| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:29 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 SimBu package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SimBu.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 1865/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SimBu 1.1.3 (landing page) Alexander Dietrich
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: SimBu |
| Version: 1.1.3 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SimBu.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SimBu_1.1.3.tar.gz |
| StartedAt: 2023-02-07 15:56:27 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 16:02:47 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 379.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SimBu.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SimBu.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SimBu_1.1.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SimBu.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 ‘SimBu/DESCRIPTION’ ... OK
* this is package ‘SimBu’ version ‘1.1.3’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
.pre-commit-config.yaml
.prettierignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SimBu’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/home/biocbuild/bbs-3.17-bioc/meat/SimBu.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 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 ... ERROR
Running examples in ‘SimBu-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dataset_h5ad
> ### Title: Build SummarizedExperiment using a h5ad file for the counts
> ### Aliases: dataset_h5ad
>
> ### ** Examples
>
> h5 <- system.file("extdata", "anndata.h5ad", package = "SimBu")
> ds_h5ad <- SimBu::dataset_h5ad(
+ h5ad_file_counts = h5,
+ name = "h5ad_dataset",
+ cell_id_col = "id", # this will use the 'id' column of the metadata as cell identifiers
+ cell_type_col = "group", # this will use the 'group' column of the metadata as cell type info
+ cells_in_obs = TRUE
+ ) # in case your cell information is stored in the var layer, switch to FALSE
Warning in check_forbidden_install("Python packages") :
cannot install Python packages during R CMD check
+ '/home/biocbuild/.cache/R/basilisk/1.11.2/0/bin/conda' 'create' '--yes' '--prefix' '/home/biocbuild/.cache/R/basilisk/1.11.2/SimBu/1.1.3/SimBu_env_1_1_1' 'python=3.9' '--quiet' '-c' 'conda-forge'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.11.2/SimBu/1.1.3/SimBu_env_1_1_1
added / updated specs:
- python=3.9
The following NEW packages will be INSTALLED:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-hf897c2e_4
ca-certificates conda-forge/linux-aarch64::ca-certificates-2022.12.7-h4fd8a4c_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-12.2.0-h607ecd0_19
libgomp conda-forge/linux-aarch64::libgomp-12.2.0-h607ecd0_19
libnsl conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.40.0-hf9034f9_0
libuuid conda-forge/linux-aarch64::libuuid-2.32.1-hf897c2e_1000
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h4e544f5_4
ncurses conda-forge/linux-aarch64::ncurses-6.3-headf329_1
openssl conda-forge/linux-aarch64::openssl-3.0.7-hb4cce97_2
pip conda-forge/noarch::pip-23.0-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.9.16-hb363c5e_0_cpython
readline conda-forge/linux-aarch64::readline-8.1.2-h38e3740_0
setuptools conda-forge/noarch::setuptools-67.1.0-pyhd8ed1ab_0
tk conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0
tzdata conda-forge/noarch::tzdata-2022g-h191b570_0
wheel conda-forge/noarch::wheel-0.38.4-pyhd8ed1ab_0
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ '/home/biocbuild/.cache/R/basilisk/1.11.2/0/bin/conda' 'install' '--yes' '--prefix' '/home/biocbuild/.cache/R/basilisk/1.11.2/SimBu/1.1.3/SimBu_env_1_1_1' 'python=3.9'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.11.2/SimBu/1.1.3/SimBu_env_1_1_1
added / updated specs:
- python=3.9
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2023.01.10-hd43f75c_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.1.0
Please update conda by running
$ conda update -n base -c defaults conda
+ '/home/biocbuild/.cache/R/basilisk/1.11.2/0/bin/conda' 'install' '--yes' '--prefix' '/home/biocbuild/.cache/R/basilisk/1.11.2/SimBu/1.1.3/SimBu_env_1_1_1' '-c' 'conda-forge' 'python=3.9' 'python=3.9' 'anndata=0.7.6' 'h5py=3.2.1' 'hdf5=1.10.6' 'natsort=7.1.1' 'numpy=1.20.2' 'packaging=20.9' 'pandas=1.2.4' 'scipy=1.6.3' 'sqlite=3.35.5'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- anndata=0.7.6
Current channels:
- https://conda.anaconda.org/conda-forge/linux-aarch64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/linux-aarch64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/linux-aarch64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
Error: one or more Python packages failed to install [error code 1]
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
▆
1. ├─testthat::expect_s4_class(...) at test_dataset.R:77:2
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─SimBu::dataset_h5ad(...)
5. └─SimBu:::h5ad_to_adata(h5ad_file_counts, cells_in_obs)
6. └─basilisk::basiliskStart(SimBu_env)
7. └─basilisk::obtainEnvironmentPath(env)
8. └─basilisk::setupBasiliskEnv(...)
