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This page was generated on 2024-05-09 11:40:52 -0400 (Thu, 09 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4748
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4484
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4514
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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 791/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.2.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 2024)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: RELEASE_3_19
git_last_commit: d1f7215
git_last_commit_date: 2024-04-30 11:49:57 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for gDRutils on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: gDRutils
Version: 1.2.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings gDRutils_1.2.0.tar.gz
StartedAt: 2024-05-09 07:36:21 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 07:40:39 -0000 (Thu, 09 May 2024)
EllapsedTime: 258.5 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings gDRutils_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/gDRutils.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.2.0’
* 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 ‘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 loading without being on the library search path ... 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 ... NOTE
checkRd: (-1) split_SE_components.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) split_SE_components.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) split_SE_components.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) split_SE_components.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) split_SE_components.Rd:35: Lost braces in \itemize; meant \describe ?
* 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 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/gDRutils.Rcheck/00check.log’
for details.


Installation output

gDRutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL gDRutils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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 version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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("gDRutils")
> library("testthat")
> 
> test_check("gDRutils")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 496 ]
> 
> proc.time()
   user  system elapsed 
 57.609   2.284  59.744 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.7280.0120.741
SE_metadata0.0530.0000.054
addClass0.0030.0000.002
aggregate_assay1.3340.0321.367
apply_bumpy_function1.9700.0912.066
assert_choices000
average_biological_replicates_dt0.3730.0000.374
cap_xc50000
convert_colData_to_json0.0690.0000.069
convert_combo_data_to_dt0.3110.0000.310
convert_combo_field_to_assay0.0020.0000.003
convert_mae_assay_to_dt0.0790.0000.080
convert_mae_to_json0.0220.0000.022
convert_metadata_to_json0.0120.0000.011
convert_rowData_to_json0.0030.0000.003
convert_se_assay_to_dt0.0770.0000.077
convert_se_to_json0.0170.0000.017
demote_fields1.2850.0031.284
df_to_bm_assay0.1620.0080.171
dot-set_invalid_fit_params000
extend_normalization_type_name0.0010.0000.000
fit_curves0.2420.0280.270
flatten0.0080.0040.012
gen_synthetic_data0.0080.0000.008
geometric_mean000
get_MAE_identifiers0.0030.0080.010
get_assay_names000
get_combo_assay_names000
get_combo_base_assay_names0.0010.0000.001
get_combo_col_settings0.0040.0000.004
get_combo_excess_field_names0.0020.0000.002
get_combo_score_assay_names0.0010.0000.001
get_combo_score_field_names000
get_default_identifiers000
get_duplicated_rows0.0020.0000.002
get_env_assay_names000
get_expect_one_identifiers000
get_experiment_groups0.0010.0000.001
get_identifiers_dt0.0060.0000.007
get_idfs_synonyms000
get_iso_colors0.0020.0000.002
get_non_empty_assays0.0690.0040.072
get_required_identifiers000
get_synthetic_data0.0160.0000.016
get_testdata0.1090.0000.109
get_testdata_codilution0.0950.0120.109
get_testdata_combo0.2870.0080.313
headers0.0150.0000.015
identifiers000
identify_unique_se_metadata_fields0.0070.0040.011
is_any_exp_empty0.0660.0000.065
is_exp_empty0.0650.0000.064
is_mae_empty0.0660.0000.066
logisticFit0.0340.0000.033
loop000
mcolData0.020.000.02
merge_SE2.4100.0122.421
merge_assay0.5240.0160.540
merge_metadata0.0090.0040.013
modifyData0.1350.0040.139
mrowData0.0210.0000.020
predict_conc_from_efficacy000
predict_efficacy_from_conc000
prettify_flat_metrics0.0290.0000.030
promote_fields0.2600.0040.264
refine_coldata0.0140.0000.014
refine_rowdata0.0620.0000.063
rename_DFrame0.0140.0000.014
rename_bumpy0.0420.0000.042
set_constant_fit_params0.0000.0000.001
shorten_normalization_type_name0.0000.0000.001
split_SE_components0.0910.0080.098
standardize_mae0.1980.0000.199
standardize_se0.0450.0000.046
update_env_idfs_from_mae0.0010.0000.002
update_idfs_synonyms0.0000.0000.001
validate_MAE0.1020.0000.103
validate_SE0.0370.0000.037
validate_identifiers0.0090.0000.009
validate_json000
validate_mae_with_schema0.5710.0830.808
validate_se_assay_name0.0110.0000.011