Philipp Angerer
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/destiny |
| Branch: RELEASE_3_8 |
| Last Commit: fd8c2e5 |
| Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:51:30 -0400 (Tue, 16 Apr 2019).
| Package 401/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| destiny 2.12.0 Philipp Angerer
| 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: destiny |
| Version: 2.12.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:destiny.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings destiny_2.12.0.tar.gz |
| StartedAt: 2019-04-15 23:27:24 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:31:11 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 226.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: destiny.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:destiny.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings destiny_2.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/destiny.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 ‘destiny/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘destiny’ version ‘2.12.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘destiny’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘SingleCellExperiment’
A package should be listed in only one of these fields.
'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 ... 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 ... 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 ... 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
destiny 8.80 0.008 8.857
Gene-Relevance-plotting 6.14 0.060 6.211
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/destiny.Rcheck/00check.log’
for details.
destiny.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL destiny ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘destiny’ ... ** libs g++ -std=gnu++11 -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/RcppEigen/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/grDevices/include" -I/usr/local/include -ggdb -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -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/RcppEigen/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/grDevices/include" -I/usr/local/include -ggdb -fpic -g -O2 -Wall -c censoring.cpp -o censoring.o g++ -std=gnu++11 -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/RcppEigen/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/grDevices/include" -I/usr/local/include -ggdb -fpic -g -O2 -Wall -c knn.cpp -o knn.o g++ -std=gnu++11 -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/RcppEigen/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/grDevices/include" -I/usr/local/include -ggdb -fpic -g -O2 -Wall -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o destiny.so RcppExports.o censoring.o knn.o utils.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.8-bioc/R/library/destiny/libs ** R ** data ** demo ** 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 (destiny)
destiny.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(destiny)
>
> test_check('destiny')
══ testthat results ═══════════════════════════════════════════════════════════
OK: 51 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
12.884 0.320 13.240
destiny.Rcheck/destiny-Ex.timings
| name | user | system | elapsed | |
| DPT-methods | 3.048 | 0.024 | 3.089 | |
| DPT | 2.208 | 0.064 | 2.308 | |
| DiffusionMap-accessors | 1.756 | 0.040 | 1.800 | |
| DiffusionMap-class | 3.824 | 0.024 | 3.854 | |
| DiffusionMap-methods | 1.028 | 0.012 | 1.043 | |
| ExpressionSet-helpers | 0.120 | 0.000 | 0.118 | |
| Gene-Relevance-methods | 3.124 | 0.020 | 3.153 | |
| Gene-Relevance-plotting | 6.140 | 0.060 | 6.211 | |
| Gene-Relevance | 4.212 | 0.012 | 4.228 | |
| Sigmas-class | 0.108 | 0.000 | 0.108 | |
| coercions | 1.004 | 0.000 | 1.005 | |
| colorlegend | 0.020 | 0.000 | 0.019 | |
| cube_helix | 0.004 | 0.000 | 0.005 | |
| destiny-deprecated | 0 | 0 | 0 | |
| destiny-generics | 1.452 | 0.020 | 1.477 | |
| destiny | 8.800 | 0.008 | 8.857 | |
| dm_predict | 0.876 | 0.000 | 0.876 | |
| eig_decomp | 0.004 | 0.000 | 0.002 | |
| extractions | 1.660 | 0.004 | 1.664 | |
| find_dm_k | 0.004 | 0.004 | 0.007 | |
| find_sigmas | 1.128 | 0.008 | 1.136 | |
| find_tips | 1.616 | 0.004 | 1.620 | |
| l_which | 0.000 | 0.000 | 0.001 | |
| plot.DPT | 3.256 | 0.020 | 3.280 | |
| plot.DiffusionMap | 1.336 | 0.000 | 1.340 | |
| plot.Sigmas | 0.172 | 0.000 | 0.175 | |
| projection_dist | 0.536 | 0.004 | 0.543 | |
| random_root | 1.152 | 0.012 | 1.166 | |