| Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:26:45 -0400 (Wed, 15 Apr 2020).
| Package 1267/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Pigengene 1.12.0 Habil Zare
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: Pigengene |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pigengene.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Pigengene_1.12.0.tar.gz |
| StartedAt: 2020-04-15 05:31:36 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:38:21 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 404.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: Pigengene.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pigengene.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Pigengene_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Pigengene.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.12.0'
* 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 ... OK
** 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 ... OK
** 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.
* 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")
* 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 ... NOTE
Output for data("pigengene", package = "Pigengene"):
* 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 object is masked from 'package:base':
expand.grid
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
Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = fullXmlQuery, :
The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1.
Please report this on the support site at http://support.bioconductor.org
Calls: gene.mapping ... gene.mapping -> hu.mouse -> <Anonymous> -> .processResults
Execution halted
** running examples for arch 'x64' ... 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 object is masked from 'package:base':
expand.grid
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
Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = fullXmlQuery, :
The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1.
Please report this on the support site at http://support.bioconductor.org
Calls: gene.mapping ... gene.mapping -> hu.mouse -> <Anonymous> -> .processResults
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: 2 ERRORs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/Pigengene.Rcheck/00check.log'
for details.
Pigengene.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/Pigengene_1.12.0.tar.gz && rm -rf Pigengene.buildbin-libdir && mkdir Pigengene.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Pigengene.buildbin-libdir Pigengene_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL Pigengene_1.12.0.zip && rm Pigengene_1.12.0.tar.gz Pigengene_1.12.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2463k 100 2463k 0 0 34.2M 0 --:--:-- --:--:-- --:--:-- 35.9M
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
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_1.12.0.zip
* DONE (Pigengene)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'Pigengene' successfully unpacked and MD5 sums checked
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Pigengene.Rcheck/examples_i386/Pigengene-Ex.timings
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Pigengene.Rcheck/examples_x64/Pigengene-Ex.timings
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