12 Apr 2018).
| Package 358/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| destiny 2.6.2 Philipp Angerer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: destiny |
| Version: 2.6.2 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings destiny_2.6.2.tar.gz |
| StartedAt: 2018-04-11 22:53:05 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:55:36 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 150.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: destiny.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings destiny_2.6.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/destiny.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘destiny/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘destiny’ version ‘2.6.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘destiny’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.2Mb
sub-directories of 1Mb or more:
doc 3.1Mb
libs 3.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
'LinkingTo' for ‘grDevices’ is unused as it has no 'include' directory
* 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 ... NOTE
Namespace in Imports field not imported from: ‘scatterplot3d’
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 ... NOTE
plot_gradient_map_impl : <anonymous>: no visible binding for global
variable ‘Gene’
scatterplot3d : <anonymous>: no visible global function definition for
‘formula’
scatterplot3d : <anonymous>: no visible global function definition for
‘predict’
Undefined global functions or variables:
Gene formula predict
Consider adding
importFrom("stats", "formula", "predict")
to your NAMESPACE file.
* 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.DPT':
‘plot.DPT’
S3 methods shown with full name in documentation object 'plot.DiffusionMap':
‘plot.DiffusionMap’
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
destiny 8.172 0.024 8.342
Gene-Relevance-plotting 5.136 0.004 5.147
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘viridis’
'library' or 'require' calls not declared from:
‘IRdisplay’ ‘IRkernel’ ‘base64enc’ ‘repr’ ‘xlsx’
* 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: 6 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/destiny.Rcheck/00check.log’
for details.
destiny.Rcheck/00install.out
* installing *source* package ‘destiny’ ... ** libs g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I/usr/local/include -ggdb -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I/usr/local/include -ggdb -fpic -g -O2 -c censoring.cpp -o censoring.o g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I/usr/local/include -ggdb -fpic -g -O2 -c knn.cpp -o knn.o g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I/usr/local/include -ggdb -fpic -g -O2 -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o destiny.so RcppExports.o censoring.o knn.o utils.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.6-bioc/meat/destiny.Rcheck/destiny/libs ** R ** data ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (destiny)
destiny.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(destiny)
>
> test_check('destiny')
══ testthat results ═══════════════════════════════════════════════════════════
OK: 10 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
5.520 0.112 5.658
destiny.Rcheck/destiny-Ex.timings
| name | user | system | elapsed | |
| DPT-methods | 3.096 | 0.028 | 3.124 | |
| DPT | 1.856 | 0.008 | 1.862 | |
| DiffusionMap-accessors | 1.216 | 0.016 | 1.236 | |
| DiffusionMap-class | 2.552 | 0.008 | 2.563 | |
| DiffusionMap-methods | 1.412 | 0.004 | 1.414 | |
| ExpressionSet-helpers | 0.124 | 0.004 | 0.128 | |
| Gene-Relevance-methods | 1.608 | 0.004 | 1.613 | |
| Gene-Relevance-plotting | 5.136 | 0.004 | 5.147 | |
| Gene-Relevance | 1.868 | 0.000 | 1.867 | |
| Sigmas-class | 0.136 | 0.000 | 0.135 | |
| coercions | 1.244 | 0.004 | 1.246 | |
| colorlegend | 0.060 | 0.004 | 0.065 | |
| cube_helix | 0.008 | 0.000 | 0.005 | |
| destiny-deprecated | 0 | 0 | 0 | |
| destiny-generics | 1.300 | 0.024 | 1.326 | |
| destiny | 8.172 | 0.024 | 8.342 | |
| dm_predict | 0.584 | 0.000 | 0.584 | |
| eig_decomp | 0.000 | 0.000 | 0.001 | |
| extractions | 1.364 | 0.004 | 1.368 | |
| find_dm_k | 0.004 | 0.000 | 0.004 | |
| find_sigmas | 0.816 | 0.000 | 0.820 | |
| find_tips | 1.036 | 0.000 | 1.038 | |
| l_which | 0 | 0 | 0 | |
| plot.DPT | 1.988 | 0.012 | 2.002 | |
| plot.DiffusionMap | 1.212 | 0.000 | 1.212 | |
| plot.Sigmas | 0.136 | 0.000 | 0.136 | |
| projection_dist | 0.428 | 0.000 | 0.429 | |
| random_root | 1.008 | 0.008 | 1.016 | |