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This page was generated on 2025-08-08 12:05 -0400 (Fri, 08 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4815
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 1119/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LinkHD 1.23.0  (landing page)
"Laura M Zingaretti"
Snapshot Date: 2025-08-07 13:45 -0400 (Thu, 07 Aug 2025)
git_url: https://git.bioconductor.org/packages/LinkHD
git_branch: devel
git_last_commit: 79426a9
git_last_commit_date: 2025-04-15 11:51:42 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for LinkHD on nebbiolo2

To the developers/maintainers of the LinkHD package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LinkHD.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: LinkHD
Version: 1.23.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:LinkHD.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings LinkHD_1.23.0.tar.gz
StartedAt: 2025-08-07 23:44:22 -0400 (Thu, 07 Aug 2025)
EndedAt: 2025-08-07 23:48:09 -0400 (Thu, 07 Aug 2025)
EllapsedTime: 227.4 seconds
RetCode: 0
Status:   OK  
CheckDir: LinkHD.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:LinkHD.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings LinkHD_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/LinkHD.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘LinkHD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LinkHD’ version ‘1.23.0’
* 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 ‘LinkHD’ 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) VarSelection.Rd:40: Lost braces; missing escapes or markup?
    40 | a general linear regression into the $X$ matrix (${Y_hat}=X(X'X)^(-1)X'Y$) and the matrix $X(X'X)^(-1)X'$ is the projection matrix
       |                                                   ^
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/LinkHD.Rcheck/00check.log’
for details.


Installation output

LinkHD.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL LinkHD
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘LinkHD’ ...
** this is package ‘LinkHD’ version ‘1.23.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (LinkHD)

Tests output


Example timings

LinkHD.Rcheck/LinkHD-Ex.timings

nameusersystemelapsed
Compromise_matrix-methods0.9860.0321.018
DataProcessing0.0050.0030.008
DistStatis-Class0.0010.0000.000
DistStatis-CompromisePlot0.4830.0140.496
DistStatis-CorrelationPlot0.6800.0210.701
DistStatis-GlobalPlot0.7540.0320.786
Euclid_Im-methods0.3180.0170.336
Inertia_RV-methods0.3210.0000.321
Inertia_comp-methods0.2970.0010.298
LinkData-LinkData0.3140.0000.314
OTU2Taxa-OTU2Taxa2.9740.0373.010
RQO-methods0.3150.0210.336
Read_Data000
Ruminotypes0.0000.0000.001
Taraoceans0.0000.0000.001
Trajectories-methods0.5090.0420.552
VarSelection-Class0.0010.0000.001
VarSelection1.5770.0201.597
VarTable-methods1.5970.0021.599
Var_coordinates-methods1.6460.0211.667
Variables-methods1.6010.0081.609
compromise_coords-methods0.3170.0000.316
correl-methods0.3020.0000.302
dAB-dAB0.6270.0010.628
sign_values-methods1.6460.0511.697