Olivier Cuvier
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/HicAggR |
| git_branch: RELEASE_3_20 |
| git_last_commit: bf7aff9 |
| git_last_commit_date: 2024-10-29 11:31:14 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 952/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HicAggR 1.2.0 (landing page) Olivier Cuvier
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the HicAggR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HicAggR.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. |
| Package: HicAggR |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HicAggR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HicAggR_1.2.0.tar.gz |
| StartedAt: 2024-11-20 04:17:50 -0500 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 04:28:22 -0500 (Wed, 20 Nov 2024) |
| EllapsedTime: 632.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: HicAggR.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HicAggR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HicAggR_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/HicAggR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘HicAggR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HicAggR’ version ‘1.2.0’
* 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 ‘HicAggR’ 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 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 ... WARNING
Undocumented code objects:
‘ImportLoops’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
compareToBackground 28.531 0.280 28.827
plotMultiAPA 19.753 0.012 19.772
Aggregation 8.238 0.221 8.473
PrepareMtxList 6.878 0.004 6.895
ggAPA 5.924 0.006 5.934
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/HicAggR.Rcheck/00check.log’
for details.
HicAggR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL HicAggR ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘HicAggR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (HicAggR)
HicAggR.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: x86_64-pc-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.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(HicAggR)
Package 'HicAggR' version 1.2.0
>
> test_check("HicAggR")
hicLst is already o/e.
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extracted : 23 Matrices on 2L_2L
extracted : 22 Matrices on 2R_2R
FILTERED extracted submat: 45
TOTAL extracted submat: 45
extracted : 23 Matrices on 2L_2L
extracted : 22 Matrices on 2R_2R
FILTERED extracted submat: 45
TOTAL extracted submat: 45
extracted : 1 Matrices on 2R_2R
FILTERED extracted submat: 1
TOTAL extracted submat: 1
24 matrices are oriented
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 24 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
112.559 49.381 119.738
HicAggR.Rcheck/HicAggR-Ex.timings
| name | user | system | elapsed | |
| Aggregation | 8.238 | 0.221 | 8.473 | |
| BalanceHiC | 1.211 | 0.015 | 1.225 | |
| Beaf32_Peaks.gnr | 0.017 | 0.001 | 0.017 | |
| BinGRanges | 0.115 | 0.000 | 0.116 | |
| CutHiC | 0.282 | 0.000 | 0.283 | |
| ExtractSubmatrix | 3.628 | 0.009 | 3.638 | |
| FilterInteractions | 3.305 | 0.013 | 3.320 | |
| GenomicSystem | 0.003 | 0.000 | 0.003 | |
| GetInfo | 0.024 | 0.000 | 0.036 | |
| GetQuantif | 3.927 | 0.005 | 3.936 | |
| HiC_Ctrl.cmx_lst | 0.033 | 0.001 | 0.033 | |
| HiC_HS.cmx_lst | 0.029 | 0.003 | 0.031 | |
| Hue | 0.002 | 0.000 | 0.003 | |
| ICEnorm | 0.056 | 0.001 | 0.056 | |
| ImportHiC | 0.937 | 0.071 | 1.019 | |
| IndexFeatures | 0.907 | 0.006 | 0.913 | |
| JoinHiC | 0.053 | 0.002 | 0.055 | |
| MergeGRanges | 0.094 | 0.000 | 0.095 | |
| OrientateMatrix | 3.531 | 0.001 | 3.535 | |
| OverExpectedHiC | 1.011 | 0.009 | 1.020 | |
| PlotAPA | 4.571 | 0.008 | 4.587 | |
| PrepareMtxList | 6.878 | 0.004 | 6.895 | |
| QtlThreshold | 0.002 | 0.000 | 0.003 | |
| SearchPairs | 2.390 | 0.000 | 2.393 | |
| SeqEnds | 0.008 | 0.000 | 0.007 | |
| StrToGRanges | 0.053 | 0.000 | 0.053 | |
| SwitchMatrix | 0.395 | 0.002 | 0.396 | |
| TADs_Domains.gnr | 0.010 | 0.001 | 0.011 | |
| TSS_Peaks.gnr | 0.010 | 0.000 | 0.009 | |
| VCnorm | 0.033 | 0.004 | 0.038 | |
| YlGnBu | 0.000 | 0.000 | 0.001 | |
| YlOrRd | 0 | 0 | 0 | |
| compareToBackground | 28.531 | 0.280 | 28.827 | |
| ggAPA | 5.924 | 0.006 | 5.934 | |
| plotMultiAPA | 19.753 | 0.012 | 19.772 | |
| preparePlotgardener | 0.058 | 0.001 | 0.059 | |
| viridis | 0.001 | 0.000 | 0.001 | |