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This page was generated on 2024-12-24 11:44 -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 kjohnson3

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.15.36.tar.gz
StartedAt: 2024-12-23 18:11:28 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 18:16:18 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 290.4 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.15.36.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 32.127  1.005  33.686
read_rnaseq_counts        8.506  0.756   9.353
rm_diann_contaminants     6.265  0.122   7.326
fit                       5.932  0.073   6.033
plot_exprs_per_coef       5.514  0.063   5.603
plot_exprs                5.381  0.027   5.458
default_formula           5.181  0.129   5.360
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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


Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 
 50.049   3.040  53.710 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
COMPOUNDDISCOVERER_PATTERNS000
CONTAMINANTSURL0.0010.0000.000
FITSEP000
LINMOD_ENGINES000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME000
TESTS0.0000.0010.000
X0.4730.0300.505
abstract_fit0.5650.0310.596
add_adjusted_pvalues0.1690.0040.173
add_assay_means0.1020.0080.111
add_facetvars0.3890.0210.415
add_opentargets_by_uniprot0.1140.0020.118
add_psp0.1510.0030.155
add_smiles0.1250.0160.145
analysis0.1080.0020.111
analyze3.5480.0363.587
annotate_maxquant0.3080.0090.321
annotate_uniprot_rest0.0300.0052.492
assert_is_valid_sumexp0.1960.0150.213
bin0.4560.0100.467
biplot0.9810.0161.011
biplot_corrections0.8720.0170.891
biplot_covariates1.4590.0251.484
block2lme0.0010.0000.001
center0.4210.0060.427
code1.3990.0171.416
coefs0.2030.0130.216
collapsed_entrezg_to_symbol000
contrast_subgroup_cols0.1570.0130.170
count_in0.0010.0000.000
counts0.0990.0010.100
counts2cpm0.0780.0010.078
counts2tpm0.0840.0010.085
cpm0.0800.0010.081
create_design0.1910.0150.207
default_coefs0.1980.0130.213
default_formula5.1810.1295.360
default_geom0.1340.0150.149
default_sfile0.0010.0000.001
demultiplex0.0040.0000.004
dequantify0.0000.0000.001
dequantify_compounddiscoverer0.0010.0000.001
dot-merge0.0070.0000.007
dot-plot_survival1.7760.2211.998
dot-read_maxquant_proteingroups0.0460.0030.048
download_contaminants000
download_data0.0000.0010.001
download_gtf000
download_mcclain210.0000.0000.001
dt2mat0.0010.0010.001
enrichment0.3680.0310.400
entrezg_to_symbol0.0000.0000.001
extract_coef_features1.5240.0221.553
extract_rectangle0.0410.0140.054
fcluster1.7670.0181.786
fcor0.3350.0090.349
fdata0.1510.0040.154
fdr2p0.2640.0160.288
filter_exprs_replicated_in_some_subgroup0.2610.0160.276
filter_features0.1470.0150.162
filter_medoid0.2100.0050.219
filter_samples0.1420.0140.155
fit5.9320.0736.033
fitcoefs0.2080.0140.221
fits0.2120.0140.226
fitvars0.2760.0150.295
fix_xlgenes0.0010.0000.000
flevels0.1120.0020.115
fnames0.1800.0120.191
formula2str000
ftype2.6300.1222.763
fvalues0.1120.0020.115
fvars0.1140.0020.117
genome_to_orgdb000
group_by_level000
guess_compounddiscoverer_quantity0.0000.0000.001
guess_fitsep0.1200.0010.121
