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This page was generated on 2024-05-04 11:38:51 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 112/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.12.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: RELEASE_3_19
git_last_commit: a23e37e
git_last_commit_date: 2024-04-30 11:31:54 -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    ERROR  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for autonomics on lconway


To the developers/maintainers of the autonomics package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/autonomics.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: autonomics
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.12.0.tar.gz
StartedAt: 2024-05-03 20:11:02 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 20:26:00 -0400 (Fri, 03 May 2024)
EllapsedTime: 898.0 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘autonomics’ 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 ... NOTE
checkRd: (-1) dequantify.Rd:24: Lost braces; missing escapes or markup?
    24 | Encode {channel} as suffix.
       |        ^
* 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
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
read_diann_proteingroups 105.359  2.427 109.048
read_rnaseq_counts        29.858  3.459  33.824
rm_diann_contaminants     22.303  0.638  23.175
plot_exprs                21.922  0.369  22.524
plot_exprs_per_coef       20.108  0.241  20.514
default_formula           15.002  0.467  15.673
read_somascan             13.625  0.136  13.880
analyze                   13.380  0.220  13.726
fit                       13.160  0.250  13.524
plot_summary              13.025  0.154  13.269
read_metabolon            12.873  0.142  13.091
plot_volcano              10.868  0.186  11.165
plot_densities             8.567  0.213   8.858
plot_sample_nas            6.652  0.084   6.807
read_fragpipe              5.941  0.190   6.184
biplot_covariates          5.710  0.107   5.870
dot-plot_survival          4.681  0.609   5.361
code                       5.095  0.100   5.245
subtract_baseline          5.001  0.127   5.213
log2transform              4.976  0.092   5.121
reset_fit                  4.958  0.100   5.119
extract_coef_features      4.916  0.138   5.089
* 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck/00check.log’
for details.


Installation output

autonomics.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘autonomics’ ...
** 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 (autonomics)

Tests output

autonomics.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup"
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(testthat)
> library(autonomics)

Attaching package: 'autonomics'

The following objects are masked from 'package:stats':

