Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1276/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
miRLAB 1.36.0 (landing page) Thuc Duy Le
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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: 1.36.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miRLAB.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings miRLAB_1.36.0.tar.gz |
StartedAt: 2024-12-20 03:31:30 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 03:36:11 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 281.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: miRLAB.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miRLAB.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings miRLAB_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/miRLAB.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'miRLAB/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'miRLAB' version '1.36.0' * 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 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 'F:/biocbuild/bbs-3.20-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 'F:/biocbuild/bbs-3.20-bioc/meat/miRLAB.Rcheck/00check.log' for details.
miRLAB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL miRLAB ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 -- Fri Dec 20 03:36:01 2024 *********************************************** 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 12.06 1.40 13.42
miRLAB.Rcheck/miRLAB-Ex.timings
name | user | system | elapsed | |
Borda | 0.06 | 0.01 | 0.11 | |
BordaTopk | 0.04 | 0.00 | 0.05 | |
Dcov | 0.02 | 0.00 | 0.01 | |
Elastic | 0.03 | 0.02 | 0.05 | |
Extopk | 0.01 | 0.00 | 0.01 | |
GOBPenrichment | 0 | 0 | 0 | |
Hoeffding | 0.02 | 0.00 | 0.02 | |
IDA | 0.03 | 0.00 | 0.03 | |
ImputeNormData | 0.02 | 0.00 | 0.02 | |
KEGGenrichment | 0 | 0 | 0 | |
Kendall | 0.03 | 0.00 | 0.03 | |
Lasso | 0.03 | 0.00 | 0.03 | |
MI | 0.02 | 0.03 | 0.05 | |
Pearson | 0.01 | 0.00 | 0.01 | |
RDC | 0.08 | 0.00 | 0.08 | |
Read | 0 | 0 | 0 | |
ReadExtResult | 0 | 0 | 0 | |
Spearman | 0 | 0 | 0 | |
Standardise | 0 | 0 | 0 | |
ValidateAll | 0 | 0 | 0 | |
Validation | 0.01 | 0.02 | 0.04 | |
ValidationT | 0 | 0 | 0 | |
Zscore | 0.02 | 0.00 | 0.02 | |
bRank | 0.02 | 0.00 | 0.01 | |
convert | 0.01 | 0.00 | 0.07 | |
filterAndCompare | 0 | 0 | 0 | |
readHeader | 0 | 0 | 0 | |