Arkadiusz Gladki
| Snapshot Date: 2025-10-30 13:45 -0400 (Thu, 30 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/gDRcore |
| git_branch: RELEASE_3_22 |
| git_last_commit: 632e500 |
| git_last_commit_date: 2025-10-29 11:24:07 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-31 12:03 -0400 (Fri, 31 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 803/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gDRcore 1.8.0 (landing page) Arkadiusz Gladki
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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. |
| Package: gDRcore |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:gDRcore.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings gDRcore_1.8.0.tar.gz |
| StartedAt: 2025-10-30 23:45:06 -0400 (Thu, 30 Oct 2025) |
| EndedAt: 2025-10-30 23:50:48 -0400 (Thu, 30 Oct 2025) |
| EllapsedTime: 341.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gDRcore.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:gDRcore.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings gDRcore_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/gDRcore.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘gDRcore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRcore’ version ‘1.8.0’
* 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 ‘gDRcore’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... 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 ... NOTE
fit_SE.combinations : <anonymous>: no visible binding for global
variable ‘hsa_score’
fit_SE.combinations : <anonymous>: no visible binding for global
variable ‘bliss_score’
Undefined global functions or variables:
bliss_score hsa_score
* 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 19.054 0.424 18.978
annotate_dt_with_cell_line 4.815 0.228 5.045
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/gDRcore.Rcheck/00check.log’
for details.
gDRcore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL gDRcore ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘gDRcore’ ... ** this is package ‘gDRcore’ version ‘1.8.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c gDRcore.cpp -o gDRcore.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o gDRcore.so gDRcore.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/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 version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 [2025-10-30 23:47:55]
INFO [2025-10-30 23:47:55]
INFO [2025-10-30 23:47:55]
INFO [2025-10-30 23:47:55]
INFO [2025-10-30 23:50:02]
INFO [2025-10-30 23:50:02]
INFO [2025-10-30 23:50:02]
INFO [2025-10-30 23:50:02] Manifest loaded successfully
INFO [2025-10-30 23:50:02] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2025-10-30 23:50:02] Loading Template_7daytreated.xlsx
INFO [2025-10-30 23:50:03] Loading Template_Untreated.xlsx
INFO [2025-10-30 23:50:03] Templates loaded successfully!
INFO [2025-10-30 23:50:03] Reading file /home/biocbuild/bbs-3.22-bioc/R/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2025-10-30 23:50:03] Plate 201904190a read; 384 wells
INFO [2025-10-30 23:50:03] Plate 201904190b read; 384 wells
INFO [2025-10-30 23:50:03] Plate 201904190c read; 384 wells
INFO [2025-10-30 23:50:03] Plate 201904190d read; 384 wells
INFO [2025-10-30 23:50:03] Plate 201904190e read; 384 wells
INFO [2025-10-30 23:50:03] Plate 201904190f read; 384 wells
INFO [2025-10-30 23:50:03] File done
INFO [2025-10-30 23:50:03] Reading file /home/biocbuild/bbs-3.22-bioc/R/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2025-10-30 23:50:03] Plate 201904197a read; 384 wells
INFO [2025-10-30 23:50:03] Plate 201904197b read; 384 wells
INFO [2025-10-30 23:50:03] Plate 201904197c read; 384 wells
INFO [2025-10-30 23:50:03] Plate 201904197d read; 384 wells
INFO [2025-10-30 23:50:03] Plate 201904197e read; 384 wells
INFO [2025-10-30 23:50:03] Plate 201904197f read; 384 wells
INFO [2025-10-30 23:50:03] File done
INFO [2025-10-30 23:50:04] Manifest loaded successfully
INFO [2025-10-30 23:50:04] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2025-10-30 23:50:04] Loading Template_7daytreated.xlsx
INFO [2025-10-30 23:50:04] Loading Template_Untreated.xlsx
INFO [2025-10-30 23:50:04] Templates loaded successfully!
