Philipp Angerer
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/destiny |
| git_branch: devel |
| git_last_commit: 48962d2 |
| git_last_commit_date: 2023-12-28 07:36:24 -0400 (Thu, 28 Dec 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:38 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 | ||||
| Package 557/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| destiny 3.17.0 (landing page) Philipp Angerer
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: destiny |
| Version: 3.17.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:destiny.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings destiny_3.17.0.tar.gz |
| StartedAt: 2024-03-28 04:42:27 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 04:47:49 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 322.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: destiny.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:destiny.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings destiny_3.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/destiny.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘destiny/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘destiny’ version ‘3.17.0’
* 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++ (GCC) 10.3.1’
* 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 code 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 loading without being on the library search path ... OK
* checking whether 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 Rd file 'coercions.Rd':
‘fortify.DiffusionMap’ ‘fortify.DPT’
S3 methods shown with full name in Rd file 'plot.DPT.Rd':
‘plot.DPT’
S3 methods shown with full name in Rd file 'plot.DiffusionMap.Rd':
‘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 8.371 0.084 8.471
destiny 5.131 0.012 5.155
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/destiny.Rcheck/00check.log’
for details.
destiny.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL destiny ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’ * installing *source* package ‘destiny’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o destiny.so RcppExports.o censoring.o utils.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/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) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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 0 | SKIP 1 | PASS 67 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• Not yet stable (1): 'test_gr.r:23:2'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 67 ]
>
> proc.time()
user system elapsed
17.753 0.641 18.410
destiny.Rcheck/destiny-Ex.timings
| name | user | system | elapsed | |
| DPT-matrix-methods | 1.962 | 0.024 | 1.989 | |
| DPT-methods | 2.008 | 0.011 | 2.024 | |
| DPT | 1.850 | 0.003 | 1.857 | |
| DiffusionMap-accessors | 0.485 | 0.008 | 0.494 | |
| DiffusionMap-class | 3.333 | 0.004 | 3.343 | |
| DiffusionMap-methods | 0.446 | 0.012 | 0.459 | |
| ExpressionSet-helpers | 0.108 | 0.004 | 0.112 | |
| Gene-Relevance-methods | 1.909 | 0.000 | 1.914 | |
| Gene-Relevance-plotting | 8.371 | 0.084 | 8.471 | |
| Gene-Relevance | 4.208 | 0.044 | 4.259 | |
| Sigmas-class | 0.171 | 0.001 | 0.172 | |
| coercions | 0.479 | 0.002 | 0.482 | |
| colorlegend | 0.008 | 0.003 | 0.012 | |
| cube_helix | 0.008 | 0.000 | 0.008 | |
| destiny-generics | 0.544 | 0.004 | 0.548 | |
| destiny | 5.131 | 0.012 | 5.155 | |
| dm_predict | 0.525 | 0.004 | 0.531 | |
| eig_decomp | 0.002 | 0.000 | 0.001 | |
| extractions | 0.987 | 0.004 | 0.992 | |
| find_dm_k | 0.009 | 0.000 | 0.010 | |
| find_sigmas | 0.644 | 0.000 | 0.651 | |
| find_tips | 0.509 | 0.004 | 0.513 | |
| l_which | 0 | 0 | 0 | |
| plot.DPT | 3.498 | 0.068 | 3.574 | |
| plot.DiffusionMap | 0.684 | 0.036 | 0.722 | |
| plot.Sigmas | 1.051 | 0.040 | 1.094 | |
| projection_dist | 0.240 | 0.004 | 0.245 | |
| random_root | 0.453 | 0.016 | 0.470 | |