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This page was generated on 2024-05-04 11:36:17 -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 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: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2024-05-03 20:47:35 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 21:03:54 -0400 (Fri, 03 May 2024)
EllapsedTime: 979.0 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* 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 ‘1.12.0’
* 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 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 91.786  4.867  91.965
read_rnaseq_counts       26.838  1.021  27.622
plot_exprs               19.349  0.311  19.533
rm_diann_contaminants    18.729  0.316  18.987
plot_exprs_per_coef      18.695  0.256  18.839
default_formula          14.516  0.379  14.450
fit                      12.973  0.537  12.337
analyze                  12.246  0.100  12.261
read_somascan            11.558  0.008  11.501
read_metabolon           11.444  0.112  11.435
plot_summary             10.955  0.132  11.004
plot_volcano              8.873  0.056   8.873
plot_densities            8.090  0.264   8.274
plot_sample_nas           6.828  0.127   6.908
read_fragpipe             6.441  0.236   6.391
biplot_covariates         5.252  0.020   5.251
extract_coef_features     4.682  0.396   5.056
* 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 beta (2024-04-15 r86425) -- "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 
126.751   4.656 129.060 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
CONTAMINANTSURL000
FITSEP000
LINMOD_ENGINES0.0010.0000.001
MAXQUANT_PATTERNS0.0010.0000.000
TAXON_TO_ORGNAME0.0010.0000.000
TESTS000
abstract_fit1.2670.0511.296
add_adjusted_pvalues0.5750.0480.623
add_assay_means1.0130.0361.049
add_facetvars1.5250.0801.584
add_opentargets_by_uniprot0.3960.0150.414
add_psp0.5110.0120.524
add_smiles0.4910.0120.483
analysis0.4050.0040.409
analyze12.246 0.10012.261
annotate_maxquant0.8340.0200.854
annotate_uniprot_rest0.4130.0082.567
assert_is_valid_sumexp0.7130.0360.728
bin1.2470.0481.295
biplot3.4650.0523.497
biplot_corrections3.2470.0193.245
biplot_covariates5.2520.0205.251
block2lme0.0020.0020.004
center1.3740.0141.389
code4.6570.0284.663
coefs0.6910.0520.721
collapsed_entrezg_to_symbol000
contrast_subgroup_cols0.5930.0200.592
count_in0.0020.0000.001
counts0.4280.0000.427
counts2cpm0.3800.0000.379
counts2tpm0.3320.0000.332
cpm0.3810.0000.380
create_design0.6710.0240.674
default_formula14.516 0.37914.450
default_geom0.5010.0090.489
default_sfile0.0020.0000.001
demultiplex0.0140.0000.013
dequantify0.0030.0000.002
dot-merge0.0150.0000.016
dot-plot_survival3.9890.1714.161
dot-read_maxquant_proteingroups0.1230.0000.123
download_contaminants0.1880.0082.576
download_data0.0000.0020.001
download_gtf000
download_mcclain210.0000.0000.001
dt2mat0.0030.0040.007
enrichment1.1910.0841.276
entrezg_to_symbol0.0010.0000.001
explore_transformations3.4180.2123.630
extract_coef_features4.6820.3965.056
extract_rectangle0.0990.0310.131
fdata0.5480.0520.600
fdr2p0.8930.0750.948
filter_exprs_replicated_in_some_subgroup1.0700.0731.030
filter_features0.5420.0160.520
filter_medoid0.7300.0240.754
filter_samples0.5490.0360.547
fit12.973 0.53712.337
fit_lmx4.3340.0964.217
fitcoefs0.7850.0440.790
fits0.6950.0190.694
fitvars1.0040.0441.028