9. └─reticulate::conda_install(...)
10. └─reticulate:::stopf(fmt, result)
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 28 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘SimBu.Rmd’ using ‘UTF-8’... OK
‘sfaira_vignette.Rmd’ using ‘UTF-8’... OK
‘simulator_scaling_factors.Rmd’ using ‘UTF-8’... OK
‘simulator_input_output.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/SimBu.Rcheck/00check.log’
for details.
SimBu.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SimBu ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘SimBu’ ... ** using non-staged installation via StagedInstall field ** R ** 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 (SimBu)
SimBu.Rcheck/tests/testthat.Rout.fail
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(SimBu)
>
> test_check("SimBu")
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
+ '/home/biocbuild/.cache/R/basilisk/1.11.2/0/bin/conda' 'create' '--yes' '--prefix' '/home/biocbuild/.cache/R/basilisk/1.11.2/SimBu/1.1.3/SimBu_env_1_1_1' 'python=3.9' '--quiet' '-c' 'conda-forge'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.11.2/SimBu/1.1.3/SimBu_env_1_1_1
added / updated specs:
- python=3.9
The following NEW packages will be INSTALLED:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-hf897c2e_4
ca-certificates conda-forge/linux-aarch64::ca-certificates-2022.12.7-h4fd8a4c_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-12.2.0-h607ecd0_19
libgomp conda-forge/linux-aarch64::libgomp-12.2.0-h607ecd0_19
libnsl conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.40.0-hf9034f9_0
libuuid conda-forge/linux-aarch64::libuuid-2.32.1-hf897c2e_1000
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h4e544f5_4
ncurses conda-forge/linux-aarch64::ncurses-6.3-headf329_1
openssl conda-forge/linux-aarch64::openssl-3.0.7-hb4cce97_2
pip conda-forge/noarch::pip-23.0-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.9.16-hb363c5e_0_cpython
readline conda-forge/linux-aarch64::readline-8.1.2-h38e3740_0
setuptools conda-forge/noarch::setuptools-67.1.0-pyhd8ed1ab_0
tk conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0
tzdata conda-forge/noarch::tzdata-2022g-h191b570_0
wheel conda-forge/noarch::wheel-0.38.4-pyhd8ed1ab_0
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ '/home/biocbuild/.cache/R/basilisk/1.11.2/0/bin/conda' 'install' '--yes' '--prefix' '/home/biocbuild/.cache/R/basilisk/1.11.2/SimBu/1.1.3/SimBu_env_1_1_1' 'python=3.9'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.11.2/SimBu/1.1.3/SimBu_env_1_1_1
added / updated specs:
- python=3.9
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2023.01.10-hd43f75c_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.1.0
Please update conda by running
$ conda update -n base -c defaults conda
+ '/home/biocbuild/.cache/R/basilisk/1.11.2/0/bin/conda' 'install' '--yes' '--prefix' '/home/biocbuild/.cache/R/basilisk/1.11.2/SimBu/1.1.3/SimBu_env_1_1_1' '-c' 'conda-forge' 'python=3.9' 'python=3.9' 'anndata=0.7.6' 'h5py=3.2.1' 'hdf5=1.10.6' 'natsort=7.1.1' 'numpy=1.20.2' 'packaging=20.9' 'pandas=1.2.4' 'scipy=1.6.3' 'sqlite=3.35.5'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- anndata=0.7.6
Current channels:
- https://conda.anaconda.org/conda-forge/linux-aarch64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/linux-aarch64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/linux-aarch64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
Filtering genes...
Created dataset.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Using EPIC scaling factors.
Finished simulation.
Using EPIC scaling factors.
Finished simulation.
Using ABIS scaling factors.
Finished simulation.
Using quanTIseq scaling factors.
Finished simulation.
Using quanTIseq scaling factors.
Finished simulation.
Using custom scaling factors.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 28 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_dataset.R:77'): can load h5ad file with cells in obs and var ───
Error: one or more Python packages failed to install [error code 1]
Backtrace:
▆
1. ├─testthat::expect_s4_class(...) at test_dataset.R:77:2
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─SimBu::dataset_h5ad(...)
5. └─SimBu:::h5ad_to_adata(h5ad_file_counts, cells_in_obs)
6. └─basilisk::basiliskStart(SimBu_env)
7. └─basilisk::obtainEnvironmentPath(env)
8. └─basilisk::setupBasiliskEnv(...)
9. └─reticulate::conda_install(...)
10. └─reticulate:::stopf(fmt, result)
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 28 ]
Error: Test failures
Execution halted
SimBu.Rcheck/SimBu-Ex.timings
| name | user | system | elapsed | |
| census | 2.278 | 0.083 | 2.363 | |
| dataset | 5.917 | 0.139 | 6.061 | |