INFO [2025-10-30 23:50:04] Reading file /home/biocbuild/bbs-3.22-bioc/R/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2025-10-30 23:50:04] Plate 201904190a read; 384 wells
INFO [2025-10-30 23:50:04] Plate 201904190b read; 384 wells
INFO [2025-10-30 23:50:04] Plate 201904190c read; 384 wells
INFO [2025-10-30 23:50:04] Plate 201904190d read; 384 wells
INFO [2025-10-30 23:50:04] Plate 201904190e read; 384 wells
INFO [2025-10-30 23:50:04] Plate 201904190f read; 384 wells
INFO [2025-10-30 23:50:04] File done
INFO [2025-10-30 23:50:04] Reading file /home/biocbuild/bbs-3.22-bioc/R/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2025-10-30 23:50:04] Plate 201904197a read; 384 wells
INFO [2025-10-30 23:50:04] Plate 201904197b read; 384 wells
INFO [2025-10-30 23:50:04] Plate 201904197c read; 384 wells
INFO [2025-10-30 23:50:04] Plate 201904197d read; 384 wells
INFO [2025-10-30 23:50:04] Plate 201904197e read; 384 wells
INFO [2025-10-30 23:50:04] Plate 201904197f read; 384 wells
INFO [2025-10-30 23:50:04] File done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 235 ]
>
> proc.time()
user system elapsed
210.663 2.559 211.760
gDRcore.Rcheck/gDRcore-Ex.timings
| name | user | system | elapsed | |
| annotate_dt_with_cell_line | 4.815 | 0.228 | 5.045 | |
| annotate_dt_with_drug | 0.014 | 0.000 | 0.015 | |
| annotate_mae_with_cell_line | 1.086 | 0.044 | 1.130 | |
| annotate_mae_with_drug | 0.126 | 0.026 | 0.152 | |
| annotate_se_with_cell_line | 0.027 | 0.003 | 0.030 | |
| annotate_se_with_drug | 0.021 | 0.002 | 0.024 | |
| calculate_GR_value | 0.002 | 0.000 | 0.003 | |
| calculate_excess | 0.071 | 0.000 | 0.071 | |
| calculate_matrix_metric | 0.016 | 0.000 | 0.016 | |
| calculate_score | 0.031 | 0.000 | 0.031 | |
| cleanup_metadata | 0.248 | 0.008 | 0.257 | |
| convert_mae_to_raw_data | 0.606 | 0.055 | 0.629 | |
| convert_se_to_raw_data | 0.105 | 0.000 | 0.085 | |
| data_model | 0.002 | 0.000 | 0.001 | |
| fit_SE.combinations | 3.104 | 0.035 | 3.136 | |
| get_cell_line_annotation | 0.004 | 0.002 | 0.006 | |
| get_cellline_annotation_from_dt | 0.009 | 0.002 | 0.011 | |
| get_default_nested_identifiers | 0 | 0 | 0 | |
| get_drug_annotation | 0.003 | 0.002 | 0.005 | |
| get_drug_annotation_from_dt | 0.004 | 0.000 | 0.004 | |
| grr_matches | 0.012 | 0.000 | 0.011 | |
| identify_data_type | 0.036 | 0.000 | 0.036 | |
| identify_keys | 0.183 | 0.007 | 0.191 | |
| map_df | 0.206 | 0.001 | 0.207 | |
| map_ids_to_fits | 0.001 | 0.000 | 0.001 | |
| merge_data | 1.456 | 0.059 | 1.477 | |
| prepare_input | 1.335 | 0.027 | 1.304 | |
| process_perturbations | 0.007 | 0.000 | 0.006 | |
| replace_conc_with_standardized_conc | 0.000 | 0.000 | 0.001 | |
| runDrugResponseProcessingPipelineFxns | 19.054 | 0.424 | 18.978 | |
| split_raw_data | 0.303 | 0.001 | 0.276 | |
| test_synthetic_data | 0.818 | 0.029 | 0.789 | |