Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2025-01-23 12:13 -0500 (Thu, 23 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4493
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4394
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 1995/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
snapcount 1.18.0  (landing page)
Rone Charles
Snapshot Date: 2025-01-20 13:00 -0500 (Mon, 20 Jan 2025)
git_url: https://git.bioconductor.org/packages/snapcount
git_branch: RELEASE_3_20
git_last_commit: a32cce4
git_last_commit_date: 2024-10-29 10:47:00 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows 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    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for snapcount on taishan

To the developers/maintainers of the snapcount package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/snapcount.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: snapcount
Version: 1.18.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:snapcount.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings snapcount_1.18.0.tar.gz
StartedAt: 2025-01-21 11:10:44 -0000 (Tue, 21 Jan 2025)
EndedAt: 2025-01-21 11:21:56 -0000 (Tue, 21 Jan 2025)
EllapsedTime: 672.0 seconds
RetCode: 0
Status:   OK  
CheckDir: snapcount.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:snapcount.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings snapcount_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/snapcount.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘snapcount/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘snapcount’ version ‘1.18.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘snapcount’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 whether startup messages can be suppressed ... 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
junction_intersection          7.669  0.901 114.989
junction_union                 3.669  0.394   8.755
Compilation                    2.824  0.299 128.838
uri_of_last_successful_request 1.187  0.259   6.550
query_jx                       0.958  0.277   5.732
percent_spliced_in             0.061  0.017   5.266
* 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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/snapcount.Rcheck/00check.log’
for details.


Installation output

snapcount.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL snapcount
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’
* installing *source* package ‘snapcount’ ...
** 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 (snapcount)

Tests output

snapcount.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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(snapcount)
> 
> test_check("snapcount")
Read 2 items
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 82 ]
> 
> proc.time()
   user  system elapsed 
 12.257   1.123 135.082 

Example timings

snapcount.Rcheck/snapcount-Ex.timings

nameusersystemelapsed
Compilation 2.824 0.299128.838
Coordinates0.0280.0000.028
QueryBuilder0.1500.0040.155
from_url0.0060.0162.652
get_column_filters0.1620.0230.188
get_compilation0.0020.0000.001
get_coordinate_modifier0.0010.0000.001
get_regions0.1350.0150.152
get_row_filters0.0020.0000.003
get_sids0.0010.0010.002
junction_inclusion_ratio0.1360.0274.715
junction_intersection 7.669 0.901114.989
junction_union3.6690.3948.755
percent_spliced_in0.0610.0175.266
query_jx0.9580.2775.732
shared_sample_counts0.1150.0083.836
tissue_specificity0.0440.0172.632
uri_of_last_successful_request1.1870.2596.550