Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-25 17:39 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 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: 2024-06-23 14:00 -0400 (Sun, 23 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    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  


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: 2024-06-23 20:41:19 -0400 (Sun, 23 Jun 2024)
EndedAt: 2024-06-23 20:54:00 -0400 (Sun, 23 Jun 2024)
EllapsedTime: 760.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: autonomics.Rcheck
Warnings: NA

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 87.786  4.303  87.549
read_rnaseq_counts       25.975  1.127  26.922
plot_exprs               18.473  0.196  18.548
plot_exprs_per_coef      17.408  0.160  17.489
rm_diann_contaminants    17.051  0.296  17.354
default_formula          13.681  0.492  13.782
fit                      12.233  0.453  11.665
analyze                  11.322  0.128  11.350
read_metabolon           11.138  0.232  11.253
read_somascan            11.179  0.060  11.131
plot_summary             10.844  0.116  10.857
plot_volcano              9.046  0.092   9.079
plot_densities            8.547  0.216   8.683
plot_sample_nas           5.543  0.024   5.499
reset_fit                 5.057  0.112   5.046
read_fragpipe             5.071  0.096   4.904
* 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 ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘autonomics_platformaware_analysis.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck/vign_test/autonomics/vignettes/autonomics_platformaware_analysis_files/figure-html/unnamed-chunk-2-1.png" but not available.
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161731/suppl//GSE161731_counts.csv.gz?tool=geoquery'
Content type 'application/x-gzip' length 8347405 bytes (8.0 MB)
==================================================
downloaded 8.0 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161731/suppl//GSE161731_counts_key.csv.gz?tool=geoquery'
Content type 'application/x-gzip' length 2443 bytes
==================================================
downloaded 2443 bytes

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161731/suppl//GSE161731_key.csv.gz?tool=geoquery'
Content type 'application/x-gzip' length 2398 bytes
==================================================
downloaded 2398 bytes

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161731/suppl//GSE161731_xpr_nlcpm.csv.gz?tool=geoquery'
Content type 'application/x-gzip' length 16839511 bytes (16.1 MB)

