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This page was generated on 2024-10-18 20:39 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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: 2024-10-16 14:00 -0400 (Wed, 16 Oct 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
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 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 palomino7

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: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings autonomics_1.12.1.tar.gz
StartedAt: 2024-10-16 22:55:52 -0400 (Wed, 16 Oct 2024)
EndedAt: 2024-10-16 23:13:09 -0400 (Wed, 16 Oct 2024)
EllapsedTime: 1037.2 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings autonomics_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'autonomics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'autonomics' version '1.12.1'
* 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 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 ... 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 143.16   4.75  144.55
read_rnaseq_counts        34.25   1.73   36.20
rm_diann_contaminants     31.35   1.47   32.34
plot_exprs                24.75   0.22   25.00
plot_exprs_per_coef       23.92   0.28   24.21
default_formula           21.27   0.53   21.75
read_metabolon            16.52   0.23   16.75
fit                       14.98   0.35   15.39
read_somascan             15.01   0.14   15.17
plot_summary              13.59   0.16   13.77
analyze                   13.32   0.17   13.51
plot_volcano              13.06   0.28   13.36
plot_densities            11.41   0.26   11.67
read_fragpipe             11.39   0.24   11.54
plot_sample_nas            7.96   0.10    8.05
biplot_covariates          6.20   0.14    6.34
dot-plot_survival          5.47   0.52    6.03
plot_subgroup_points       5.73   0.04    5.79
reset_fit                  5.58   0.11    5.69
code                       5.22   0.14    5.36
extract_coef_features      5.19   0.10    5.28
fit_lmx                    5.16   0.09    5.26
* 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: 2 NOTEs
See
  'E:/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck/00check.log'
for details.


Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.19-bioc/R/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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
 176.79   12.37  196.57 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
CONTAMINANTSURL000
FITSEP000
LINMOD_ENGINES000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME000
TESTS000
abstract_fit1.430.111.58
add_adjusted_pvalues0.720.010.74
add_assay_means0.530.000.53
add_facetvars2.760.112.87
add_opentargets_by_uniprot0.390.020.41
add_psp0.490.030.51
add_smiles0.680.060.75
analysis0.610.020.63
analyze13.32 0.1713.51
annotate_maxquant0.840.040.89
annotate_uniprot_rest0.030.022.09
assert_is_valid_sumexp0.580.080.66
bin0.410.010.42
biplot3.900.134.05
biplot_corrections3.800.113.91
biplot_covariates6.200.146.34
block2lme000
center2.800.012.81
code5.220.145.36
coefs0.730.140.87
collapsed_entrezg_to_symbol000
contrast_subgroup_cols0.610.030.64
count_in000
counts0.470.000.47
counts2cpm0.620.000.63
counts2tpm0.520.000.51
cpm0.370.000.38
create_design0.860.060.92
default_formula21.27 0.5321.75
default_geom0.760.090.86
default_sfile0.020.000.02
demultiplex0.010.000.01
dequantify000
dot-merge0.020.020.03
dot-plot_survival5.470.526.03
dot-read_maxquant_proteingroups0.170.010.19
download_contaminants0.000.021.11
download_data000
download_gtf000
download_mcclain21000
dt2mat0.020.000.02
enrichment1.340.181.53
entrezg_to_symbol000
explore_transformations4.220.194.40
extract_coef_features5.190.105.28
extract_rectangle0.120.040.18
fdata0.550.020.56
fdr2p1.060.071.13
filter_exprs_replicated_in_some_subgroup1.310.071.41
filter_features0.660.040.68
filter_medoid0.940.061.00
filter_samples0.560.040.63
fit14.98 0.3515.39
fit_lmx5.160.095.26
fitcoefs1.030.061.10
fits0.920.020.94
fitvars1.210.111.31
fix_xlgenes000
flevels0.450.000.46
fnames0.610.030.64
formula2str000
fvalues0.590.040.64
fvars0.640.020.65
genome_to_orgdb0.000.010.02
group_by_level000
guess_fitsep0.520.020.53
guess_maxquant_quantity000
guess_sep0.610.080.69
has_multiple_levels0.050.000.05
hdlproteins0.030.060.11
impute3.640.053.69
invert_subgroups0.990.000.98
is_collapsed_subset000
is_diann_report0.360.060.60
is_fastadt0.100.000.11
is_file000
is_fraction000
is_imputed1.080.021.09
is_positive_number000
is_scalar_subset0.470.010.48
is_sig1.750.051.80
is_valid_formula0.060.000.06
keep_connected_blocks0.580.150.75
keep_connected_features0.970.081.20
keep_replicated_features1.040.071.13
label2index000
list2mat000
log2counts0.610.000.61
log2cpm0.380.010.39
log2diffs0.560.020.58
log2proteins0.580.000.57
log2sites0.390.030.43
log2tpm0.500.010.51
log2transform4.480.114.59
logical2factor0.020.000.02
make_alpha_palette0.620.020.64
make_colors0.020.000.02
make_volcano_dt1.230.031.26
map_fvalues0.630.020.64
matrix2sumexp0.970.041.02
merge_sample_file0.780.020.80
merge_sdata0.720.000.72
message_df000
modelvar1.530.111.64
order_on_p0.990.061.05
pca3.450.093.54
pg_to_canonical000
plot_contrast_venn2.220.032.25
plot_contrastogram2.660.132.84
plot_data1.620.091.72
plot_densities11.41 0.2611.67
plot_design0.650.000.66
plot_exprs24.75 0.2225.00
plot_exprs_per_coef23.92 0.2824.21
plot_fit_summary2.330.082.41
plot_heatmap2.360.032.39
plot_matrix0.450.080.55
plot_sample_nas7.960.108.05
plot_subgroup_points5.730.045.79
plot_summary13.59 0.1613.77
plot_venn0.020.000.01
plot_venn_heatmap0.060.010.08
plot_violins4.690.214.89
plot_volcano13.06 0.2813.36
preprocess_rnaseq_counts0.420.000.42
pull_columns000
read_affymetrix000
read_contaminants0.000.000.39
read_diann_proteingroups143.16 4.75144.55
read_fragpipe11.39 0.2411.54
read_maxquant_phosphosites2.280.122.41
read_maxquant_proteingroups1.560.041.59
read_metabolon16.52 0.2316.75
read_msigdt000
read_olink1.230.061.44
read_rectangles0.290.020.30
read_rnaseq_counts34.25 1.7336.20
read_salmon000
read_somascan15.01 0.1415.17
read_uniprotdt0.270.030.30
reset_fit5.580.115.69
rm_diann_contaminants31.35 1.4732.34
rm_missing_in_some_samples0.690.050.73
rm_unmatched_samples0.790.010.81
scaledlibsizes0.580.020.58
scoremat1.080.111.19
slevels0.500.020.51
snames0.670.030.71
split_extract_fixed0.750.040.81
split_samples1.470.051.52
stri_any_regex000
stri_detect_fixed_in_collapsed0.410.000.40
subgroup_matrix0.470.090.58
subtract_baseline4.840.054.89
sumexp_to_longdt2.200.132.33
sumexp_to_tsv0.580.040.62
sumexplist_to_longdt2.360.082.44
summarize_fit1.860.051.92
svalues0.480.010.50
svars0.570.020.58
systematic_nas0.760.010.78
tag_features1.220.071.28
tag_hdlproteins0.630.040.68
taxon2org000
tpm0.450.000.45
uncollapse0.020.000.01
values0.530.000.53
varlevels_dont_clash0.030.000.03
venn_detects0.900.000.91
weights0.450.020.47
write_xl0.940.081.02
zero_to_na0.020.000.01