Back to Multiple platform build/check report for BioC 3.21:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-12-24 11:39 -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 116/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.15.36  (landing page)
Aditya Bhagwat
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: devel
git_last_commit: 5cb516d
git_last_commit_date: 2024-12-04 06:05:33 -0500 (Wed, 04 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 autonomics on nebbiolo1

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: 1.15.36
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings autonomics_1.15.36.tar.gz
StartedAt: 2024-12-23 19:50:18 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 20:05:25 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 907.0 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings autonomics_1.15.36.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.15.36’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
read_diann_proteingroups 103.026  1.031  98.899
read_rnaseq_counts        27.181  1.982  28.839
fit                       21.070  0.343  20.676
rm_diann_contaminants     20.707  0.703  21.499
plot_exprs_per_coef       18.681  0.275  18.860
plot_exprs                18.441  0.481  18.784
default_formula           16.822  1.034  17.430
plot_volcano              16.296  0.237  16.441
read_somascan             12.704  0.473  13.124
read_metabolon            13.114  0.020  13.040
plot_summary              12.031  0.179  12.117
analyze                   11.910  0.180  11.973
plot_densities             8.810  0.391   9.109
ftype                      6.985  0.083   6.806
plot_sample_nas            6.229  0.085   6.255
fcluster                   5.898  0.198   6.040
extract_coef_features      5.437  0.218   5.623
read_fragpipe              5.539  0.019   5.251
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck/00check.log’
for details.


Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(testthat)
> library(autonomics)

Attaching package: 'autonomics'

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

    biplot, loadings

The following object is masked from 'package:base':

