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This page was generated on 2024-06-07 20:24 -0400 (Fri, 07 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4755
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4489
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4520
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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 1.12.1  (landing page)
Aditya Bhagwat
Snapshot Date: 2024-06-05 14:00:26 -0400 (Wed, 05 Jun 2024)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: RELEASE_3_19
git_last_commit: 1da6999
git_last_commit_date: 2024-06-05 05:58:13 -0400 (Wed, 05 Jun 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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 1.12.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings autonomics_1.12.1.tar.gz
StartedAt: 2024-06-05 20:38:23 -0400 (Wed, 05 Jun 2024)
EndedAt: 2024-06-05 20:53:17 -0400 (Wed, 05 Jun 2024)
EllapsedTime: 893.8 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings autonomics_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.12.1’
* 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 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) 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 87.538  3.773  86.795
read_rnaseq_counts       27.176  0.896  27.821
plot_exprs               19.262  0.272  19.440
rm_diann_contaminants    18.418  0.296  18.722
plot_exprs_per_coef      16.994  0.224  17.142
default_formula          14.351  0.551  14.493
fit                      12.013  0.468  11.681
read_somascan            11.913  0.016  11.881
analyze                  11.568  0.175  11.655
read_metabolon           11.552  0.052  11.475
plot_summary             10.959  0.123  10.999
plot_volcano              9.083  0.045   9.069
plot_densities            7.897  0.127   7.952
plot_sample_nas           5.649  0.008   5.608
read_fragpipe             5.508  0.144   5.340
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck/00check.log’
for details.


Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
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

> 
> test_check("autonomics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 159 ]
> 
> proc.time()
   user  system elapsed 
129.750   3.975 131.257 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
CONTAMINANTSURL000
FITSEP0.0010.0010.000
LINMOD_ENGINES000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME0.0000.0010.000
TESTS0.0000.0000.001
abstract_fit1.1960.0571.232
add_adjusted_pvalues0.5950.0290.629
add_assay_means0.9980.0401.038
add_facetvars1.4640.0521.496
add_opentargets_by_uniprot0.3830.0040.389
add_psp0.5170.0110.529
add_smiles0.4480.0080.436
analysis0.370.000.37
analyze11.568 0.17511.655
annotate_maxquant0.8040.0440.848
annotate_uniprot_rest0.3130.0082.323
assert_is_valid_sumexp0.6590.0680.704
bin0.4010.0160.416
biplot4.1860.3164.479
biplot_corrections2.8900.1363.005
biplot_covariates4.6860.1484.813
block2lme0.0030.0000.004
center1.3340.0361.370
code4.6960.1124.787
coefs0.6660.0160.662
collapsed_entrezg_to_symbol0.0010.0000.000
contrast_subgroup_cols0.5640.0120.555
count_in0.0010.0000.001
counts0.3950.0040.399
counts2cpm0.3890.0160.405
counts2tpm0.3330.0040.337
cpm0.3610.0000.360
create_design0.6800.0360.697
default_formula14.351 0.55114.493
default_geom0.5330.0080.512
default_sfile0.0010.0000.001
demultiplex0.0140.0000.014
dequantify0.0020.0000.002
dot-merge0.0160.0000.016
dot-plot_survival4.0350.3404.375
dot-read_maxquant_proteingroups0.1230.0000.124
download_contaminants0.1300.0032.625
download_data0.0010.0000.001
download_gtf000
download_mcclain210.0010.0000.001
dt2mat0.0070.0000.008
enrichment1.0990.1131.213
entrezg_to_symbol0.0010.0000.001
explore_transformations3.4940.4033.898
