Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-11-02 11:40:43 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 781/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.0.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: RELEASE_3_18
git_last_commit: b8a1d96
git_last_commit_date: 2023-10-24 11:49:34 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

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: 1.0.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings gDRutils_1.0.0.tar.gz
StartedAt: 2023-11-02 10:43:34 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 10:48:00 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 265.4 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings gDRutils_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/gDRutils.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* 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 ‘1.0.0’
* 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 R 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 ... 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

gDRutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL gDRutils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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 461 ]
> 
> proc.time()
   user  system elapsed 
 59.664   1.695  61.192 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply1.3360.0401.396
SE_metadata0.0460.0000.046
aggregate_assay0.7350.0440.780
apply_bumpy_function2.1850.0952.285
assert_choices000
cap_xc50000
convert_combo_data_to_dt1.6230.0761.704
convert_mae_assay_to_dt0.0760.0000.076
convert_mae_to_json0.1030.0110.115
convert_se_assay_to_dt0.0740.0030.077
convert_se_to_json0.0240.0000.024
demote_fields0.4690.0200.481
df_to_bm_assay0.1440.0040.148
dot-convert_colData_to_json0.0030.0000.003
dot-convert_metadata_to_json0.0060.0000.005
dot-convert_rowData_to_json0.0040.0000.003
dot-set_constant_fit_params0.0010.0000.001
dot-set_invalid_fit_params000
extend_normalization_type_name0.0010.0000.000
fit_curves0.2410.0160.264
flatten0.0120.0000.012
gen_synthetic_data0.0030.0000.003
get_MAE_identifiers0.0060.0040.009
get_assay_names0.0010.0000.000
get_combo_assay_names0.0010.0000.001
get_combo_base_assay_names0.0010.0000.001
get_combo_col_settings0.0050.0000.005
get_combo_score_assay_names0.0010.0000.001
get_default_identifiers0.0010.0000.000
get_env_assay_names000
get_expect_one_identifiers000
get_experiment_groups0.0000.0000.001
get_identifiers_dt0.0070.0000.007
get_idfs_synonyms000
get_iso_colors0.0020.0000.002
get_non_empty_assays0.0710.0000.071
get_required_identifiers000
get_synthetic_data0.0130.0000.013
get_testdata0.0880.0080.096
headers0.0070.0000.007
identifiers000
identify_unique_se_metadata_fields0.0080.0000.008
is_any_exp_empty0.0640.0000.062
is_exp_empty0.0640.0000.063
is_mae_empty0.0640.0000.062
logisticFit0.0250.0000.025
loop000
mcolData0.0170.0000.017
merge_SE2.2620.0122.266
merge_assay0.4340.0040.439
merge_metadata0.0090.0000.009
mrowData0.0170.0000.017
predict_conc_from_efficacy000
predict_efficacy_from_conc000
prettify_flat_metrics0.0060.0000.007
promote_fields0.2990.0080.306
refine_coldata0.0110.0000.012
refine_rowdata0.060.000.06
rename_DFrame0.0110.0000.012
rename_bumpy0.0360.0040.041
shorten_normalization_type_name0.0000.0000.001
split_SE_components0.0390.0000.040
standardize_mae0.1990.0000.204
standardize_se0.0410.0000.042
update_env_idfs_from_mae0.0010.0000.002
update_idfs_synonyms0.0000.0000.001
validate_MAE0.0970.0000.097
validate_SE0.0340.0040.038
validate_identifiers0.0070.0040.011
validate_json000
validate_mae_with_schema0.5760.0480.768
validate_se_assay_name0.0060.0030.008