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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1253/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRNApath 1.65.0  (landing page)
James M. Ward
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/miRNApath
git_branch: devel
git_last_commit: 33c05f0
git_last_commit_date: 2024-04-30 10:18:18 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for miRNApath on palomino4

To the developers/maintainers of the miRNApath package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miRNApath.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: miRNApath
Version: 1.65.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miRNApath.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings miRNApath_1.65.0.tar.gz
StartedAt: 2024-06-10 05:29:29 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 05:32:03 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 153.1 seconds
RetCode: 0
Status:   OK  
CheckDir: miRNApath.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miRNApath.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings miRNApath_1.65.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/miRNApath.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'miRNApath/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'miRNApath' version '1.65.0'
* 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 'miRNApath' can be installed ... OK
* 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 ... NOTE
Problems with news in 'NEWS':
  Cannot process chunk/lines:
    Initial release.
  Cannot process chunk/lines:
    Changed objects to S4 format
  Cannot process chunk/lines:
    Updated runEnrichment and mirnaTable to remove the "Enriched by miRNA"
  Cannot process chunk/lines:
    concatenated strings, which were way too long to be useful.
  Cannot process chunk/lines:
    Updated the miRNA-gene counts methodology; fixed
  Cannot process chunk/lines:
    the strategy for ignoring pathways with no hits.
  Cannot process chunk/lines:
    Updated permutation logic to handle empty when permutations
  Cannot process chunk/lines:
    show enrichment in only a subset of overall pathways.
* 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 ... NOTE
Warning: no function found corresponding to methods exports from 'miRNApath' for: 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
loadmirnapath: no visible global function definition for 'read.table'
loadmirnapath: no visible global function definition for 'new'
loadmirnapathways: no visible global function definition for
  'read.table'
loadmirnatogene: no visible global function definition for 'read.table'
mirnaTable: no visible global function definition for 'reshape'
runEnrichment : <anonymous> : <anonymous>: no visible global function
  definition for 'phyper'
runEnrichment: no visible global function definition for 'slotNames'
Undefined global functions or variables:
  new phyper read.table reshape slotNames
Consider adding
  importFrom("methods", "new", "slotNames")
  importFrom("stats", "phyper", "reshape")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) runEnrichment.Rd:119: Escaped LaTeX specials: \$
* 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 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
mirnaTable 31.3   2.05   33.34
* 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: 5 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/miRNApath.Rcheck/00check.log'
for details.


Installation output

miRNApath.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL miRNApath
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'miRNApath' ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (miRNApath)

Tests output


Example timings

miRNApath.Rcheck/miRNApath-Ex.timings

nameusersystemelapsed
checkColumns000
convertFoldChange000
filtermirnapath0.100.280.41
loadmirnapath0.050.020.08
loadmirnapathways0.100.000.12
loadmirnatogene0.160.010.19
miRNApath-package000
mirnaTable31.30 2.0533.34
mirnaobj0.010.000.02
mirnapath-class0.020.000.01
runEnrichment000