extract_coef_features4.4500.3484.777
extract_rectangle0.1020.0240.125
fdata0.5580.0320.590
fdr2p0.9170.0480.944
filter_exprs_replicated_in_some_subgroup1.1200.0601.081
filter_features0.5440.0270.533
filter_medoid0.7180.0880.805
filter_samples0.5220.0150.499
fit12.013 0.46811.681
fit_lmx4.1470.1004.064
fitcoefs0.7540.0480.780
fits0.700.040.72
fitvars0.9970.0321.008
fix_xlgenes0.0000.0020.002
flevels0.3980.0130.411
fnames0.4690.0080.478
formula2str0.0000.0000.001
fvalues0.4290.0080.437
fvars0.4440.0160.461
genome_to_orgdb0.0010.0000.001
group_by_level0.0020.0000.001
guess_fitsep0.4520.0000.452
guess_maxquant_quantity0.0060.0000.005
guess_sep0.5010.0120.491
has_multiple_levels0.0560.0040.059
hdlproteins0.0620.0400.104
impute2.9280.0482.975
invert_subgroups0.6280.0000.628
is_collapsed_subset0.0010.0000.001
is_diann_report0.3990.0470.418
is_fastadt0.0620.0000.062
is_file000
is_fraction0.0020.0000.002
is_imputed0.6950.0280.723
is_positive_number0.0020.0000.002
is_scalar_subset0.3420.0160.358
is_sig1.1330.0161.149
is_valid_formula0.0340.0080.042
keep_connected_blocks0.5470.0280.549
keep_connected_features0.6790.0570.696
keep_replicated_features0.8360.0320.812
label2index0.0010.0000.001
list2mat0.0010.0000.001
log2counts0.5120.0160.528
log2cpm0.3790.0000.379
log2diffs0.3410.0030.345
log2proteins0.3310.0080.339
log2sites0.3240.0080.332
log2tpm0.4060.0040.410
log2transform3.5360.0163.552
logical2factor0.0010.0000.001
make_alpha_palette0.5330.0040.516
make_colors0.010.000.01
make_volcano_dt0.8070.0000.808
map_fvalues0.4160.0000.417
matrix2sumexp0.8990.0160.894
merge_sample_file0.4280.0200.449
merge_sdata0.6190.0160.599
message_df0.0030.0000.002
modelvar1.5990.0241.517
order_on_p0.8970.0360.894
pca2.8000.0762.838
pg_to_canonical0.0050.0000.005
plot_contrast_venn1.7690.0481.737
plot_contrastogram2.1870.0522.154
plot_data1.2100.0121.200
plot_densities7.8970.1277.952
plot_design0.6070.0080.616
plot_exprs19.262 0.27219.440
plot_exprs_per_coef16.994 0.22417.142
plot_fit_summary1.6620.0371.640
plot_heatmap1.6310.0081.639
plot_matrix0.4900.0080.476
plot_sample_nas5.6490.0085.608
plot_subgroup_points4.1800.0364.175
plot_summary10.959 0.12310.999
plot_venn0.0170.0000.017
plot_venn_heatmap0.0370.0040.041
plot_violins3.5250.0563.559
plot_volcano9.0830.0459.069
preprocess_rnaseq_counts0.3420.0000.342
pull_columns0.0000.0020.002
read_affymetrix0.0000.0010.000
read_contaminants0.0880.0121.259
read_diann_proteingroups87.538 3.77386.795
read_fragpipe5.5080.1445.340
read_maxquant_phosphosites1.5470.0081.555
read_maxquant_proteingroups1.2990.0121.311
read_metabolon11.552 0.05211.475
read_msigdt0.0010.0000.000
read_olink1.2390.0651.265
read_rectangles0.1680.0160.184
read_rnaseq_counts27.176 0.89627.821
read_salmon0.0010.0000.000
read_somascan11.913 0.01611.881
read_uniprotdt0.2740.0120.286
reset_fit4.1570.0044.072
rm_diann_contaminants18.418 0.29618.722
rm_missing_in_some_samples0.4920.0080.479
rm_unmatched_samples0.5270.0400.566
scaledlibsizes0.4110.0560.466
scoremat0.9820.0881.033
slevels0.4920.0760.567
snames0.4160.0320.449
split_extract_fixed0.5140.0560.548
split_samples1.2110.1681.341
stri_any_regex0.0010.0000.001
stri_detect_fixed_in_collapsed0.3650.0280.393
subgroup_matrix0.5410.0400.558
subtract_baseline4.2980.4074.644
sumexp_to_longdt1.8980.0931.935
sumexp_to_tsv0.4970.0320.529
sumexplist_to_longdt1.6600.1081.769
summarize_fit1.5010.0641.503
svalues0.4250.0000.425
svars0.4150.0000.415
systematic_nas0.6040.0400.644
tag_features0.8270.1280.955
tag_hdlproteins0.5430.0280.571
taxon2org0.0010.0000.002
tpm0.4280.0560.484
uncollapse0.0090.0020.010
values0.4250.0130.438
varlevels_dont_clash0.0290.0000.029
venn_detects0.6000.0040.603
weights0.390.000.39
write_xl0.7710.0080.759
zero_to_na0.0020.0000.002