Package: MGFR

Version: 1.9.2

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MGFR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MGFR_1.9.2.tar.gz

StartedAt: 2019-04-07 04:26:36 -0400 (Sun, 07 Apr 2019)

EndedAt: 2019-04-07 04:45:15 -0400 (Sun, 07 Apr 2019)

EllapsedTime: 1119.2 seconds

RetCode: 1

Status:  ERROR

CheckDir: MGFR.Rcheck

Warnings: NA

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MGFR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MGFR_1.9.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MGFR.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MGFR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MGFR' version '1.9.2'
* 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 'MGFR' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'MGFR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getMarkerGenes.rnaseq.html
> ### Title: Marker Gene Detection
> ### Aliases: getMarkerGenes.rnaseq.html
> ### Keywords: marker genes RNA-seq data
> 
> ### ** Examples
> 
> data(ref.mat)
> getMarkerGenes.rnaseq.html(ref.mat, class.vec = colnames(ref.mat), samples2compare="all", gene.ids.type="ensembl", score.cutoff=1,directory = getwd())
Detecting marker genes...
Mapping gene IDs to gene symbols...
Error in getBM(filters = "ensembl_gene_id", attributes = c("ensembl_gene_id",  : 
  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: getMarkerGenes.rnaseq.html -> .get.genes.rnaseq -> getBM
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'MGFR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MGFR-package
> ### Title: Marker Gene Finder in RNA-seq data
> ### Aliases: MGFR-package MGFR
> ### Keywords: package
> 
> ### ** Examples
> 
> data(ref.mat)
> res.list <- getMarkerGenes.rnaseq(ref.mat, class.vec=colnames(ref.mat), samples2compare="all", annotate=TRUE, gene.ids.type="ensembl", score.cutoff=1)
Detecting marker genes...
Mapping gene IDs to gene symbols...
Error in getBM(filters = "ensembl_gene_id", attributes = c("ensembl_gene_id",  : 
  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: getMarkerGenes.rnaseq -> .get.genes.rnaseq -> getBM
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
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/MGFR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MGFR_1.9.2.tar.gz && rm -rf MGFR.buildbin-libdir && mkdir MGFR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MGFR.buildbin-libdir MGFR_1.9.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MGFR_1.9.2.zip && rm MGFR_1.9.2.tar.gz MGFR_1.9.2.zip
###
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100 1568k  100 1568k    0     0  22.5M      0 --:--:-- --:--:-- --:--:-- 25.1M

install for i386

* installing *source* package 'MGFR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MGFR'
    finding HTML links ... done
    MGFR-internal                           html  
    MGFR-package                            html  
    getMarkerGenes.rnaseq                   html  
    getMarkerGenes.rnaseq.html              html  
    ref.mat                                 html  
** building package indices
** installing vignettes
   'MGFR.Rnw' using 'UTF-8' 
** 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 'MGFR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MGFR' as MGFR_1.9.2.zip
* DONE (MGFR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MGFR' successfully unpacked and MD5 sums checked