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This page was generated on 2021-07-23 15:06:45 -0400 (Fri, 23 Jul 2021).

CHECK results for Pigengene on machv2

To the developers/maintainers of the Pigengene package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Pigengene.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1394/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pigengene 1.18.0  (landing page)
Habil Zare
Snapshot Date: 2021-07-22 04:50:13 -0400 (Thu, 22 Jul 2021)
URL: https://git.bioconductor.org/packages/Pigengene
Branch: RELEASE_3_13
Last Commit: 848d21a
Last Changed Date: 2021-05-19 12:20:45 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: Pigengene
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pigengene_1.18.0.tar.gz
StartedAt: 2021-07-22 22:01:05 -0400 (Thu, 22 Jul 2021)
EndedAt: 2021-07-22 22:06:58 -0400 (Thu, 22 Jul 2021)
EllapsedTime: 352.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: Pigengene.Rcheck
Warnings: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pigengene_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/Pigengene.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pigengene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pigengene’ version ‘1.18.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Pigengene’ 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 ... 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 ... WARNING
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘Pigengene’
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘AnnotationDbi’ ‘biomaRt’ ‘energy’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘BiocStyle’
  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
Found the following possibly unsafe calls:
File ‘Pigengene/R/bn.calculation.R’:
  assignInNamespace("supported.clusters", fixArgs, "bnlearn")

combine.networks: no visible binding for global variable ‘netwok’
Undefined global functions or variables:
  netwok
* 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 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 ... ERROR
Running examples in ‘Pigengene-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gene.mapping
> ### Title: Maps gene IDs
> ### Aliases: gene.mapping
> ### Keywords: misc
> 
> ### ** Examples
> 
>      library(org.Hs.eg.db)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname


>      g1 <- gene.mapping(ids="NM_001159995")
Loading required package: org.Mm.eg.db

'select()' returned 1:1 mapping between keys and columns
>      print(g1)
             input          output1 output2
NM_001159995 "NM_001159995" "NRG1"  "NRG1" 
> 
>      ## Mapping to multiple convention
>      library(org.Mm.eg.db)
>      g2 <- gene.mapping(ids=c("NM_170730", "NM_001013580"),
+         inputType="REFSEQ", inputDb=org.Mm.eg.db,
+         outputType=c("SYMBOL","ENTREZID"),
+         outputDb=list(org.Hs.eg.db,org.Mm.eg.db), verbose=1)
[1] "Mapping to:"
[1] "org.Hs.eg.db-SYMBOL"
'select()' returned 1:1 mapping between keys and columns
Loading required package: biomaRt
Error: Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://useast.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Execution halted
* 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 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/Pigengene.Rcheck/00check.log’
for details.


Installation output

Pigengene.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Pigengene
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘Pigengene’ ...
** 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 (Pigengene)

Tests output


Example timings

Pigengene.Rcheck/Pigengene-Ex.timings

nameusersystemelapsed
Pigengene-package77.101 2.17979.389
aml0.2290.0030.232
balance0.7100.0310.741
calculate.beta1.2970.0321.329
check.nas0.0640.0030.066
check.pigengene.input0.0640.0030.066
combine.networks11.596 0.03511.639
compact.tree15.580 0.72916.325
compute.pigengene7.6510.3327.996
dcor.matrix0.2280.0310.260
draw.bn000
eigengenes330.0870.0040.092