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This page was generated on 2024-05-04 11:40:16 -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 kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: autonomics
Version: 1.12.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings autonomics_1.12.0.tar.gz
StartedAt: 2024-05-04 04:57:05 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 05:13:19 -0000 (Sat, 04 May 2024)
EllapsedTime: 973.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: autonomics.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --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: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 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 ... ERROR
Running examples in ‘autonomics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: .read_rnaseq_bams
> ### Title: Read rnaseq counts/bams
> ### Aliases: .read_rnaseq_bams .read_rnaseq_counts read_rnaseq_bams
> ###   read_rnaseq_counts
> 
> ### ** Examples
> 
> # read_rnaseq_bams
>     if (requireNamespace('Rsubread')){
+        dir <- download_data('billing16.bam.zip')
+        object <- read_rnaseq_bams(dir, paired = TRUE, genome = 'hg38')  
+        object <- read_rnaseq_bams(dir, paired = TRUE, genome = 'hg38', plot = TRUE)  
+     }
Loading required namespace: Rsubread
unzip
Warning in unzip(filepath, exdir = substr(filepath, 1, nchar(filepath) -  :
  error 1 in extracting from zip file
NCBI RefSeq annotation for hg38 (build 38.2) is used.
Error in (function (files, annot.inbuilt = "mm39", annot.ext = NULL, isGTFAnnotationFile = FALSE,  : 
  No read files provided!
Calls: read_rnaseq_bams ... .read_rnaseq_bams -> count_reads -> do.call -> <Anonymous>
Execution halted
* 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 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/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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: aarch64-unknown-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 
191.877   2.771 193.884 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0010.0000.000
CONTAMINANTSURL000
FITSEP000
LINMOD_ENGINES000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME000
TESTS0.0000.0000.001
abstract_fit1.7980.0401.847
add_adjusted_pvalues0.7970.0510.855
add_assay_means0.6510.0200.673
add_facetvars3.1740.1883.365
add_opentargets_by_uniprot0.5580.0200.584
add_psp0.7010.0160.721
add_smiles0.6550.0080.660
analysis0.5360.0040.540
analyze17.572 0.08417.683
annotate_maxquant1.1440.0201.168
annotate_uniprot_rest0.0790.0204.935
assert_is_valid_sumexp0.7840.1070.891
bin0.5620.0080.575
biplot5.1490.0725.229
biplot_corrections4.4260.0044.436
biplot_covariates7.1450.0247.182
block2lme0.0030.0000.004
center2.7980.0672.870
code6.8130.0246.847
coefs1.0330.0041.036
collapsed_entrezg_to_symbol000
contrast_subgroup_cols0.8410.0040.844
count_in0.0010.0000.001
counts0.5880.0000.590
counts2cpm0.5550.0000.557
counts2tpm0.5160.0040.522
cpm0.5610.0000.563
create_design1.0150.0041.018
default_formula21.541 0.53521.931
default_geom0.7080.0240.731
default_sfile0.0000.0020.001
demultiplex0.0180.0010.019
dequantify0.0030.0000.003
dot-merge0.0210.0000.021
dot-plot_survival5.3270.1275.465
dot-read_maxquant_proteingroups0.1340.0040.138
download_contaminants0.0280.0005.266
download_data0.0010.0000.000
download_gtf000
download_mcclain21000
dt2mat0.0050.0000.004
enrichment1.6220.0441.669
entrezg_to_symbol0.0010.0000.000
explore_transformations4.8420.0444.895
extract_coef_features6.8900.0526.952
extract_rectangle0.1460.0120.158
fdata0.7890.0000.790
fdr2p1.2930.0001.293
filter_exprs_replicated_in_some_subgroup1.4560.0201.473
filter_features0.7570.0160.771
filter_medoid1.0930.0201.114
filter_samples0.8280.0040.830
fit17.162 0.08817.221
fit_lmx5.9550.1286.077
fitcoefs1.1150.0121.125
fits1.0280.0121.038
fitvars1.5110.0081.519
fix_xlgenes0.0020.0000.003
flevels0.6010.0440.647
fnames0.6520.1270.783
formula2str0.0000.0000.001
fvalues0.5960.0160.614
fvars0.5680.0040.573
genome_to_orgdb000
group_by_level0.0010.0000.001
guess_fitsep0.7360.0400.777
guess_maxquant_quantity0.0070.0000.007
guess_sep0.6940.0040.696
has_multiple_levels0.0730.0000.074
hdlproteins0.0510.0280.089
impute4.1950.0084.212
invert_subgroups0.9330.0040.938
is_collapsed_subset0.0010.0000.000
is_diann_report0.5530.0320.749
is_fastadt0.0870.0000.087
is_file0.0010.0000.001
is_fraction0.0000.0020.002
is_imputed1.0290.0851.115
is_positive_number0.0030.0000.003
is_scalar_subset0.4980.1320.630
is_sig1.6830.0681.754
is_valid_formula0.0690.0120.081
keep_connected_blocks0.7390.0200.757
keep_connected_features1.0270.0241.047
keep_replicated_features1.1300.0041.131
label2index0.0010.0000.001
list2mat0.0010.0000.000
log2counts0.5680.0000.569
log2cpm0.6070.0000.609
log2diffs0.4740.0000.475
log2proteins0.4720.0040.477
log2sites0.4670.0080.475
log2tpm0.5450.0000.546
log2transform5.2680.1275.407
logical2factor0.0010.0000.001
make_alpha_palette0.7880.0120.799
make_colors0.0100.0000.011
make_volcano_dt1.1990.0001.201
map_fvalues0.5680.0000.570
matrix2sumexp1.3990.0081.407
merge_sample_file0.6440.0000.646
merge_sdata0.7720.0120.782
message_df0.0030.0000.002
modelvar2.3390.0162.353
order_on_p1.3840.0161.400
pca4.2710.0164.293
pg_to_canonical0.0080.0000.008
plot_contrast_venn2.6750.0042.673
plot_contrastogram3.2690.0603.330
plot_data1.8080.0161.824
plot_densities12.826 0.15213.008
plot_design0.8770.0000.879
plot_exprs29.191 0.19129.436
plot_exprs_per_coef27.752 0.11227.910
plot_fit_summary2.5700.0162.585
plot_heatmap2.4050.0162.426
plot_matrix0.7550.0120.765
plot_sample_nas8.6630.0208.698
plot_subgroup_points6.4940.0286.532
plot_summary17.085 0.05617.167
plot_venn0.0150.0000.015
plot_venn_heatmap0.0450.0040.050
plot_violins5.3660.0245.397
plot_volcano14.076 0.13914.241
preprocess_rnaseq_counts0.5510.0040.557
pull_columns0.0030.0010.003
read_affymetrix000
read_contaminants0.0110.0000.011
read_diann_proteingroups137.036 1.324135.195
read_fragpipe8.0480.0767.967
read_maxquant_phosphosites2.1960.0162.216
read_maxquant_proteingroups1.8000.0081.811
read_metabolon17.285 0.06017.375
read_msigdt0.0010.0000.001
read_olink1.7230.0281.741
read_rectangles0.2180.0080.227