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This page was generated on 2024-06-11 14:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 1114/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LinkHD 1.18.0  (landing page)
"Laura M Zingaretti"
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/LinkHD
git_branch: RELEASE_3_19
git_last_commit: 038d19e
git_last_commit_date: 2024-04-30 11:18:28 -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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for LinkHD on lconway

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: 1.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LinkHD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LinkHD_1.18.0.tar.gz
StartedAt: 2024-06-09 21:11:56 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 21:15:42 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 225.7 seconds
RetCode: 0
Status:   OK  
CheckDir: LinkHD.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LinkHD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LinkHD_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/LinkHD.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LinkHD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LinkHD’ 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 ‘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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/LinkHD.Rcheck/00check.log’
for details.


Installation output

LinkHD.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL LinkHD
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘LinkHD’ ...
** 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-methods0.5170.1370.656
DataProcessing0.0070.0010.008
DistStatis-Class0.0010.0000.001
DistStatis-CompromisePlot1.2960.0301.328
DistStatis-CorrelationPlot0.8000.0390.841
DistStatis-GlobalPlot0.8210.0380.862
Euclid_Im-methods0.4440.0210.466
Inertia_RV-methods0.3320.0120.344
Inertia_comp-methods0.3440.0150.359
LinkData-LinkData0.3620.0110.373
OTU2Taxa-OTU2Taxa3.9410.0774.022
RQO-methods0.2940.0160.311
Read_Data0.0000.0010.001
Ruminotypes0.0010.0010.002
Taraoceans0.0010.0010.003
Trajectories-methods0.7000.3201.031
VarSelection-Class0.0000.0010.000
VarSelection1.8060.0171.827
VarTable-methods1.8340.0161.851
Var_coordinates-methods1.6140.0331.648
Variables-methods1.8570.0191.880
compromise_coords-methods0.3510.0090.361
correl-methods0.4340.0500.486
dAB-dAB0.6130.0220.636
sign_values-methods1.5650.0281.595