    biplot, loadings

> 
> test_check("autonomics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 159 ]
> 
> proc.time()
   user  system elapsed 
149.329   9.048 160.828 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0000.001
CONTAMINANTSURL000
FITSEP000
LINMOD_ENGINES000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME0.0000.0000.001
TESTS000
abstract_fit1.4950.0971.616
add_adjusted_pvalues0.6840.0290.721
add_assay_means0.5180.0140.537
add_facetvars2.4020.1352.567
add_opentargets_by_uniprot0.4670.0120.486
add_psp0.5730.0160.594
add_smiles0.5740.0560.643
analysis0.4710.0130.491
analyze13.380 0.22013.726
annotate_maxquant0.8980.0420.952
annotate_uniprot_rest0.0850.0172.525
assert_is_valid_sumexp0.6540.0650.730
bin0.4280.0130.444
biplot4.0070.1134.162
biplot_corrections3.5040.0943.634
biplot_covariates5.7100.1075.870
block2lme0.0040.0010.005
center2.3750.0392.433
code5.0950.1005.245
coefs0.7520.0480.807
collapsed_entrezg_to_symbol0.0010.0000.001
contrast_subgroup_cols0.6220.0530.684
count_in0.0010.0000.001
counts0.4210.0060.431
counts2cpm0.4100.0050.416
counts2tpm0.3990.0060.409
cpm0.4090.0060.420
create_design0.7280.0470.781
default_formula15.002 0.46715.673
default_geom0.6410.0640.720
default_sfile0.0010.0000.002
demultiplex0.0130.0000.013
dequantify0.0030.0000.003
dot-merge0.0250.0010.025
dot-plot_survival4.6810.6095.361
dot-read_maxquant_proteingroups0.1160.0050.124
download_contaminants0.0240.0072.740
download_data0.0000.0010.002
download_gtf000
download_mcclain210.0000.0000.002
dt2mat0.0030.0000.004
enrichment1.1800.0391.225
entrezg_to_symbol0.0010.0000.001
explore_transformations3.6710.1123.814
extract_coef_features4.9160.1385.089
extract_rectangle0.1560.0500.209
fdata0.5400.0120.553
fdr2p0.9980.0671.076
filter_exprs_replicated_in_some_subgroup1.0920.0611.164
filter_features0.6120.0560.678
filter_medoid0.9160.0300.954
filter_samples0.5910.0460.642
fit13.160 0.25013.524
fit_lmx4.7370.1104.898
fitcoefs0.8500.0580.924
fits0.7980.0510.855
fitvars1.1720.0571.244
fix_xlgenes0.0020.0000.003
flevels0.4830.0090.497
fnames0.4580.0090.470
formula2str0.0010.0010.001
fvalues0.3920.0070.401
fvars0.4620.0100.477
genome_to_orgdb0.0010.0000.000
group_by_level0.0010.0000.002
guess_fitsep0.5010.0100.517
guess_maxquant_quantity0.0070.0020.008
guess_sep0.5400.0400.583
has_multiple_levels0.0500.0010.053
hdlproteins0.0480.0350.089
impute3.2280.0493.295
invert_subgroups0.7270.0080.739
is_collapsed_subset0.0010.0000.000
is_diann_report0.2470.0540.376
is_fastadt0.0740.0020.076
is_file000
is_fraction0.0020.0000.002
is_imputed0.8110.0100.823
is_positive_number0.0020.0000.003
is_scalar_subset0.3860.0070.394
is_sig1.3850.0181.411
is_valid_formula0.0580.0020.060
keep_connected_blocks0.6360.0490.691
keep_connected_features0.8310.0540.895
keep_replicated_features0.9210.0520.984
label2index0.0010.0010.001
list2mat0.0010.0000.002
log2counts0.4890.0060.498
log2cpm0.4270.0040.434
log2diffs0.3740.0060.383
log2proteins0.3990.0070.408
log2sites0.3890.0080.401
log2tpm0.4690.0070.479
log2transform4.9760.0925.121
logical2factor0.0010.0000.002
make_alpha_palette0.5010.0480.557
make_colors0.0110.0020.013
make_volcano_dt0.8770.0180.904
map_fvalues0.4480.0120.464
matrix2sumexp0.9890.0541.053
merge_sample_file0.5110.0140.529
merge_sdata0.6850.0740.772
message_df0.0030.0000.004
modelvar1.6780.0731.774
order_on_p1.0890.0601.162
pca3.1620.0923.283
pg_to_canonical0.0060.0000.007
plot_contrast_venn1.9360.0662.024
plot_contrastogram2.5920.1952.826
plot_data1.3020.0651.390
plot_densities8.5670.2138.858
plot_design0.6550.0140.678
plot_exprs21.922 0.36922.524
plot_exprs_per_coef20.108 0.24120.514
plot_fit_summary2.0220.0692.109
plot_heatmap1.9840.0322.038
plot_matrix0.6080.0580.674
plot_sample_nas6.6520.0846.807
plot_subgroup_points4.8380.0974.980
plot_summary13.025 0.15413.269
plot_venn0.0170.0010.019
plot_venn_heatmap0.0470.0040.052
plot_violins4.3950.1154.549
plot_volcano10.868 0.18611.165
preprocess_rnaseq_counts0.4660.0060.476
pull_columns0.0030.0010.004
read_affymetrix0.0000.0010.001
read_contaminants0.0110.0020.014
read_diann_proteingroups105.359 2.427109.048
read_fragpipe5.9410.1906.184
read_maxquant_phosphosites1.7170.0321.825
read_maxquant_proteingroups1.3500.0271.386
read_metabolon12.873 0.14213.091
read_msigdt0.0010.0000.001
read_olink1.4490.0691.534
read_rectangles0.2130.0270.242
read_rnaseq_counts29.858 3.45933.824
read_salmon000
read_somascan13.625 0.13613.880
read_uniprotdt0.2790.0170.298
reset_fit4.9580.1005.119
rm_diann_contaminants22.303 0.63823.175
rm_missing_in_some_samples0.6070.0610.674
rm_unmatched_samples0.6580.0110.678
scaledlibsizes0.4870.0080.502
scoremat1.2350.0801.336
slevels0.5230.0160.550
snames0.5300.0110.547
split_extract_fixed0.5540.0530.614
split_samples1.3600.0751.455
stri_any_regex0.0000.0010.002
stri_detect_fixed_in_collapsed0.3960.0100.414
subgroup_matrix0.6190.0510.677
subtract_baseline5.0010.1275.213
sumexp_to_longdt2.1470.1052.278
sumexp_to_tsv0.5360.0110.554
sumexplist_to_longdt1.8610.0361.915
summarize_fit1.7170.0691.811
svalues0.4350.0090.449
svars0.4320.0090.447
systematic_nas0.6650.0100.680
tag_features1.0110.0401.067
tag_hdlproteins0.5760.0410.625
taxon2org0.0010.0000.001
tpm0.4550.0060.467
uncollapse0.0110.0000.011
values0.5680.0200.596
varlevels_dont_clash0.0220.0010.023
venn_detects0.6490.0120.668
weights0.4980.0070.512
write_xl0.8750.0650.958
zero_to_na0.0020.0000.003