Arkadiusz Gladki
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/gDRcore |
| git_branch: RELEASE_3_20 |
| git_last_commit: 13ad3fa |
| git_last_commit_date: 2024-10-29 11:22:09 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 778/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gDRcore 1.4.0 (landing page) Arkadiusz Gladki
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 1.4.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gDRcore.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings gDRcore_1.4.0.tar.gz |
| StartedAt: 2024-12-20 01:45:42 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 01:53:01 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 438.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gDRcore.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gDRcore.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings gDRcore_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/gDRcore.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'gDRcore/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gDRcore' version '1.4.0'
* 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 whether package 'gDRcore' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 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 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 ... 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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/gDRcore/libs/x64/gDRcore.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runDrugResponseProcessingPipelineFxns 21.98 1.56 23.67
annotate_dt_with_cell_line 6.17 0.60 8.17
fit_SE.combinations 3.98 0.21 5.68
* 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: 1 NOTE
See
'F:/biocbuild/bbs-3.20-bioc/meat/gDRcore.Rcheck/00check.log'
for details.
gDRcore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL gDRcore ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'gDRcore' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gDRcore.cpp -o gDRcore.o g++ -std=gnu++17 -shared -s -static-libgcc -o gDRcore.dll tmp.def gDRcore.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-gDRcore/00new/gDRcore/libs/x64 ** 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 ** 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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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 [2024-12-20 01:52:14]
INFO [2024-12-20 01:52:14]
INFO [2024-12-20 01:52:14]
INFO [2024-12-20 01:52:34] Manifest loaded successfully
INFO [2024-12-20 01:52:34] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2024-12-20 01:52:34] Loading Template_7daytreated.xlsx
INFO [2024-12-20 01:52:34] Loading Template_Untreated.xlsx
INFO [2024-12-20 01:52:35] Templates loaded successfully!
INFO [2024-12-20 01:52:35] Reading file F:/biocbuild/bbs-3.20-bioc/R/library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-12-20 01:52:35] Plate 201904190a read; 384 wells
INFO [2024-12-20 01:52:35] Plate 201904190b read; 384 wells
INFO [2024-12-20 01:52:35] Plate 201904190c read; 384 wells
INFO [2024-12-20 01:52:35] Plate 201904190d read; 384 wells
INFO [2024-12-20 01:52:35] Plate 201904190e read; 384 wells
INFO [2024-12-20 01:52:35] Plate 201904190f read; 384 wells
INFO [2024-12-20 01:52:35] File done
INFO [2024-12-20 01:52:35] Reading file F:/biocbuild/bbs-3.20-bioc/R/library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-12-20 01:52:36] Plate 201904197a read; 384 wells
INFO [2024-12-20 01:52:36] Plate 201904197b read; 384 wells
INFO [2024-12-20 01:52:36] Plate 201904197c read; 384 wells
INFO [2024-12-20 01:52:36] Plate 201904197d read; 384 wells
INFO [2024-12-20 01:52:36] Plate 201904197e read; 384 wells
INFO [2024-12-20 01:52:36] Plate 201904197f read; 384 wells
INFO [2024-12-20 01:52:36] File done
INFO [2024-12-20 01:52:36] Manifest loaded successfully
INFO [2024-12-20 01:52:36] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2024-12-20 01:52:36] Loading Template_7daytreated.xlsx
INFO [2024-12-20 01:52:37] Loading Template_Untreated.xlsx
INFO [2024-12-20 01:52:37] Templates loaded successfully!
INFO [2024-12-20 01:52:37] Reading file F:/biocbuild/bbs-3.20-bioc/R/library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-12-20 01:52:37] Plate 201904190a read; 384 wells
INFO [2024-12-20 01:52:37] Plate 201904190b read; 384 wells
INFO [2024-12-20 01:52:37] Plate 201904190c read; 384 wells
INFO [2024-12-20 01:52:37] Plate 201904190d read; 384 wells
INFO [2024-12-20 01:52:37] Plate 201904190e read; 384 wells
INFO [2024-12-20 01:52:37] Plate 201904190f read; 384 wells
INFO [2024-12-20 01:52:37] File done
INFO [2024-12-20 01:52:37] Reading file F:/biocbuild/bbs-3.20-bioc/R/library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-12-20 01:52:38] Plate 201904197a read; 384 wells
INFO [2024-12-20 01:52:38] Plate 201904197b read; 384 wells
INFO [2024-12-20 01:52:38] Plate 201904197c read; 384 wells
INFO [2024-12-20 01:52:38] Plate 201904197d read; 384 wells
INFO [2024-12-20 01:52:38] Plate 201904197e read; 384 wells
INFO [2024-12-20 01:52:38] Plate 201904197f read; 384 wells
INFO [2024-12-20 01:52:38] File done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 225 ]
>
> proc.time()
user system elapsed
284.17 7.04 298.37
gDRcore.Rcheck/gDRcore-Ex.timings
| name | user | system | elapsed | |
| annotate_dt_with_cell_line | 6.17 | 0.60 | 8.17 | |
| annotate_dt_with_drug | 0.11 | 0.14 | 0.33 | |
| calculate_GR_value | 0 | 0 | 0 | |
| calculate_excess | 0.03 | 0.05 | 0.08 | |
| calculate_matrix_metric | 0.03 | 0.00 | 0.03 | |
| calculate_score | 0.02 | 0.01 | 0.03 | |
| cleanup_metadata | 1.01 | 0.25 | 2.81 | |
| convert_mae_to_raw_data | 2.13 | 0.09 | 3.52 | |
| convert_se_to_raw_data | 0.14 | 0.00 | 0.14 | |
| data_model | 0 | 0 | 0 | |
| dot-standardize_conc | 0 | 0 | 0 | |
| fit_SE.combinations | 3.98 | 0.21 | 5.68 | |
| get_cell_line_annotation | 0.10 | 0.25 | 0.35 | |
| get_cellline_annotation_from_dt | 0.01 | 0.00 | 0.01 | |
| get_default_nested_identifiers | 0 | 0 | 0 | |
| get_drug_annotation | 0.09 | 0.17 | 0.27 | |
| get_drug_annotation_from_dt | 0.02 | 0.00 | 0.01 | |
| grr_matches | 0.02 | 0.00 | 0.02 | |
| identify_data_type | 0.04 | 0.00 | 0.05 | |
| identify_keys | 0.21 | 0.02 | 0.22 | |
| map_conc_to_standardized_conc | 0 | 0 | 0 | |
| map_df | 0.23 | 0.02 | 0.25 | |
| map_ids_to_fits | 0 | 0 | 0 | |
| merge_data | 2.38 | 0.51 | 3.31 | |
| prepare_input | 1.95 | 0.38 | 2.33 | |
| process_perturbations | 0 | 0 | 0 | |
| remove_drug_batch | 0 | 0 | 0 | |
| replace_conc_with_standardized_conc | 0 | 0 | 0 | |
| runDrugResponseProcessingPipelineFxns | 21.98 | 1.56 | 23.67 | |
| split_raw_data | 0.41 | 0.00 | 0.44 | |
| test_synthetic_data | 0.98 | 0.06 | 1.22 | |