Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:39 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 516/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
destiny 3.13.0 (landing page) Philipp Angerer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: destiny |
Version: 3.13.0 |
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/library --timings destiny_3.13.0.tar.gz |
StartedAt: 2023-02-28 01:47:06 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 02:01:44 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 878.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: destiny.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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/library --timings destiny_3.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/destiny.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * 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 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘destiny/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘destiny’ version ‘3.13.0’ * 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 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 dependencies in R code ... OK * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: plot.DPT plot.DiffusionMap See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Gene-Relevance-plotting 7.736 0.132 7.868 destiny 5.125 0.008 5.136 * 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: 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/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/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/lib -L/usr/local/lib -o destiny.so RcppExports.o censoring.o utils.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "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 17.279 0.839 18.104
destiny.Rcheck/destiny-Ex.timings
name | user | system | elapsed | |
DPT-matrix-methods | 1.890 | 0.096 | 1.986 | |
DPT-methods | 1.582 | 0.056 | 1.638 | |
DPT | 1.785 | 0.080 | 1.866 | |
DiffusionMap-accessors | 0.488 | 0.027 | 0.516 | |
DiffusionMap-class | 3.087 | 0.084 | 3.172 | |
DiffusionMap-methods | 0.455 | 0.004 | 0.459 | |
ExpressionSet-helpers | 0.104 | 0.000 | 0.104 | |
Gene-Relevance-methods | 1.896 | 0.012 | 1.908 | |
Gene-Relevance-plotting | 7.736 | 0.132 | 7.868 | |
Gene-Relevance | 3.404 | 0.040 | 3.443 | |
Sigmas-class | 0.114 | 0.008 | 0.122 | |
coercions | 0.519 | 0.004 | 0.523 | |
colorlegend | 0.026 | 0.000 | 0.027 | |
cube_helix | 0.008 | 0.000 | 0.008 | |
destiny-generics | 1.309 | 0.072 | 1.382 | |
destiny | 5.125 | 0.008 | 5.136 | |
dm_predict | 0.540 | 0.032 | 0.572 | |
eig_decomp | 0.001 | 0.000 | 0.002 | |
extractions | 1.048 | 0.020 | 1.068 | |
find_dm_k | 0.013 | 0.000 | 0.012 | |
find_sigmas | 0.599 | 0.000 | 0.599 | |
find_tips | 0.556 | 0.000 | 0.556 | |
l_which | 0 | 0 | 0 | |
plot.DPT | 2.633 | 0.056 | 2.689 | |
plot.DiffusionMap | 0.783 | 0.032 | 0.816 | |
plot.Sigmas | 0.132 | 0.008 | 0.140 | |
projection_dist | 0.274 | 0.000 | 0.274 | |
random_root | 0.565 | 0.008 | 0.574 | |