| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:29 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the destiny package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/destiny.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 533/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| destiny 3.15.0 (landing page) Philipp Angerer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: destiny |
| Version: 3.15.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:destiny.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings destiny_3.15.0.tar.gz |
| StartedAt: 2023-05-09 14:21:48 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 14:37:06 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 917.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: destiny.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:destiny.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings destiny_3.15.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/destiny.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘destiny/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘destiny’ version ‘3.15.0’
* 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
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘rgl’ ‘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 startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) Gene-Relevance.Rd:94: Escaped LaTeX specials: \_
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: 'as(<dsCMatrix>, "dsTMatrix")' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Gene-Relevance-plotting 7.824 0.220 8.044
destiny 5.128 0.052 5.183
* 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 ...
‘DPT.Rmd’ using ‘UTF-8’... OK
‘Diffusion-Map-recap.Rmd’ using ‘UTF-8’... OK
‘Diffusion-Maps.Rmd’ using ‘UTF-8’... OK
‘Gene-Relevance.Rmd’ using ‘UTF-8’... OK
‘Global-Sigma.Rmd’ using ‘UTF-8’... OK
‘tidyverse.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 5 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/destiny.Rcheck/00check.log’
for details.
destiny.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL destiny ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘destiny’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/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-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/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-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/grDevices/include' -I/usr/local/include -ggdb -fPIC -g -O2 -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/usr/local/lib -o destiny.so RcppExports.o censoring.o utils.o installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-destiny/00new/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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (destiny)
destiny.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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')
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 67 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• Not yet stable (1)
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 67 ]
>
> proc.time()
user system elapsed
18.350 0.886 19.220
destiny.Rcheck/destiny-Ex.timings
| name | user | system | elapsed | |
| DPT-matrix-methods | 1.228 | 0.016 | 1.245 | |
| DPT-methods | 2.424 | 0.012 | 2.436 | |
| DPT | 1.834 | 0.036 | 1.869 | |
| DiffusionMap-accessors | 0.533 | 0.040 | 0.572 | |
| DiffusionMap-class | 3.612 | 0.008 | 3.620 | |
| DiffusionMap-methods | 0.473 | 0.004 | 0.477 | |
| ExpressionSet-helpers | 0.105 | 0.000 | 0.105 | |
| Gene-Relevance-methods | 1.954 | 0.056 | 2.010 | |
| Gene-Relevance-plotting | 7.824 | 0.220 | 8.044 | |
| Gene-Relevance | 3.437 | 0.024 | 3.463 | |
| Sigmas-class | 0.130 | 0.004 | 0.133 | |
| coercions | 0.541 | 0.008 | 0.549 | |
| colorlegend | 0.015 | 0.000 | 0.015 | |
| cube_helix | 0.003 | 0.004 | 0.007 | |
| destiny-generics | 1.401 | 0.084 | 1.485 | |
| destiny | 5.128 | 0.052 | 5.183 | |
| dm_predict | 0.574 | 0.040 | 0.613 | |
| eig_decomp | 0.001 | 0.000 | 0.002 | |
| extractions | 1.016 | 0.148 | 1.165 | |
| find_dm_k | 0.014 | 0.000 | 0.013 | |
| find_sigmas | 0.604 | 0.032 | 0.635 | |
| find_tips | 0.502 | 0.058 | 0.560 | |
| l_which | 0 | 0 | 0 | |
| plot.DPT | 2.454 | 0.180 | 2.634 | |
| plot.DiffusionMap | 0.674 | 0.024 | 0.698 | |
| plot.Sigmas | 0.130 | 0.004 | 0.134 | |
| projection_dist | 0.272 | 0.008 | 0.281 | |
| random_root | 0.502 | 0.036 | 0.538 | |