downloaded 16 KB


Quitting from lines 62-73 [unnamed-chunk-3] (autonomics_platformaware_analysis.Rmd)
Error: processing vignette 'autonomics_platformaware_analysis.Rmd' failed with diagnostics:
Failed to download /tmp/Rtmpw5KiR7/datasets/GSE161731/GSE161731_xpr_nlcpm.csv.gz!
--- failed re-building ‘autonomics_platformaware_analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘autonomics_platformaware_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 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 
126.299   3.951 127.667 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0000.001
CONTAMINANTSURL000
FITSEP000
LINMOD_ENGINES0.0000.0000.001
MAXQUANT_PATTERNS0.0010.0000.001
TAXON_TO_ORGNAME0.0010.0000.000
TESTS000
abstract_fit1.1990.0241.202
add_adjusted_pvalues0.5350.0240.560
add_assay_means0.4330.0160.449
add_facetvars2.2250.0642.268
add_opentargets_by_uniprot0.3940.0010.396
add_psp0.4920.0080.500
add_smiles0.4630.0160.452
analysis0.3670.0080.375
analyze11.322 0.12811.350
annotate_maxquant0.7900.0480.838
annotate_uniprot_rest0.2620.0162.288
assert_is_valid_sumexp0.5440.0240.547
bin0.3660.0030.369
biplot3.3540.0333.366
biplot_corrections2.9220.0672.968
biplot_covariates4.7010.0404.721
block2lme0.0030.0000.003
center2.0810.0642.145
code4.5980.0434.618
coefs0.6720.0160.668
collapsed_entrezg_to_symbol0.0000.0000.001
contrast_subgroup_cols0.5450.0230.550
count_in0.0010.0000.001
counts0.3590.0120.371
counts2cpm0.3470.0000.348
counts2tpm0.3260.0000.325
cpm0.3360.0000.336
create_design0.6700.0120.661
default_formula13.681 0.49213.782
default_geom0.5180.0160.505
default_sfile0.0000.0010.002
demultiplex0.0120.0020.014
dequantify0.0020.0000.002
dot-merge0.0180.0000.018
dot-plot_survival3.9780.1604.139
dot-read_maxquant_proteingroups0.1210.0000.121
download_contaminants0.1890.0002.769
download_data0.0010.0000.001
download_gtf000
download_mcclain210.0000.0010.001
dt2mat0.0020.0030.004
enrichment1.1050.0001.105
entrezg_to_symbol0.0000.0000.001
explore_transformations3.2600.2243.485
extract_coef_features4.5360.4524.950
extract_rectangle0.0950.0240.119
fdata0.5060.0360.542
fdr2p0.8580.0270.864
filter_exprs_replicated_in_some_subgroup1.0550.0721.020
filter_features0.5230.0520.536
filter_medoid0.7110.0800.790
filter_samples0.5340.0360.531
fit12.233 0.45311.665
fit_lmx4.3620.1004.152
fitcoefs0.7240.0350.740
fits0.6730.0230.661
fitvars0.9780.0521.009
fix_xlgenes0.0020.0000.002
flevels0.4160.0000.417
fnames0.460.000.46
formula2str0.0010.0000.000
fvalues0.4050.0080.412
fvars0.3940.0000.393
genome_to_orgdb0.0010.0000.000
group_by_level0.0010.0010.001
guess_fitsep0.4840.0220.506
guess_maxquant_quantity0.0060.0000.006
guess_sep0.4950.0360.509
has_multiple_levels0.0500.0040.054
hdlproteins0.0480.0240.075
impute2.9300.1043.034
invert_subgroups0.6090.0040.612
is_collapsed_subset0.0010.0000.001
is_diann_report0.4500.0520.462
is_fastadt0.0590.0000.058
is_file0.0010.0010.000
is_fraction0.0000.0020.001
is_imputed0.6830.0010.684
is_positive_number0.0020.0000.002
is_scalar_subset0.3480.0080.356
is_sig1.0940.0041.099
is_valid_formula0.0360.0040.040
keep_connected_blocks0.5230.0360.530
keep_connected_features0.7170.0240.697
keep_replicated_features0.8240.0160.773
label2index0.0010.0000.000
list2mat0.0010.0000.001
log2counts0.4270.0040.432
log2cpm0.3860.0120.399
log2diffs0.3390.0200.358
log2proteins0.3370.0040.341
log2sites0.3160.0040.320
log2tpm0.5090.0680.576
log2transform3.3610.0363.397
logical2factor0.0020.0000.001
make_alpha_palette0.5440.0200.540
make_colors0.0100.0000.009
make_volcano_dt0.7790.0070.787
map_fvalues0.3690.0040.372
matrix2sumexp0.8960.0370.909
merge_sample_file0.4420.0040.445
merge_sdata0.5420.0110.532
message_df0.0020.0010.003
modelvar1.5530.0321.525
order_on_p0.8940.0200.891
pca2.7250.0682.771
pg_to_canonical0.0050.0000.005
plot_contrast_venn1.8480.0281.788
plot_contrastogram2.2440.0752.225
plot_data1.1600.0211.156
plot_densities8.5470.2168.683
plot_design0.5550.0120.567
plot_exprs18.473 0.19618.548
plot_exprs_per_coef17.408 0.16017.489
plot_fit_summary1.7190.0161.677
plot_heatmap1.5900.0121.602
plot_matrix0.4620.0120.454
plot_sample_nas5.5430.0245.499
plot_subgroup_points4.0830.0324.052
plot_summary10.844 0.11610.857
plot_venn0.0160.0000.016
plot_venn_heatmap0.0380.0000.038
plot_violins3.3950.0403.415
plot_volcano9.0460.0929.079
preprocess_rnaseq_counts0.3360.0040.340
pull_columns0.0020.0000.002
read_affymetrix0.0000.0000.001
read_contaminants0.0820.0041.241
read_diann_proteingroups87.786 4.30387.549
read_fragpipe5.0710.0964.904
read_maxquant_phosphosites1.4280.0161.444
read_maxquant_proteingroups1.1950.0361.231
read_metabolon11.138 0.23211.253
read_msigdt0.0010.0000.001
read_olink1.2950.0161.239
read_rectangles0.1560.0160.172
read_rnaseq_counts25.975 1.12726.922
read_salmon0.0010.0000.000
read_somascan11.179 0.06011.131
read_uniprotdt0.2620.0160.278
reset_fit5.0570.1125.046
rm_diann_contaminants17.051 0.29617.354
rm_missing_in_some_samples0.5170.0320.527
rm_unmatched_samples0.5520.0070.560
scaledlibsizes0.3250.0000.325
scoremat0.8980.0320.909
slevels0.4320.0120.444
snames0.3860.0080.394
split_extract_fixed0.4730.0280.480
split_samples1.1100.0121.101
stri_any_regex0.0010.0000.000
stri_detect_fixed_in_collapsed0.3290.0040.333
subgroup_matrix0.5230.0080.510
subtract_baseline4.0020.0283.976
sumexp_to_longdt1.7460.0601.750
sumexp_to_tsv0.5360.0040.541
sumexplist_to_longdt1.4640.0121.476
summarize_fit1.6580.0321.628
svalues0.4830.0040.487
svars0.3910.0000.392
systematic_nas0.5150.0040.519
tag_features0.8770.0080.886
tag_hdlproteins0.5860.0040.591
taxon2org0.0010.0000.001
tpm0.3570.0000.356
uncollapse0.0110.0000.011
values0.4180.0000.418
varlevels_dont_clash0.020.000.02
venn_detects0.5870.0040.591
weights0.3590.0000.359
write_xl0.6670.0000.645
zero_to_na0.0020.0010.002