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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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: 2024-06-12 14:00 -0400 (Wed, 12 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


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: 2024-06-12 20:39:21 -0400 (Wed, 12 Jun 2024)
EndedAt: 2024-06-12 20:54:11 -0400 (Wed, 12 Jun 2024)
EllapsedTime: 890.8 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
###
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* 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 88.182  1.344  85.005
read_rnaseq_counts       28.334  2.598  30.667
rm_diann_contaminants    19.214  0.548  19.605
plot_exprs               18.696  0.232  18.801
plot_exprs_per_coef      17.579  0.160  17.584
default_formula          14.090  0.544  14.248
fit                      12.333  0.400  11.941
read_somascan            12.034  0.316  12.273
analyze                  12.033  0.096  12.049
read_metabolon           11.642  0.024  11.557
plot_summary             11.039  0.080  11.035
plot_volcano              8.998  0.048   8.993
plot_densities            8.860  0.184   8.978
plot_sample_nas           5.661  0.036   5.648
read_fragpipe             5.349  0.060   5.135
biplot_covariates         4.867  0.156   5.002
* 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

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###
### 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 
125.097   3.829 126.052 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0010.0000.001
CONTAMINANTSURL000
FITSEP000
LINMOD_ENGINES0.0000.0000.001
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME000
TESTS000
abstract_fit1.2340.0161.227
add_adjusted_pvalues0.5380.0200.559
add_assay_means0.4320.0110.444
add_facetvars2.1400.0642.182
add_opentargets_by_uniprot0.3950.0030.401
add_psp0.5010.0130.514
add_smiles0.4620.0200.462
analysis0.3750.0080.383
analyze12.033 0.09612.049
annotate_maxquant0.8700.0280.898
annotate_uniprot_rest0.3810.0272.732
assert_is_valid_sumexp0.6480.0480.671
bin0.3810.0240.405
biplot3.4860.2123.664
biplot_corrections3.0360.0963.111
biplot_covariates4.8670.1565.002
block2lme0.0030.0000.003
center2.0810.1002.182
code4.4860.0844.550
coefs0.6660.0040.651
collapsed_entrezg_to_symbol0.0010.0000.001
contrast_subgroup_cols0.5440.0250.549
count_in0.0000.0010.001
counts0.3720.0100.383
counts2cpm0.3560.0080.364
counts2tpm0.3340.0040.338
cpm0.3480.0080.357
create_design0.6750.0440.697
default_formula14.090 0.54414.248
default_geom0.5120.0120.504
default_sfile0.0010.0000.001
demultiplex0.0140.0000.014
dequantify0.0010.0020.002
dot-merge0.0160.0010.018
dot-plot_survival4.1920.2244.416
dot-read_maxquant_proteingroups0.1210.0000.121
download_contaminants0.170.022.17
download_data0.0010.0000.000
download_gtf0.0010.0000.000
download_mcclain210.0010.0000.000
dt2mat0.0020.0030.004
enrichment1.1190.1241.244
entrezg_to_symbol0.0010.0000.001
explore_transformations3.4790.3573.836
extract_coef_features4.5890.3444.896
extract_rectangle0.1020.0160.118
fdata0.5160.0200.537
fdr2p0.8270.0520.858
filter_exprs_replicated_in_some_subgroup1.0100.0561.010
filter_features0.5130.0360.524
filter_medoid0.7260.0680.794
filter_samples0.5050.0240.496
fit12.333 0.40011.941
fit_lmx4.2180.0404.072
fitcoefs0.7370.0760.793
fits0.7000.0200.699
