Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
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" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 772/2274 | 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: 2024-12-24 06:54:09 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 07:01:16 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 427.4 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 22.292 0.145 22.446 annotate_dt_with_cell_line 6.603 0.204 6.823 * 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 [2024-12-24 07:00:37] INFO [2024-12-24 07:00:37] INFO [2024-12-24 07:00:37] INFO [2024-12-24 07:01:01] Manifest loaded successfully INFO [2024-12-24 07:01:01] Reading Template_7daytreated.xlsx with load_templates_xlsx INFO [2024-12-24 07:01:01] Loading Template_7daytreated.xlsx INFO [2024-12-24 07:01:02] Loading Template_Untreated.xlsx INFO [2024-12-24 07:01:02] Templates loaded successfully! INFO [2024-12-24 07:01:02] 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 [2024-12-24 07:01:02] Plate 201904190a read; 384 wells INFO [2024-12-24 07:01:02] Plate 201904190b read; 384 wells INFO [2024-12-24 07:01:02] Plate 201904190c read; 384 wells INFO [2024-12-24 07:01:02] Plate 201904190d read; 384 wells INFO [2024-12-24 07:01:02] Plate 201904190e read; 384 wells INFO [2024-12-24 07:01:02] Plate 201904190f read; 384 wells INFO [2024-12-24 07:01:02] File done INFO [2024-12-24 07:01:02] 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 [2024-12-24 07:01:03] Plate 201904197a read; 384 wells INFO [2024-12-24 07:01:03] Plate 201904197b read; 384 wells INFO [2024-12-24 07:01:03] Plate 201904197c read; 384 wells INFO [2024-12-24 07:01:03] Plate 201904197d read; 384 wells INFO [2024-12-24 07:01:03] Plate 201904197e read; 384 wells INFO [2024-12-24 07:01:03] Plate 201904197f read; 384 wells INFO [2024-12-24 07:01:03] File done INFO [2024-12-24 07:01:03] Manifest loaded successfully INFO [2024-12-24 07:01:03] Reading Template_7daytreated.xlsx with load_templates_xlsx INFO [2024-12-24 07:01:03] Loading Template_7daytreated.xlsx INFO [2024-12-24 07:01:03] Loading Template_Untreated.xlsx INFO [2024-12-24 07:01:03] Templates loaded successfully! INFO [2024-12-24 07:01:03] 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 [2024-12-24 07:01:04] Plate 201904190a read; 384 wells INFO [2024-12-24 07:01:04] Plate 201904190b read; 384 wells INFO [2024-12-24 07:01:04] Plate 201904190c read; 384 wells INFO [2024-12-24 07:01:04] Plate 201904190d read; 384 wells INFO [2024-12-24 07:01:04] Plate 201904190e read; 384 wells INFO [2024-12-24 07:01:04] Plate 201904190f read; 384 wells INFO [2024-12-24 07:01:04] File done INFO [2024-12-24 07:01:04] 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 [2024-12-24 07:01:04] Plate 201904197a read; 384 wells INFO [2024-12-24 07:01:04] Plate 201904197b read; 384 wells INFO [2024-12-24 07:01:04] Plate 201904197c read; 384 wells INFO [2024-12-24 07:01:04] Plate 201904197d read; 384 wells INFO [2024-12-24 07:01:04] Plate 201904197e read; 384 wells INFO [2024-12-24 07:01:04] Plate 201904197f read; 384 wells INFO [2024-12-24 07:01:04] File done [ FAIL 0 | WARN 0 | SKIP 0 | PASS 226 ] > > proc.time() user system elapsed 307.198 2.117 309.812
gDRcore.Rcheck/gDRcore-Ex.timings
name | user | system | elapsed | |
annotate_dt_with_cell_line | 6.603 | 0.204 | 6.823 | |
annotate_dt_with_drug | 0.019 | 0.000 | 0.020 | |
calculate_GR_value | 0.002 | 0.000 | 0.003 | |
calculate_excess | 0.087 | 0.008 | 0.094 | |
calculate_matrix_metric | 0.021 | 0.004 | 0.025 | |
calculate_score | 0.052 | 0.000 | 0.052 | |
cleanup_metadata | 0.364 | 0.036 | 0.401 | |
convert_mae_to_raw_data | 1.923 | 0.060 | 1.989 | |
convert_se_to_raw_data | 0.137 | 0.000 | 0.136 | |
data_model | 0.002 | 0.000 | 0.001 | |
dot-standardize_conc | 0.002 | 0.000 | 0.001 | |
fit_SE.combinations | 3.888 | 0.072 | 3.974 | |
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 | 0.006 | 0.000 | 0.006 | |
get_drug_annotation_from_dt | 0.006 | 0.000 | 0.006 | |
grr_matches | 0.017 | 0.000 | 0.018 | |
identify_data_type | 0.054 | 0.000 | 0.054 | |
identify_keys | 0.148 | 0.000 | 0.149 | |
map_conc_to_standardized_conc | 0.004 | 0.000 | 0.004 | |
map_df | 0.158 | 0.000 | 0.158 | |
map_ids_to_fits | 0.002 | 0.000 | 0.002 | |
merge_data | 1.945 | 0.072 | 2.037 | |
prepare_input | 1.770 | 0.028 | 1.792 | |
process_perturbations | 0.008 | 0.000 | 0.007 | |
remove_drug_batch | 0.000 | 0.000 | 0.001 | |
replace_conc_with_standardized_conc | 0.001 | 0.000 | 0.001 | |
runDrugResponseProcessingPipelineFxns | 22.292 | 0.145 | 22.446 | |
split_raw_data | 0.394 | 0.008 | 0.401 | |
test_synthetic_data | 1.194 | 0.016 | 1.203 | |