fix_xlgenes0.0020.0000.002
flevels0.4210.0150.436
fnames0.4650.0050.468
formula2str0.0000.0000.001
fvalues0.4150.0080.423
fvars0.3920.0000.391
genome_to_orgdb0.0010.0000.000
group_by_level0.0020.0000.001
guess_fitsep0.4870.0030.491
guess_maxquant_quantity0.0060.0010.006
guess_sep0.4930.0160.486
has_multiple_levels0.0480.0040.051
hdlproteins0.0540.0360.092
impute3.0200.0563.075
invert_subgroups0.6880.0240.712
is_collapsed_subset0.0010.0000.001
is_diann_report0.4410.0630.461
is_fastadt0.0580.0080.066
is_file0.0010.0000.001
is_fraction0.0020.0000.002
is_imputed0.7290.0560.785
is_positive_number0.0020.0000.002
is_scalar_subset0.3590.0320.391
is_sig1.2840.1161.401
is_valid_formula0.0440.0040.048
keep_connected_blocks0.5660.0480.574
keep_connected_features0.8170.1040.847
keep_replicated_features0.9130.0520.867
label2index0.0000.0000.001
list2mat0.0010.0000.001
log2counts0.3950.0360.432
log2cpm0.4330.0680.501
log2diffs0.3580.0320.390
log2proteins0.3510.0360.387
log2sites0.3560.0400.396
log2tpm0.3960.0320.428
log2transform3.6870.2243.912
logical2factor0.0020.0000.002
make_alpha_palette0.5890.0360.603
make_colors0.010.000.01
make_volcano_dt0.8530.0400.893
map_fvalues0.4010.0280.430
matrix2sumexp0.9650.0480.990
merge_sample_file0.4540.0160.469
merge_sdata0.5510.0410.569
message_df0.0030.0000.003
modelvar1.6120.0441.599
order_on_p0.8920.0600.931
pca2.8570.1042.940
pg_to_canonical0.0060.0000.006
plot_contrast_venn1.8300.0441.797
plot_contrastogram2.3780.1082.371
plot_data1.1910.0401.210
plot_densities8.0900.2648.274
plot_design0.6150.0280.643
plot_exprs19.349 0.31119.533
plot_exprs_per_coef18.695 0.25618.839
plot_fit_summary1.7730.0281.744
plot_heatmap1.6350.0511.688
plot_matrix0.5010.0080.488
plot_sample_nas6.8280.1276.908
plot_subgroup_points3.9990.0293.988
plot_summary10.955 0.13211.004
plot_venn0.0120.0040.016
plot_venn_heatmap0.0340.0040.039
plot_violins3.4120.0643.455
plot_volcano8.8730.0568.873
preprocess_rnaseq_counts0.3420.0000.342
pull_columns0.0020.0000.002
read_affymetrix000
read_contaminants0.0670.0041.254
read_diann_proteingroups91.786 4.86791.965
read_fragpipe6.4410.2366.391
read_maxquant_phosphosites1.5610.0081.568
read_maxquant_proteingroups1.2680.0121.280
read_metabolon11.444 0.11211.435
read_msigdt0.0010.0000.001
read_olink1.2620.0721.284
read_rectangles0.1810.0040.185
read_rnaseq_counts26.838 1.02127.622
read_salmon000
read_somascan11.558 0.00811.501
read_uniprotdt0.2660.0150.282
reset_fit4.0450.0203.968
rm_diann_contaminants18.729 0.31618.987
rm_missing_in_some_samples0.5200.0080.506
rm_unmatched_samples0.5290.0040.534
scaledlibsizes0.3580.0040.362
scoremat1.0110.0161.005
slevels0.4430.0000.444
snames0.4100.0040.414
split_extract_fixed0.5480.0120.539
split_samples1.1920.0041.175
stri_any_regex0.0010.0000.001
stri_detect_fixed_in_collapsed0.3400.0000.341
subgroup_matrix0.5370.0080.522
subtract_baseline4.3460.0124.304
sumexp_to_longdt1.8430.0521.840
sumexp_to_tsv0.5000.0080.508
sumexplist_to_longdt1.6100.0081.619
summarize_fit1.5550.0161.483
svalues0.4230.0000.423
svars0.4000.0080.408
systematic_nas0.7270.0160.744
tag_features1.1230.0321.156
tag_hdlproteins0.5400.0080.548
taxon2org0.0010.0000.001
tpm0.5110.0000.510
uncollapse0.0060.0030.010
values0.4130.0040.417
varlevels_dont_clash0.0180.0000.018
venn_detects0.5460.0040.551
weights0.3740.0000.374
write_xl0.8290.0120.802
zero_to_na0.0020.0000.002