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This page was generated on 2023-10-20 09:38:06 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1247/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRNApath 1.60.0  (landing page)
James M. Ward
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/miRNApath
git_branch: RELEASE_3_17
git_last_commit: a9d8b7e
git_last_commit_date: 2023-04-25 09:47:06 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for miRNApath on kjohnson2


To the developers/maintainers of the miRNApath package:
- 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: 1.60.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miRNApath.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miRNApath_1.60.0.tar.gz
StartedAt: 2023-10-18 08:04:10 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 08:05:41 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 91.4 seconds
RetCode: 0
Status:   OK  
CheckDir: miRNApath.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miRNApath.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miRNApath_1.60.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/miRNApath.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘miRNApath/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRNApath’ version ‘1.60.0’
* 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 ‘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 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 ... 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 27.04  0.603  42.057
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/miRNApath.Rcheck/00check.log’
for details.



Installation output

miRNApath.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL miRNApath
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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
filtermirnapath0.0440.0050.074
loadmirnapath0.0510.0050.086
loadmirnapathways0.0640.0060.106
loadmirnatogene0.1210.0070.197
miRNApath-package0.0000.0010.001
mirnaTable27.040 0.60342.057
mirnaobj0.0210.0020.035
mirnapath-class0.0210.0020.033
runEnrichment0.0000.0000.001