Shun Hang Yip
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/Linnorm |
| git_branch: devel |
| git_last_commit: 0b5e85a |
| git_last_commit_date: 2025-04-15 11:00:39 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:05 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1143/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Linnorm 2.33.0 (landing page) Shun Hang Yip
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
To the developers/maintainers of the Linnorm package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Linnorm.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: Linnorm |
| Version: 2.33.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Linnorm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Linnorm_2.33.0.tar.gz |
| StartedAt: 2025-10-23 22:03:01 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 22:09:17 -0400 (Thu, 23 Oct 2025) |
| EllapsedTime: 376.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Linnorm.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Linnorm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Linnorm_2.33.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Linnorm.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Linnorm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Linnorm’ version ‘2.33.0’
* 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 ‘Linnorm’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 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 ... NOTE
Linnorm.HClust: no visible binding for global variable ‘y’
Linnorm.HClust: no visible binding for global variable ‘xend’
Linnorm.HClust: no visible binding for global variable ‘yend’
Linnorm.HClust: no visible binding for global variable ‘cluster’
Linnorm.HClust: no visible binding for global variable ‘X1’
Linnorm.HClust: no visible binding for global variable ‘X2’
Linnorm.HVar: no visible binding for global variable ‘SD’
Linnorm.HVar: no visible binding for global variable ‘group’
Undefined global functions or variables:
SD X1 X2 cluster group xend y yend
* checking Rd files ... NOTE
checkRd: (-1) Linnorm.Cor.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HClust.Rd:37: Lost braces; missing escapes or markup?
37 | \item{method_hclust}{Charcter. Method to be used in hierarchical clustering. (From hclust {fastcluster}: the agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median" or "centroid".) Defaults to "ward.D".}
| ^
checkRd: (-1) Linnorm.HClust.Rd:39: Lost braces; missing escapes or markup?
39 | \item{method_dist}{Charcter. Method to be used in hierarchical clustering. (From Dist {amap}: the distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary", "pearson", "correlation", "spearman" or "kendall". Any unambiguous substring can be given.) Defaults to "pearson".}
| ^
checkRd: (-1) Linnorm.HClust.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HClust.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HClust.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HVar.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HVar.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HVar.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HVar.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HVar.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HVar.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HVar.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HVar.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.PCA.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.PCA.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.PCA.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.PCA.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.limma.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.limma.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.limma.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.limma.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.limma.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.limma.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.limma.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.limma.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.tSNE.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.tSNE.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.tSNE.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.tSNE.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
RnaXSim 78.498 1.496 80.526
Linnorm.Cor 58.357 0.545 59.334
Linnorm.limma 22.131 1.075 23.400
Linnorm 21.811 0.976 22.976
Linnorm.Norm 21.953 0.743 22.863
Linnorm.HClust 5.243 0.069 3.236
* 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/Linnorm.Rcheck/00check.log’
for details.
Linnorm.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Linnorm ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘Linnorm’ ... ** this is package ‘Linnorm’ version ‘2.33.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Misc.cpp -o Misc.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o Linnorm.so Misc.o -std=c++11 -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -DARMA_64BIT_WORD=1 -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-Linnorm/00new/Linnorm/libs ** R ** data ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Linnorm)
Linnorm.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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.
> library(testthat)
> library(Linnorm)
>
> test_check("Linnorm")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
>
> proc.time()
user system elapsed
21.939 0.959 27.186
Linnorm.Rcheck/Linnorm-Ex.timings
| name | user | system | elapsed | |
| LinearRegression | 0.001 | 0.001 | 0.002 | |
| LinearRegressionFP | 0.000 | 0.000 | 0.001 | |
| Linnorm.Cor | 58.357 | 0.545 | 59.334 | |
| Linnorm.DataImput | 1.916 | 0.158 | 2.082 | |
| Linnorm.HClust | 5.243 | 0.069 | 3.236 | |
| Linnorm.HVar | 1.019 | 0.059 | 1.081 | |
| Linnorm.Norm | 21.953 | 0.743 | 22.863 | |
| Linnorm.PCA | 3.551 | 0.132 | 3.717 | |
| Linnorm | 21.811 | 0.976 | 22.976 | |
| Linnorm.SGenes | 0.386 | 0.013 | 0.401 | |
| Linnorm.limma | 22.131 | 1.075 | 23.400 | |
| Linnorm.tSNE | 4.422 | 0.158 | 4.622 | |
| RnaXSim | 78.498 | 1.496 | 80.526 | |