guess_maxquant_quantity0.0010.0010.002
guess_sep0.1440.0140.158
has_multiple_levels0.0150.0000.015
hdlproteins0.0190.0110.031
impute0.8260.0080.841
invert_subgroups0.1660.0010.168
is_collapsed_subset0.0000.0000.001
is_correlation_matrix000
is_diann_report0.1120.0140.174
is_fastadt0.020.000.02
is_file000
is_fraction0.0000.0000.001
is_imputed0.1970.0010.198
is_positive_number000
is_scalar_subset0.0860.0010.087
is_sig0.3820.0030.386
is_valid_formula0.0120.0000.012
keep_connected_blocks0.1410.0150.155
keep_connected_features0.1910.0140.205
keep_replicated_features0.2160.0150.233
label2index0.0000.0000.001
list2mat0.0010.0000.000
log2counts0.0840.0010.086
log2cpm0.0840.0000.084
log2diffs0.0870.0010.087
log2proteins0.0980.0020.100
log2sites0.0870.0010.089
log2tpm0.0850.0010.085
log2transform1.0660.0141.081
logical2factor0.0010.0000.001
make_alpha_palette0.1370.0140.151
make_colors0.0040.0010.005
make_volcano_dt0.2240.0020.236
map_fvalues0.1120.0020.114
matrix2sumexp0.2400.0170.257
merge_sample_file0.1280.0030.136
merge_sdata0.1610.0240.187
message_df0.0000.0000.001
model_coefs0.1950.0170.218
modelvar0.8600.0160.889
order_on_p0.2460.0170.263
pca0.8050.0170.826
pg_to_canonical0.0020.0000.002
plot_contrast_venn0.6520.0510.710
plot_contrastogram0.8750.0650.958
plot_data0.3590.0160.378
plot_densities2.3780.0602.453
plot_design0.1710.0020.174
plot_exprs5.3810.0275.458
plot_exprs_per_coef5.5140.0635.603
plot_fit_summary0.5530.0160.569
plot_heatmap0.5060.0020.511
plot_joint_density0.8560.0280.899
plot_matrix0.1410.0160.157
plot_sample_nas1.7480.0111.786
plot_subgroup_points1.2480.0191.275
plot_summary3.5710.0213.661
plot_venn0.0080.0000.008
plot_venn_heatmap0.0070.0000.007
plot_violins1.1970.0331.273
plot_volcano4.5270.0434.671
preprocess_rnaseq_counts0.0800.0010.086
pull_columns0.0010.0000.001
read_affymetrix0.0000.0000.001
read_contaminants0.0220.0021.819
read_diann_proteingroups32.127 1.00533.686
read_fragpipe2.3530.0962.474
read_maxquant_phosphosites0.4380.0100.448
read_maxquant_proteingroups0.3520.0060.371
read_metabolon3.3540.0333.429
read_msigdt000
read_olink0.4310.0190.451
read_rectangles0.0590.0070.065
read_rnaseq_counts8.5060.7569.353
read_salmon000
read_somascan3.6090.0483.750
read_uniprotdt0.0980.0060.103
reset_fit1.1640.0181.181
rm_diann_contaminants6.2650.1227.326
rm_missing_in_some_samples0.1700.0190.193
rm_unmatched_samples0.1750.0020.178
scaledlibsizes0.0820.0010.083
scoremat0.3070.0150.323
slevels0.1170.0020.122
snames0.1320.0020.136
split_extract_fixed0.1710.0170.192
split_samples0.3250.0180.343
stri_any_regex0.0000.0000.001
stri_detect_fixed_in_collapsed0.2450.0390.295
subgroup_matrix0.1460.0150.162
subtract_baseline1.3240.0221.424
sumexp_to_longdt0.5300.0240.609
sumexp_to_tsv0.1340.0020.142
sumexplist_to_longdt0.4560.0070.476
summarize_fit0.4610.0210.498
svalues0.1160.0010.117
svars0.1150.0040.119
systematic_nas0.1430.0010.144
tag_features0.4240.0130.440
tag_hdlproteins0.1570.0070.164
taxon2org0.0010.0000.000
tpm0.0810.0000.086
uncollapse0.0070.0010.008
values0.1160.0010.118
varlevels_dont_clash0.0410.0010.042
venn_detects0.1590.0040.165
weights0.0860.0000.086
write_xl0.1880.0130.208
zero_to_na0.0000.0010.001