fitvars0.9820.0320.993
fix_xlgenes0.0020.0000.002
flevels0.4080.0040.412
fnames0.4460.0080.454
formula2str000
fvalues0.4040.0360.440
fvars0.3930.0120.405
genome_to_orgdb0.0010.0000.001
group_by_level0.0000.0020.002
guess_fitsep0.4850.0060.491
guess_maxquant_quantity0.0060.0000.006
guess_sep0.5130.0160.508
has_multiple_levels0.0460.0120.057
hdlproteins0.0450.0280.076
impute3.0100.0443.054
invert_subgroups0.7090.0160.724
is_collapsed_subset000
is_diann_report0.4500.0360.438
is_fastadt0.0630.0000.062
is_file0.0010.0000.000
is_fraction0.0010.0000.002
is_imputed0.7290.0040.733
is_positive_number0.0020.0000.002
is_scalar_subset0.3770.0200.397
is_sig1.1800.0921.273
is_valid_formula0.0400.0040.043
keep_connected_blocks0.5270.0160.515
keep_connected_features0.7500.0160.725
keep_replicated_features0.8460.0390.826
label2index0.0010.0000.001
list2mat0.0010.0000.001
log2counts0.4080.0120.420
log2cpm0.3780.0040.382
log2diffs0.3200.0000.321
log2proteins0.3140.0160.330
log2sites0.3450.0000.345
log2tpm0.5300.0320.562
log2transform3.3960.0163.412
logical2factor0.0020.0000.002
make_alpha_palette0.5340.0240.538
make_colors0.010.000.01
make_volcano_dt0.7720.0080.780
map_fvalues0.3870.0080.395
matrix2sumexp0.9280.0240.932
merge_sample_file0.4380.0160.453
merge_sdata0.5470.0080.533
message_df0.0030.0000.002
modelvar1.5840.0361.565
order_on_p0.8960.0150.890
pca2.8290.0522.845
pg_to_canonical0.0060.0000.006
plot_contrast_venn1.8730.0721.865
plot_contrastogram2.3200.0602.298
plot_data1.2950.0161.291
plot_densities8.8600.1848.978
plot_design0.6430.0040.646
plot_exprs18.696 0.23218.801
plot_exprs_per_coef17.579 0.16017.584
plot_fit_summary1.7190.0281.642
plot_heatmap1.5840.0081.592
plot_matrix0.5080.0080.478
plot_sample_nas5.6610.0365.648
plot_subgroup_points4.1330.0364.131
plot_summary11.039 0.08011.035
plot_venn0.0120.0040.016
plot_venn_heatmap0.0330.0040.038
plot_violins3.5200.0683.569
plot_volcano8.9980.0488.993
preprocess_rnaseq_counts0.3930.0040.397
pull_columns0.0030.0000.002
read_affymetrix0.0000.0000.001
read_contaminants0.1220.0041.296
read_diann_proteingroups88.182 1.34485.005
read_fragpipe5.3490.0605.135
read_maxquant_phosphosites1.5510.0041.555
read_maxquant_proteingroups1.3140.0041.318
read_metabolon11.642 0.02411.557
read_msigdt0.0010.0000.001
read_olink1.2970.0561.307
read_rectangles0.1610.0120.173
read_rnaseq_counts28.334 2.59830.667
read_salmon000
read_somascan12.034 0.31612.273
read_uniprotdt0.2640.0320.297
reset_fit4.3220.1004.331
rm_diann_contaminants19.214 0.54819.605
rm_missing_in_some_samples0.6130.0720.657
rm_unmatched_samples0.5720.0760.647
scaledlibsizes0.4420.0880.531
scoremat1.0080.1081.095
slevels0.5060.0760.582
snames0.3930.0520.446
split_extract_fixed0.5320.0520.562
split_samples1.1580.1681.305
stri_any_regex000
stri_detect_fixed_in_collapsed0.3550.0400.395
subgroup_matrix0.5410.0480.568
subtract_baseline4.1830.3724.496
sumexp_to_longdt1.9290.1201.994
sumexp_to_tsv0.4920.0360.528
sumexplist_to_longdt1.5790.0761.654
summarize_fit1.4830.1041.530
svalues0.3990.0400.438
svars0.4530.0320.484
systematic_nas0.5160.0080.523
tag_features0.8330.0440.877
tag_hdlproteins0.4960.0320.528
taxon2org0.0010.0000.001
tpm0.4040.0280.431
uncollapse0.0070.0040.011
values0.4390.0320.472
varlevels_dont_clash0.0200.0070.028
venn_detects0.5290.0600.589
weights0.5720.0840.657
write_xl0.6760.0160.672
zero_to_na0.0000.0020.002