Thuc Duy Le
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/miRLAB |
| git_branch: devel |
| git_last_commit: c4f5519 |
| git_last_commit_date: 2025-04-15 10:52:10 -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 1318/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miRLAB 1.39.0 (landing page) Thuc Duy Le
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
To the developers/maintainers of the miRLAB package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miRLAB.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: miRLAB |
| Version: 1.39.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miRLAB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miRLAB_1.39.0.tar.gz |
| StartedAt: 2025-10-23 22:27:37 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 22:32:08 -0400 (Thu, 23 Oct 2025) |
| EllapsedTime: 270.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: miRLAB.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miRLAB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miRLAB_1.39.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/miRLAB.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 ‘miRLAB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRLAB’ version ‘1.39.0’
* 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 ‘miRLAB’ can be installed ... WARNING
Found the following significant warnings:
Note: possible error in 'GDCquery(project = project, ': unused arguments (file.type = file_type, legacy = TRUE)
See ‘/Users/biocbuild/bbs-3.22-bioc/meat/miRLAB.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 ... NOTE
TCGAdownload: possible error in GDCquery(project = project,
data.category = data_category, data.type = data_type, platform =
"Illumina HiSeq", file.type = file_type, legacy = TRUE, access =
"open", experimental.strategy = experimental_strategy, ): unused
arguments (file.type = file_type, legacy = TRUE)
TCGAdownload: possible error in GDCquery(project = project,
data.category = data_category, data.type = data_type, file.type =
file_type, legacy = TRUE, access = "open", experimental.strategy =
experimental_strategy, sample.type = sample_type, barcode =
getcases): unused arguments (file.type = file_type, legacy = TRUE)
* checking Rd files ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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-3.22-bioc/meat/miRLAB.Rcheck/00check.log’
for details.
miRLAB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL miRLAB ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘miRLAB’ ... ** this is package ‘miRLAB’ version ‘1.39.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Note: possible error in 'GDCquery(project = project, ': unused arguments (file.type = file_type, legacy = TRUE) Note: possible error in 'GDCquery(project = project, ': unused arguments (file.type = file_type, legacy = TRUE) ** 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 (miRLAB)
miRLAB.Rcheck/tests/runTests.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.
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Type 'q()' to quit R.
> BiocGenerics:::testPackage("miRLAB")
Loading required package: amap
RUNIT TEST PROTOCOL -- Thu Oct 23 22:31:58 2025
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
miRLAB RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
12.157 0.784 13.051
miRLAB.Rcheck/miRLAB-Ex.timings
| name | user | system | elapsed | |
| Borda | 0.136 | 0.009 | 0.148 | |
| BordaTopk | 0.050 | 0.003 | 0.054 | |
| Dcov | 0.020 | 0.004 | 0.024 | |
| Elastic | 0.055 | 0.003 | 0.058 | |
| Extopk | 0.006 | 0.001 | 0.007 | |
| GOBPenrichment | 0.000 | 0.000 | 0.001 | |
| Hoeffding | 0.018 | 0.001 | 0.020 | |
| IDA | 0.043 | 0.002 | 0.045 | |
| ImputeNormData | 0.009 | 0.001 | 0.010 | |
| KEGGenrichment | 0.000 | 0.000 | 0.001 | |
| Kendall | 0.008 | 0.002 | 0.009 | |
| Lasso | 0.030 | 0.002 | 0.031 | |
| MI | 0.054 | 0.004 | 0.058 | |
| Pearson | 0.006 | 0.001 | 0.007 | |
| RDC | 0.084 | 0.004 | 0.089 | |
| Read | 0.003 | 0.000 | 0.003 | |
| ReadExtResult | 0 | 0 | 0 | |
| Spearman | 0.005 | 0.001 | 0.007 | |
| Standardise | 0.000 | 0.000 | 0.001 | |
| ValidateAll | 0 | 0 | 0 | |
| Validation | 0.012 | 0.002 | 0.014 | |
| ValidationT | 0.001 | 0.000 | 0.000 | |
| Zscore | 0.007 | 0.001 | 0.008 | |
| bRank | 0.008 | 0.001 | 0.009 | |
| convert | 0.015 | 0.002 | 0.017 | |
| filterAndCompare | 0 | 0 | 0 | |
| readHeader | 0.003 | 0.000 | 0.004 | |