Thuc Duy Le
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/miRLAB |
| git_branch: RELEASE_3_17 |
| git_last_commit: 64b3130 |
| git_last_commit_date: 2023-04-25 10:40:34 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:15 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1244/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miRLAB 1.30.0 (landing page) Thuc Duy Le
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 1.30.0 |
| 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_1.30.0.tar.gz |
| StartedAt: 2023-10-16 04:00:34 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 04:10:04 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 570.3 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_1.30.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/miRLAB.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘miRLAB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRLAB’ version ‘1.30.0’
* 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-3.17-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 R 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 in ‘inst/doc’ ... 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-3.17-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/4.3-x86_64/Resources/library’ * installing *source* package ‘miRLAB’ ... ** 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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
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.
> BiocGenerics:::testPackage("miRLAB")
Loading required package: amap
RUNIT TEST PROTOCOL -- Mon Oct 16 04:09:48 2023
***********************************************
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
20.084 1.261 27.816
miRLAB.Rcheck/miRLAB-Ex.timings
| name | user | system | elapsed | |
| Borda | 0.207 | 0.008 | 0.276 | |
| BordaTopk | 0.104 | 0.003 | 0.133 | |
| Dcov | 0.812 | 0.010 | 1.033 | |
| Elastic | 0.102 | 0.003 | 0.133 | |
| Extopk | 0.012 | 0.002 | 0.016 | |
| GOBPenrichment | 0.001 | 0.000 | 0.001 | |
| Hoeffding | 0.042 | 0.002 | 0.057 | |
| IDA | 0.090 | 0.001 | 0.114 | |
| ImputeNormData | 0.017 | 0.002 | 0.021 | |
| KEGGenrichment | 0.001 | 0.000 | 0.000 | |
| Kendall | 0.013 | 0.002 | 0.019 | |
| Lasso | 0.071 | 0.002 | 0.095 | |
| MI | 0.126 | 0.007 | 0.166 | |
| Pearson | 0.010 | 0.002 | 0.014 | |
| RDC | 0.152 | 0.007 | 0.205 | |
| Read | 0.004 | 0.002 | 0.009 | |
| ReadExtResult | 0.001 | 0.001 | 0.001 | |
| Spearman | 0.013 | 0.002 | 0.017 | |
| Standardise | 0.000 | 0.000 | 0.001 | |
| ValidateAll | 0.000 | 0.000 | 0.001 | |
| Validation | 0.022 | 0.003 | 0.032 | |
| ValidationT | 0 | 0 | 0 | |
| Zscore | 0.016 | 0.002 | 0.027 | |
| bRank | 0.015 | 0.002 | 0.023 | |
| convert | 0.025 | 0.004 | 0.037 | |
| filterAndCompare | 0.000 | 0.001 | 0.000 | |
| readHeader | 0.005 | 0.001 | 0.010 | |