| Back to Using R 4.1.3 to BUILD/CHECK a small subset of 3.18 packages |
This page was generated on 2024-03-08 16:41:48 -0500 (Fri, 08 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 655 |
| 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 117/118 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
| zellkonverter 1.12.1 (landing page) Luke Zappia
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||
|
To the developers/maintainers of the zellkonverter package: - 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. |
| Package: zellkonverter |
| Version: 1.12.1 |
| Command: /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/hpages/bbs-3.18-bioc-R41/R/site-library --timings zellkonverter_1.12.1.tar.gz |
| StartedAt: 2024-03-08 16:20:09 -0500 (Fri, 08 Mar 2024) |
| EndedAt: 2024-03-08 16:28:53 -0500 (Fri, 08 Mar 2024) |
| EllapsedTime: 523.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: zellkonverter.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/hpages/bbs-3.18-bioc-R41/R/site-library --timings zellkonverter_1.12.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/hpages/bbs-3.18-bioc-R41/meat/zellkonverter.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘zellkonverter/DESCRIPTION’ ... OK
* this is package ‘zellkonverter’ version ‘1.12.1’
* 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 ‘zellkonverter’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/home/hpages/bbs-3.18-bioc-R41/meat/zellkonverter.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AnnData-Conversion 24.122 4.350 28.941
writeH5AD 7.701 1.124 9.545
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘zellkonverter.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/hpages/bbs-3.18-bioc-R41/meat/zellkonverter.Rcheck/00check.log’
for details.
zellkonverter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL zellkonverter ### ############################################################################## ############################################################################## * installing to library ‘/home/hpages/bbs-3.18-bioc-R41/R/site-library’ * installing *source* package ‘zellkonverter’ ... ** using non-staged installation via StagedInstall field ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (zellkonverter)
zellkonverter.Rcheck/tests/spelling.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> if (requireNamespace("spelling", quietly = TRUE)) {
+ spelling::spell_check_test(
+ vignettes = TRUE,
+ error = FALSE,
+ skip_on_cran = TRUE
+ )
+ }
NULL
>
> proc.time()
user system elapsed
0.144 0.027 0.162
zellkonverter.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(zellkonverter)
Registered S3 methods overwritten by 'zellkonverter':
method from
py_to_r.numpy.ndarray reticulate
py_to_r.pandas.core.arrays.categorical.Categorical reticulate
>
> test_check("zellkonverter")
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
... storing 'tissue' as categorical
... storing 'level1class' as categorical
... storing 'level2class' as categorical
... storing 'featureType' as categorical
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
[ FAIL 0 | WARN 20 | SKIP 3 | PASS 134 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-read.R:147:5', 'test-zzz-anndata.R:6:5',
'test-zzz-anndata.R:54:5'
[ FAIL 0 | WARN 20 | SKIP 3 | PASS 134 ]
>
> proc.time()
user system elapsed
122.173 36.497 286.780
zellkonverter.Rcheck/zellkonverter-Ex.timings
| name | user | system | elapsed | |
| AnnData-Conversion | 24.122 | 4.350 | 28.941 | |
| AnnData-Environment | 0.006 | 0.000 | 0.005 | |
| readH5AD | 1.213 | 0.120 | 1.332 | |
| setZellkonverterVerbose | 0.001 | 0.000 | 0.000 | |
| writeH5AD | 7.701 | 1.124 | 9.545 | |