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This page was generated on 2024-06-25 11:38 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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 1252/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRLAB 1.35.0  (landing page)
Thuc Duy Le
Snapshot Date: 2024-06-24 14:00 -0400 (Mon, 24 Jun 2024)
git_url: https://git.bioconductor.org/packages/miRLAB
git_branch: devel
git_last_commit: 71301a0
git_last_commit_date: 2024-04-30 10:44:45 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for miRLAB on nebbiolo2

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.

raw results


Summary

Package: miRLAB
Version: 1.35.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:miRLAB.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings miRLAB_1.35.0.tar.gz
StartedAt: 2024-06-25 00:50:15 -0400 (Tue, 25 Jun 2024)
EndedAt: 2024-06-25 00:54:10 -0400 (Tue, 25 Jun 2024)
EllapsedTime: 234.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: miRLAB.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:miRLAB.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings miRLAB_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/miRLAB.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘miRLAB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRLAB’ version ‘1.35.0’
* 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 ‘/home/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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/miRLAB.Rcheck/00check.log’
for details.


Installation output

miRLAB.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL miRLAB
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)

Tests output

miRLAB.Rcheck/tests/runTests.Rout


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 -- Tue Jun 25 00:54:05 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 
 10.274   0.490  10.753 

Example timings

miRLAB.Rcheck/miRLAB-Ex.timings

nameusersystemelapsed
Borda0.0810.0040.086
BordaTopk0.0350.0000.034
Dcov0.0120.0010.012
Elastic0.0420.0000.041
Extopk0.0050.0000.005
GOBPenrichment000
Hoeffding0.0170.0000.017
IDA0.0300.0000.029
ImputeNormData0.0070.0000.007
KEGGenrichment000
Kendall0.0030.0030.007
Lasso0.0220.0040.026
MI0.0480.0000.049
Pearson0.0040.0010.005
RDC0.0850.0070.093
Read0.0020.0010.002
ReadExtResult0.0010.0000.000
Spearman0.0050.0000.005
Standardise000
ValidateAll0.0010.0000.000
Validation0.010.000.01
ValidationT0.0010.0000.000
Zscore0.0060.0000.006
bRank0.0050.0000.006
convert0.0120.0000.012
filterAndCompare000
readHeader0.0020.0000.003