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This page was generated on 2024-05-04 11:37:25 -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 palomino3


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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings autonomics_1.12.0.tar.gz
StartedAt: 2024-05-04 00:37:48 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 00:54:20 -0400 (Sat, 04 May 2024)
EllapsedTime: 992.1 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings autonomics_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 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 '1.12.0'
* 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 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 131.86   5.81  134.99
read_rnaseq_counts        32.40   1.97   39.92
rm_diann_contaminants     26.22   1.35   27.35
plot_exprs                22.56   0.27   22.92
plot_exprs_per_coef       21.48   0.20   21.81
default_formula           17.89   0.55   18.42
read_metabolon            14.97   0.26   15.34
read_somascan             14.71   0.19   14.92
fit                       14.26   0.37   14.70
plot_summary              13.17   0.30   13.56
analyze                   12.58   0.25   12.95
plot_volcano              11.28   0.21   11.64
plot_densities            10.55   0.29   10.89
read_fragpipe              9.70   0.28    9.97
plot_sample_nas            6.67   0.15    6.86
code                       6.30   0.10    6.52
extract_coef_features      5.63   0.24    5.95
reset_fit                  5.39   0.15    5.68
subtract_baseline          5.39   0.12    5.65
biplot_covariates          5.20   0.14    5.40
plot_violins               4.92   0.25    5.22
plot_subgroup_points       5.00   0.11    5.27
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck/00check.log'
for details.


Installation output

autonomics.Rcheck/00install.out

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


* installing to library 'F:/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 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup"
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 
 162.34   14.65  185.59 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
CONTAMINANTSURL000
FITSEP000
LINMOD_ENGINES000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME000
TESTS000
abstract_fit1.330.221.66
add_adjusted_pvalues0.620.040.67
add_assay_means1.220.031.27
add_facetvars1.830.102.01
add_opentargets_by_uniprot0.360.040.44
add_psp0.450.080.55
add_smiles0.610.130.84
analysis0.360.030.41
analyze12.58 0.2512.95
annotate_maxquant0.970.051.03
annotate_uniprot_rest0.050.031.75
assert_is_valid_sumexp0.750.040.92
bin1.170.021.22
biplot3.500.123.75
biplot_corrections3.140.113.27
biplot_covariates5.200.145.40
block2lme000
center1.530.081.61
code6.300.106.52
coefs1.030.111.20
collapsed_entrezg_to_symbol000
contrast_subgroup_cols0.660.090.84
count_in0.010.000.02
counts0.490.000.48
counts2cpm0.390.010.41
counts2tpm0.330.000.34
cpm0.430.000.44
create_design0.790.080.99
default_formula17.89 0.5518.42
default_geom0.640.140.88
default_sfile0.020.000.01
demultiplex000
dequantify0.010.000.02
dot-merge0.020.000.02
dot-plot_survival4.340.384.71
dot-read_maxquant_proteingroups0.160.010.21
download_contaminants0.000.030.95
download_data0.000.020.02
download_gtf000
download_mcclain21000
dt2mat000
enrichment1.330.171.50
entrezg_to_symbol000
explore_transformations3.930.174.11
extract_coef_features5.630.245.95
extract_rectangle0.160.110.31
fdata0.530.030.56
fdr2p1.230.061.35
filter_exprs_replicated_in_some_subgroup1.310.051.47
filter_features0.570.140.78
filter_medoid0.780.010.79
filter_samples0.690.050.93
fit14.26 0.3714.70
fit_lmx4.660.114.87
fitcoefs0.900.101.05
fits0.910.141.16
fitvars1.110.081.29
fix_xlgenes0.010.000.02
flevels0.400.040.45
fnames0.620.050.69
formula2str000
fvalues0.560.050.61
fvars0.390.030.42
genome_to_orgdb000
group_by_level0.020.000.02
guess_fitsep0.510.000.53
guess_maxquant_quantity0.020.000.01
guess_sep0.610.140.80
has_multiple_levels0.030.030.06
hdlproteins0.020.060.13
impute3.970.154.15
invert_subgroups0.950.051.01
is_collapsed_subset000
is_diann_report0.370.110.58
is_fastadt0.080.000.08
is_file000
is_fraction000
is_imputed0.750.000.76
is_positive_number000
is_scalar_subset0.530.000.55
is_sig1.600.031.62
is_valid_formula0.070.000.08
keep_connected_blocks0.720.060.90
keep_connected_features0.990.081.13
keep_replicated_features1.110.061.36
label2index000
list2mat000
log2counts0.470.000.47
log2cpm0.610.000.61
log2diffs0.480.000.52
log2proteins0.470.010.50
log2sites0.520.020.57
log2tpm0.640.040.68
log2transform4.520.084.61
logical2factor000
make_alpha_palette0.730.100.96
make_colors0.020.000.01
make_volcano_dt1.260.031.30
map_fvalues0.470.010.50
matrix2sumexp1.250.131.47
merge_sample_file0.560.040.65
merge_sdata0.890.071.02
message_df000
modelvar1.880.112.06
order_on_p1.010.111.21
pca3.520.043.68
pg_to_canonical000
plot_contrast_venn1.840.102.11
plot_contrastogram2.530.202.89
plot_data1.270.081.46
plot_densities10.55 0.2910.89
plot_design0.720.020.78
plot_exprs22.56 0.2722.92
plot_exprs_per_coef21.48 0.2021.81
plot_fit_summary1.960.112.16
plot_heatmap1.840.001.89
plot_matrix0.550.080.76
plot_sample_nas6.670.156.86
plot_subgroup_points5.000.115.27
plot_summary13.17 0.3013.56
plot_venn0.020.000.02
plot_venn_heatmap0.110.000.11
plot_violins4.920.255.22
plot_volcano11.28 0.2111.64
preprocess_rnaseq_counts0.400.000.42
pull_columns0.020.000.02
read_affymetrix000
read_contaminants0.000.000.37
read_diann_proteingroups131.86 5.81134.99
read_fragpipe9.700.289.97
read_maxquant_phosphosites2.050.112.20
read_maxquant_proteingroups1.720.021.80
read_metabolon14.97 0.2615.34
read_msigdt000
read_olink1.730.111.94
read_rectangles0.190.030.28
read_rnaseq_counts32.40 1.9739.92
read_salmon000
read_somascan14.71 0.1914.92
read_uniprotdt0.250.050.34
reset_fit5.390.155.68
rm_diann_contaminants26.22 1.3527.35
rm_missing_in_some_samples0.640.070.79
rm_unmatched_samples0.680.020.68
scaledlibsizes0.460.000.47
scoremat0.940.081.16
slevels0.500.010.55
snames0.490.030.53
split_extract_fixed0.560.100.70
split_samples1.550.111.75
stri_any_regex000
stri_detect_fixed_in_collapsed0.370.000.41
subgroup_matrix0.520.110.72
subtract_baseline5.390.125.65
sumexp_to_longdt1.980.102.25
sumexp_to_tsv0.520.000.52
sumexplist_to_longdt1.670.031.75
summarize_fit1.840.122.00
svalues0.410.000.42
svars0.530.060.59
systematic_nas0.810.000.85
tag_features1.190.051.23
tag_hdlproteins0.810.060.92
taxon2org000
tpm0.570.020.58
uncollapse0.010.000.02
values0.580.020.59
varlevels_dont_clash0.020.000.02
venn_detects0.570.030.60
weights0.480.000.49
write_xl1.080.121.21
zero_to_na000