Arkadiusz Gladki
| Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/gDRcore |
| git_branch: devel |
| git_last_commit: a08b10a |
| git_last_commit_date: 2024-12-18 10:52:50 -0500 (Wed, 18 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-04 11:46 -0500 (Sat, 04 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| 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 773/2275 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gDRcore 1.5.3 (landing page) Arkadiusz Gladki
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the gDRcore package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gDRcore.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: gDRcore |
| Version: 1.5.3 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:gDRcore.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gDRcore_1.5.3.tar.gz |
| StartedAt: 2025-01-04 06:27:24 -0000 (Sat, 04 Jan 2025) |
| EndedAt: 2025-01-04 06:34:34 -0000 (Sat, 04 Jan 2025) |
| EllapsedTime: 430.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gDRcore.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:gDRcore.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gDRcore_1.5.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/gDRcore.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRcore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRcore’ version ‘1.5.3’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gDRcore’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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 ...Warning: program compiled against libxml 212 using older 211
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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
fit_SE.combinations.Rd: SummarizedExperiment-class
runDrugResponseProcessingPipelineFxns.Rd: SummarizedExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘gDRcore/libs/gDRcore.so’:
Found non-API call to R: ‘STRING_PTR’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runDrugResponseProcessingPipelineFxns 22.666 0.560 23.243
annotate_dt_with_cell_line 6.563 0.136 6.714
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/gDRcore.Rcheck/00check.log’
for details.
gDRcore.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL gDRcore
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘gDRcore’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c gDRcore.cpp -o gDRcore.o
gDRcore.cpp:6:9: warning: "R_NO_REMAP" redefined
6 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o gDRcore.so gDRcore.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-gDRcore/00new/gDRcore/libs
** 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 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 (gDRcore)
gDRcore.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "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("gDRcore")
> library("testthat")
>
> test_check("gDRcore")
INFO [2025-01-04 06:33:55]
INFO [2025-01-04 06:33:55]
INFO [2025-01-04 06:33:55]
INFO [2025-01-04 06:34:19] Manifest loaded successfully
INFO [2025-01-04 06:34:19] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2025-01-04 06:34:19] Loading Template_7daytreated.xlsx
INFO [2025-01-04 06:34:19] Loading Template_Untreated.xlsx
INFO [2025-01-04 06:34:19] Templates loaded successfully!
INFO [2025-01-04 06:34:19] Reading file /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2025-01-04 06:34:20] Plate 201904190a read; 384 wells
INFO [2025-01-04 06:34:20] Plate 201904190b read; 384 wells
INFO [2025-01-04 06:34:20] Plate 201904190c read; 384 wells
INFO [2025-01-04 06:34:20] Plate 201904190d read; 384 wells
INFO [2025-01-04 06:34:20] Plate 201904190e read; 384 wells
INFO [2025-01-04 06:34:20] Plate 201904190f read; 384 wells
INFO [2025-01-04 06:34:20] File done
INFO [2025-01-04 06:34:20] Reading file /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2025-01-04 06:34:20] Plate 201904197a read; 384 wells
INFO [2025-01-04 06:34:20] Plate 201904197b read; 384 wells
INFO [2025-01-04 06:34:21] Plate 201904197c read; 384 wells
INFO [2025-01-04 06:34:21] Plate 201904197d read; 384 wells
INFO [2025-01-04 06:34:21] Plate 201904197e read; 384 wells
INFO [2025-01-04 06:34:21] Plate 201904197f read; 384 wells
INFO [2025-01-04 06:34:21] File done
INFO [2025-01-04 06:34:21] Manifest loaded successfully
INFO [2025-01-04 06:34:21] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2025-01-04 06:34:21] Loading Template_7daytreated.xlsx
INFO [2025-01-04 06:34:21] Loading Template_Untreated.xlsx
INFO [2025-01-04 06:34:21] Templates loaded successfully!
INFO [2025-01-04 06:34:21] Reading file /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2025-01-04 06:34:21] Plate 201904190a read; 384 wells
INFO [2025-01-04 06:34:21] Plate 201904190b read; 384 wells
INFO [2025-01-04 06:34:21] Plate 201904190c read; 384 wells
INFO [2025-01-04 06:34:22] Plate 201904190d read; 384 wells
INFO [2025-01-04 06:34:22] Plate 201904190e read; 384 wells
INFO [2025-01-04 06:34:22] Plate 201904190f read; 384 wells
INFO [2025-01-04 06:34:22] File done
INFO [2025-01-04 06:34:22] Reading file /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2025-01-04 06:34:22] Plate 201904197a read; 384 wells
INFO [2025-01-04 06:34:22] Plate 201904197b read; 384 wells
INFO [2025-01-04 06:34:22] Plate 201904197c read; 384 wells
INFO [2025-01-04 06:34:22] Plate 201904197d read; 384 wells
INFO [2025-01-04 06:34:22] Plate 201904197e read; 384 wells
INFO [2025-01-04 06:34:22] Plate 201904197f read; 384 wells
INFO [2025-01-04 06:34:22] File done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 226 ]
>
> proc.time()
user system elapsed
308.422 2.439 311.396
gDRcore.Rcheck/gDRcore-Ex.timings
| name | user | system | elapsed | |
| annotate_dt_with_cell_line | 6.563 | 0.136 | 6.714 | |
| annotate_dt_with_drug | 0.018 | 0.000 | 0.019 | |
| calculate_GR_value | 0.003 | 0.000 | 0.003 | |
| calculate_excess | 0.084 | 0.008 | 0.093 | |
| calculate_matrix_metric | 0.024 | 0.000 | 0.023 | |
| calculate_score | 0.049 | 0.000 | 0.049 | |
| cleanup_metadata | 0.382 | 0.016 | 0.399 | |
| convert_mae_to_raw_data | 1.908 | 0.064 | 1.976 | |
| convert_se_to_raw_data | 0.128 | 0.000 | 0.126 | |
| data_model | 0.001 | 0.000 | 0.001 | |
| dot-standardize_conc | 0.001 | 0.000 | 0.001 | |
| fit_SE.combinations | 3.985 | 0.192 | 4.199 | |
| get_cell_line_annotation | 0.006 | 0.000 | 0.007 | |
| get_cellline_annotation_from_dt | 0.01 | 0.00 | 0.01 | |
| get_default_nested_identifiers | 0.001 | 0.000 | 0.001 | |
| get_drug_annotation | 0.002 | 0.004 | 0.007 | |
| get_drug_annotation_from_dt | 0.006 | 0.000 | 0.006 | |
| grr_matches | 0.018 | 0.000 | 0.018 | |
| identify_data_type | 0.055 | 0.000 | 0.055 | |
| identify_keys | 0.149 | 0.004 | 0.153 | |
| map_conc_to_standardized_conc | 0.004 | 0.000 | 0.004 | |
| map_df | 0.152 | 0.004 | 0.156 | |
| map_ids_to_fits | 0.001 | 0.000 | 0.002 | |
| merge_data | 2.003 | 0.107 | 2.126 | |
| prepare_input | 1.757 | 0.037 | 1.786 | |
| process_perturbations | 0.003 | 0.004 | 0.007 | |
| remove_drug_batch | 0 | 0 | 0 | |
| replace_conc_with_standardized_conc | 0.001 | 0.000 | 0.001 | |
| runDrugResponseProcessingPipelineFxns | 22.666 | 0.560 | 23.243 | |
| split_raw_data | 0.376 | 0.008 | 0.383 | |
| test_synthetic_data | 1.152 | 0.075 | 1.222 | |