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This page was generated on 2024-12-24 11:43 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R 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 775/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.5.5  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: devel
git_last_commit: 10a0dcc
git_last_commit_date: 2024-12-17 02:41:58 -0500 (Tue, 17 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  


CHECK results for gDRutils on lconway

To the developers/maintainers of the gDRutils package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gDRutils.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.

raw results


Summary

Package: gDRutils
Version: 1.5.5
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gDRutils_1.5.5.tar.gz
StartedAt: 2024-12-23 20:33:02 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 20:37:15 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 253.3 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gDRutils_1.5.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/gDRutils.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.5.5’
* 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 ‘gDRutils’ can be installed ... OK
* 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 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:
  SE_metadata.Rd: SummarizedExperiment-class
  convert_mae_assay_to_dt.Rd: SummarizedExperiment-class,
    MultiAssayExperiment-class
  convert_se_assay_to_dt.Rd: SummarizedExperiment-class
  is_exp_empty.Rd: SummarizedExperiment-class
  split_SE_components.Rd: SummarizedExperiment-class
  validate_se_assay_name.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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/gDRutils.Rcheck/00check.log’
for details.


Installation output

gDRutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gDRutils
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘gDRutils’ ...
** using staged installation
** 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 (gDRutils)

Tests output

gDRutils.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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("gDRutils")
> library("testthat")
> 
> test_check("gDRutils")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 690 ]
> 
> proc.time()
   user  system elapsed 
 56.196   2.128  58.789 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.4730.0260.503
SE_metadata0.0400.0050.046
addClass0.0030.0000.003
aggregate_assay1.1920.0351.235
apply_bumpy_function1.8140.0931.925
assert_choices0.0010.0000.000
average_biological_replicates_dt0.0570.0070.064
calc_sd0.0000.0010.001
capVals0.2950.0200.317
cap_xc500.0000.0000.001
convert_colData_to_json0.0570.0010.059
convert_combo_data_to_dt0.3520.0200.375
convert_combo_field_to_assay0.0020.0000.002
convert_mae_assay_to_dt0.0720.0030.076
convert_mae_to_json0.0190.0010.021
convert_metadata_to_json0.0110.0000.011
convert_rowData_to_json0.0030.0000.004
convert_se_assay_to_custom_dt1.0410.0471.094
convert_se_assay_to_dt0.0570.0030.059
convert_se_to_json0.0120.0010.012
define_matrix_grid_positions0.0480.0030.052
demote_fields0.3850.0050.393
df_to_bm_assay0.1490.0040.154
dot-set_invalid_fit_params0.0000.0000.001
extend_normalization_type_name000
fit_curves0.1750.0280.205
flatten0.0080.0000.008
gen_synthetic_data0.0050.0010.006
geometric_mean0.0010.0000.000
get_MAE_identifiers0.0080.0010.009
get_additional_variables0.0060.0000.006
get_assay_dt_duplicated_rows0.0910.0020.093
get_assay_names0.0010.0010.000
get_assay_req_uniq_cols0.0680.0020.070
get_combo_assay_names0.0000.0000.001
get_combo_base_assay_names0.0010.0000.001
get_combo_excess_field_names0.0020.0000.002
get_combo_score_assay_names0.0010.0000.001
get_combo_score_field_names0.0020.0010.001
get_default_identifiers0.0010.0010.001
get_duplicated_rows0.0030.0000.003
get_env_assay_names000
get_env_var0.0000.0010.000
get_expect_one_identifiers0.0000.0000.001
get_experiment_groups0.0010.0000.001
get_identifiers_dt0.0060.0040.010
get_idfs_synonyms0.0000.0000.001
get_isobologram_columns0.0370.0020.037
get_non_empty_assays0.0460.0010.047
get_required_identifiers0.0010.0000.000
get_settings_from_json0.0010.0000.002
get_supported_experiments000
get_synthetic_data0.0120.0020.014
get_testdata0.0860.0210.108
get_testdata_codilution0.0790.0060.086
get_testdata_combo0.1940.0220.220
has_assay_dt_duplicated_rows0.0900.0040.096
has_dt_duplicated_rows0.0010.0000.001
has_single_codrug_data0.0810.0020.084
has_valid_codrug_data0.0900.0020.092
headers0.0130.0090.022
identifiers000
identify_unique_se_metadata_fields0.0060.0010.007
is_any_exp_empty0.0470.0020.051
is_combo_data0.1220.0140.140
is_exp_empty0.0620.0040.067
is_mae_empty0.0460.0010.046
logisticFit0.0250.0010.027
loop000
mcolData0.0150.0010.017
merge_SE1.6640.0241.703
merge_assay0.3450.0050.354
merge_metadata0.0080.0010.008
modifyData0.1210.0030.125
mrowData0.0150.0010.017
predict_conc_from_efficacy000
predict_efficacy_from_conc0.0000.0000.001
prettify_flat_metrics0.0210.0020.023
promote_fields0.2220.0050.228
refine_coldata0.0090.0010.011
refine_rowdata0.0520.0010.053
remove_codrug_data0.0380.0000.039
rename_DFrame0.0100.0010.011
rename_bumpy0.0320.0010.033
round_concentration000
set_constant_fit_params0.0000.0010.001
set_unique_cl_names0.0520.0000.053
set_unique_cl_names_dt0.0240.0000.024
set_unique_drug_names0.0630.0010.067
set_unique_drug_names_dt0.0390.0010.040
set_unique_identifiers0.3420.0040.347
set_unique_names_dt0.0230.0000.024
shorten_normalization_type_name0.0000.0010.001
split_SE_components0.1140.0050.119
standardize_mae0.1110.0010.113
standardize_se0.0380.0020.039
throw_msg_if_duplicates0.0880.0030.094
update_env_idfs_from_mae0.0020.0010.001
update_idfs_synonyms0.0010.0000.000
validate_MAE0.0850.0010.087
validate_SE0.0260.0010.028
validate_identifiers0.0060.0010.007
validate_json0.0000.0000.001
validate_mae_with_schema0.3970.0610.490
validate_se_assay_name0.0070.0010.008