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This page was generated on 2021-07-30 15:06:04 -0400 (Fri, 30 Jul 2021).

CHECK results for Pigengene on tokay2

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: 2021-07-29 04:50:02 -0400 (Thu, 29 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    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Pigengene
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pigengene.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Pigengene_1.18.0.tar.gz
StartedAt: 2021-07-30 03:46:51 -0400 (Fri, 30 Jul 2021)
EndedAt: 2021-07-30 04:02:59 -0400 (Fri, 30 Jul 2021)
EllapsedTime: 968.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: Pigengene.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pigengene.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Pigengene_1.18.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/Pigengene.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows


>      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
Ensembl site unresponsive, trying www mirror
Warning in hu.mouse(verbose = verbose) :
  Some genes with multiple homologs are selected arbitrarily.
'select()' returned 1:1 mapping between keys and columns
[1] "Mapping to:"
[1] "org.Hs.eg.db-ENTREZID"
'select()' returned 1:1 mapping between keys and columns
Ensembl site unresponsive, trying asia mirror
Warning in if (BioMartVersion == "\n" | BioMartVersion == "") { :
  the condition has length > 1 and only the first element will be used
Error in textConnection(BioMartVersion) : invalid 'text' argument
Calls: gene.mapping ... <Anonymous> -> .useMart -> bmVersion -> textConnection
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
Pigengene-package  73.51   2.39   76.78
one.step.pigengene 63.00   2.34   66.78
module.heatmap     39.71   4.43   49.36
gene.mapping       19.42   0.50   89.16
learn.bn           17.13   0.12   18.06
make.decision.tree 13.81   0.14   14.22
compact.tree       13.63   0.18   13.81
combine.networks   12.62   0.05   12.72
wgcna.one.step     11.44   0.02   11.47
compute.pigengene   7.34   0.31    7.69
plot.pigengene      6.49   0.58    7.06
pigengene           6.34   0.45    8.95
project.eigen       6.41   0.35    6.75
* 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, 2 WARNINGs, 2 NOTEs
See
  'C:/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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/Pigengene_1.18.0.tar.gz && rm -rf Pigengene.buildbin-libdir && mkdir Pigengene.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Pigengene.buildbin-libdir Pigengene_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Pigengene_1.18.0.zip && rm Pigengene_1.18.0.tar.gz Pigengene_1.18.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2464k  100 2464k    0     0  4493k      0 --:--:-- --:--:-- --:--:-- 4489k

install for i386

* installing *source* package 'Pigengene' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Pigengene'
    finding HTML links ... done
    Pigengene-package                       html  
    aml                                     html  
    balance                                 html  
    calculate.beta                          html  
    check.nas                               html  
    check.pigengene.input                   html  
    combine.networks                        html  
    compact.tree                            html  
    compute.pigengene                       html  
    dcor.matrix                             html  
    draw.bn                                 html  
    eigengenes33                            html  
    gene.mapping                            html  
    get.fitted.leaf                         html  
    get.genes                               html  
    get.used.features                       html  
    learn.bn                                html  
    make.decision.tree                      html  
    mds                                     html  
    message.if                              html  
    module.heatmap                          html  
    one.step.pigengene                      html  
    pheatmap.type                           html  
    pigengene-class                         html  
    pigengene                               html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/Pigengene.buildbin-libdir/00LOCK-Pigengene/00new/Pigengene/help/pigengene.html
    plot.pigengene                          html  
    preds.at                                html  
    project.eigen                           html  
    pvalues.manova                          html  
    save.if                                 html  
    wgcna.one.step                          html  
** 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

install for x64

* installing *source* package 'Pigengene' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Pigengene' as Pigengene_1.18.0.zip
* DONE (Pigengene)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'Pigengene' successfully unpacked and MD5 sums checked

Tests output


Example timings

Pigengene.Rcheck/examples_i386/Pigengene-Ex.timings

nameusersystemelapsed
Pigengene-package62.95 2.9667.03
aml0.100.040.15
balance0.400.100.49
calculate.beta1.200.031.23
check.nas0.060.000.06
check.pigengene.input0.060.000.07
combine.networks10.61 0.0310.76
compact.tree14.50 0.1914.69
compute.pigengene7.60.48.0
dcor.matrix0.210.030.24
draw.bn000
eigengenes330.090.020.11

Pigengene.Rcheck/examples_x64/Pigengene-Ex.timings

nameusersystemelapsed
Pigengene-package73.51 2.3976.78
aml0.140.040.17
balance0.400.040.45
calculate.beta1.330.031.36
check.nas0.080.000.08
check.pigengene.input0.080.020.09
combine.networks12.62 0.0512.72
compact.tree13.63 0.1813.81
compute.pigengene7.340.317.69
dcor.matrix0.200.020.22
draw.bn000
eigengenes330.100.000.09
gene.mapping19.42 0.5089.16
get.fitted.leaf0.650.010.67
get.genes0.610.070.67
get.used.features0.500.060.57
learn.bn17.13 0.1218.06
make.decision.tree13.81 0.1414.22
mds0.20.00.2
message.if000
module.heatmap39.71 4.4349.36
one.step.pigengene63.00 2.3466.78
pheatmap.type0.160.030.19
pigengene6.340.458.95
plot.pigengene6.490.587.06
preds.at1.070.031.11
project.eigen6.410.356.75
pvalues.manova0.040.000.04
save.if0.720.010.74
wgcna.one.step11.44 0.0211.47