    beta

> 
> test_check("autonomics")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 156 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test-8_fit.R:89:5', 'test-8_fit.R:99:5'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 156 ]
> 
> proc.time()
   user  system elapsed 
136.466   3.683 137.453 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0010.0000.000
COMPOUNDDISCOVERER_PATTERNS0.0000.0000.001
CONTAMINANTSURL0.0000.0000.001
FITSEP0.0010.0000.000
LINMOD_ENGINES000
MAXQUANT_PATTERNS0.0000.0000.001
TAXON_TO_ORGNAME0.0000.0000.001
TESTS0.0000.0010.000
X1.4850.0671.528
abstract_fit1.0730.1031.153
add_adjusted_pvalues1.1770.0801.258
add_assay_means0.3240.0360.360
add_facetvars1.3070.0711.356
add_opentargets_by_uniprot0.3600.0070.370
add_psp0.4610.0150.477
add_smiles0.4140.0280.417
analysis0.3320.0030.335
analyze11.910 0.18011.973
annotate_maxquant0.8840.0200.905
annotate_uniprot_rest0.2550.0131.895
assert_is_valid_sumexp0.5170.0230.503
bin1.1640.1661.331
biplot3.3340.1513.464
biplot_corrections2.9410.1433.063
biplot_covariates4.8460.1394.964
block2lme0.0010.0020.003
center1.3690.0321.400
code4.7910.1424.910
coefs0.6880.0210.689
collapsed_entrezg_to_symbol0.0000.0000.001
contrast_subgroup_cols0.5450.0610.583
count_in0.0020.0000.002
counts0.2930.0180.312
counts2cpm0.2750.0040.280
counts2tpm0.2510.0010.253
cpm0.2940.0020.296
create_design0.6410.0220.642
default_coefs0.6320.0160.626
default_formula16.822 1.03417.430
default_geom0.4590.0100.447
default_sfile0.0010.0010.002
demultiplex0.0120.0020.013
dequantify0.0030.0000.002
dequantify_compounddiscoverer0.0010.0000.001
dot-merge0.0150.0000.016
dot-plot_survival4.0140.2674.280
dot-read_maxquant_proteingroups0.1060.0070.112
download_contaminants000
download_data0.0000.0010.000
download_gtf000
download_mcclain210.0000.0000.001
dt2mat0.0020.0010.003
enrichment1.2520.0541.306
entrezg_to_symbol0.0000.0000.001
extract_coef_features5.4370.2185.623
extract_rectangle0.0950.0200.115
fcluster5.8980.1986.040
fcor1.0080.0511.059
fdata0.5050.0150.520
fdr2p0.8540.0240.856
filter_exprs_replicated_in_some_subgroup0.9470.0370.924
filter_features0.4690.0140.462
filter_medoid0.6200.0090.630
filter_samples0.5110.0090.499
fit21.070 0.34320.676
fitcoefs0.6930.0160.687
fits0.6890.0170.684
fitvars0.9630.0140.955
fix_xlgenes0.0020.0000.002
flevels0.3760.0110.386
fnames0.4610.0420.503
formula2str0.0000.0010.001
ftype6.9850.0836.806
fvalues0.3830.0050.388
fvars0.3680.0040.372
genome_to_orgdb0.0000.0000.001
group_by_level0.0020.0000.002
guess_compounddiscoverer_quantity0.0000.0010.001
guess_fitsep0.4180.0090.427
guess_maxquant_quantity0.0040.0020.006
guess_sep0.4630.0160.456
has_multiple_levels0.0540.0030.056
hdlproteins0.0410.0210.064
impute2.8470.0212.868
invert_subgroups0.5820.0050.587
is_collapsed_subset0.0010.0000.001
is_correlation_matrix0.0020.0000.001
is_diann_report0.4530.0440.480
is_fastadt0.0790.0040.083
is_file0.0000.0000.001
is_fraction0.0010.0010.002
is_imputed0.7080.0200.727
is_positive_number0.0020.0000.002
is_scalar_subset0.2960.0030.300
is_sig1.3040.0111.316
is_valid_formula0.0430.0080.051
keep_connected_blocks0.4820.0530.506
keep_connected_features0.6660.0910.711
keep_replicated_features0.8180.1120.867
label2index0.0010.0000.001
list2mat0.0000.0010.001
log2counts0.2990.0340.334
log2cpm0.2890.0350.324
log2diffs0.2980.0340.333
log2proteins0.2890.0340.323
log2sites0.2940.0300.324
log2tpm0.4730.0960.569
log2transform3.5660.3563.924
logical2factor0.0000.0020.003
make_alpha_palette0.5080.0840.569
make_colors0.0100.0010.011
make_volcano_dt0.7850.0510.836
map_fvalues0.3560.0270.383
matrix2sumexp0.8650.0940.931
merge_sample_file0.4090.0270.436
merge_sdata0.5060.0440.529
message_df0.0020.0010.003
model_coefs0.7260.0800.769
modelvar3.1390.1703.227
order_on_p0.9530.1001.019
pca2.7670.0912.836
pg_to_canonical0.0060.0000.005
plot_contrast_venn2.2150.0742.143
plot_contrastogram2.8000.1952.905
plot_data1.2080.0491.222
plot_densities8.8100.3919.109
plot_design0.5430.0200.562
plot_exprs18.441 0.48118.784
plot_exprs_per_coef18.681 0.27518.860
plot_fit_summary1.8480.0531.843
plot_heatmap1.7310.0141.744
plot_joint_density2.8250.1112.905
plot_matrix0.5310.0420.532
plot_sample_nas6.2290.0856.255
plot_subgroup_points4.4800.0404.481
plot_summary12.031 0.17912.117
plot_venn0.0150.0020.017
plot_venn_heatmap0.0210.0010.023
plot_violins3.8710.0943.932
plot_volcano16.296 0.23716.441
preprocess_rnaseq_counts0.2680.0050.273
pull_columns0.0020.0010.003
read_affymetrix0.0010.0000.000
read_contaminants0.0970.0042.920
read_diann_proteingroups103.026 1.031 98.899
read_fragpipe5.5390.0195.251
read_maxquant_phosphosites1.3940.0041.398
read_maxquant_proteingroups1.1920.0041.196
read_metabolon13.114 0.02013.040
read_msigdt0.0010.0000.001
read_olink1.1530.0081.102
read_rectangles0.1620.0060.169
read_rnaseq_counts27.181 1.98228.839
read_salmon000
read_somascan12.704 0.47313.124
read_uniprotdt0.2810.0200.301
reset_fit4.1670.0794.152
rm_diann_contaminants20.707 0.70321.499
rm_missing_in_some_samples0.6320.0160.623
rm_unmatched_samples0.5890.0020.590
scaledlibsizes0.2830.0000.282
scoremat1.0240.0291.028
slevels0.3930.0060.399
snames0.3870.0040.391
split_extract_fixed0.6250.0580.659
split_samples1.1900.0181.182
stri_any_regex0.0010.0000.000
stri_detect_fixed_in_collapsed0.3410.0060.347
subgroup_matrix0.5390.0140.527
subtract_baseline4.3360.0254.304
sumexp_to_longdt1.7930.0591.791
sumexp_to_tsv0.4660.0030.468
sumexplist_to_longdt1.4230.0161.438
summarize_fit1.6780.0211.585
svalues0.3880.0320.421
svars0.4050.0060.410
systematic_nas0.6330.0190.653
tag_features0.9270.0370.965
tag_hdlproteins0.5180.0280.545
taxon2org0.0020.0000.001
tpm0.2870.0170.304
uncollapse0.0320.0020.033
values0.4910.0360.527
varlevels_dont_clash0.0280.0000.028
venn_detects0.5270.0070.534
weights0.2960.0040.300
write_xl0.6460.0150.639
zero_to_na0.0010.0010.002