Olivier Cuvier
| Snapshot Date: 2024-12-02 13:40 -0500 (Mon, 02 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/HicAggR |
| git_branch: devel |
| git_last_commit: 1905b6c |
| git_last_commit_date: 2024-10-29 11:31:14 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-03 11:45 -0500 (Tue, 03 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4461 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4405 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4360 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 1457 |
| 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 945/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HicAggR 1.3.0 (landing page) Olivier Cuvier
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
|
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: 1.3.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HicAggR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HicAggR_1.3.0.tar.gz |
| StartedAt: 2024-12-02 23:13:06 -0500 (Mon, 02 Dec 2024) |
| EndedAt: 2024-12-02 23:19:12 -0500 (Mon, 02 Dec 2024) |
| EllapsedTime: 365.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: HicAggR.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HicAggR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HicAggR_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/HicAggR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HicAggR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HicAggR’ version ‘1.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
ExtractSubmatrix.Rd: GRanges
ImportHiC.Rd: GRanges
IndexFeatures.Rd: GRanges
MergeGRanges.Rd: GRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 11.354 0.158 11.516
plotMultiAPA 7.528 0.110 7.648
* 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 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/HicAggR.Rcheck/00check.log’
for details.
HicAggR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HicAggR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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 1.3.0
>
> 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
37.424 11.053 40.150
HicAggR.Rcheck/HicAggR-Ex.timings
| name | user | system | elapsed | |
| Aggregation | 3.069 | 0.042 | 3.111 | |
| BalanceHiC | 0.473 | 0.009 | 0.481 | |
| Beaf32_Peaks.gnr | 0.006 | 0.001 | 0.007 | |
| BinGRanges | 0.043 | 0.000 | 0.043 | |
| CutHiC | 0.114 | 0.005 | 0.119 | |
| ExtractSubmatrix | 1.390 | 0.017 | 1.407 | |
| FilterInteractions | 1.397 | 0.026 | 1.426 | |
| GenomicSystem | 0.001 | 0.000 | 0.001 | |
| GetInfo | 0.012 | 0.003 | 0.032 | |
| GetQuantif | 1.651 | 0.036 | 1.688 | |
| HiC_Ctrl.cmx_lst | 0.016 | 0.001 | 0.016 | |
| HiC_HS.cmx_lst | 0.015 | 0.001 | 0.015 | |
| Hue | 0.001 | 0.000 | 0.001 | |
| ICEnorm | 0.030 | 0.003 | 0.032 | |
| ImportHiC | 0.124 | 0.023 | 0.149 | |
| IndexFeatures | 0.361 | 0.012 | 0.373 | |
| JoinHiC | 0.028 | 0.001 | 0.029 | |
| MergeGRanges | 0.038 | 0.000 | 0.039 | |
| OrientateMatrix | 1.763 | 0.046 | 1.808 | |
| OverExpectedHiC | 0.167 | 0.011 | 0.178 | |
| PlotAPA | 1.922 | 0.042 | 1.967 | |
| PrepareMtxList | 2.624 | 0.066 | 2.692 | |
| QtlThreshold | 0.001 | 0.000 | 0.001 | |
| SearchPairs | 0.929 | 0.021 | 0.949 | |
| SeqEnds | 0.003 | 0.000 | 0.003 | |
| StrToGRanges | 0.019 | 0.000 | 0.019 | |
| SwitchMatrix | 0.173 | 0.007 | 0.180 | |
| TADs_Domains.gnr | 0.004 | 0.000 | 0.005 | |
| TSS_Peaks.gnr | 0.003 | 0.001 | 0.004 | |
| VCnorm | 0.018 | 0.002 | 0.020 | |
| YlGnBu | 0 | 0 | 0 | |
| YlOrRd | 0 | 0 | 0 | |
| compareToBackground | 11.354 | 0.158 | 11.516 | |
| ggAPA | 2.226 | 0.059 | 2.286 | |
| plotMultiAPA | 7.528 | 0.110 | 7.648 | |
| preparePlotgardener | 0.029 | 0.002 | 0.031 | |
| viridis | 0.001 | 0.000 | 0.001 | |