Package: maser

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:maser.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings maser_1.4.0.tar.gz

StartedAt: 2020-04-15 04:27:40 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:36:44 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 543.9 seconds

RetCode: 1

Status:  ERROR

CheckDir: maser.Rcheck

Warnings: NA

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:maser.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings maser_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/maser.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 'maser/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'maser' version '1.4.0'
* package encoding: UTF-8
* 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 'maser' 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 ... NOTE
filterByIds: no visible binding for global variable 'ID'
mapTranscriptsA3SSevent: no visible global function definition for
  'subjectHits'
mapTranscriptsA5SSevent: no visible global function definition for
  'subjectHits'
mapTranscriptsMXEevent: no visible global function definition for
  'subjectHits'
mapTranscriptsRIevent: no visible global function definition for
  'subjectHits'
mapTranscriptsSEevent: no visible global function definition for
  'subjectHits'
overlappingFeatures: no visible global function definition for
  'subjectHits'
urlTracksUniprotKB: no visible binding for global variable 'Name'
Undefined global functions or variables:
  ID Name subjectHits
* 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 R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'maser-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: availableFeaturesUniprotKB
> ### Title: Query available human protein features in UniprotKB.
> ### Aliases: availableFeaturesUniprotKB
> 
> ### ** Examples
> 
> head(availableFeaturesUniprotKB(), 10)
Warning in file(con, "r") :
  InternetOpenUrl failed: 'A connection with the server could not be established
'
Error in file(con, "r") : cannot open the connection
Calls: head ... availableFeaturesUniprotKB -> urlTracksUniprotKB -> readLines -> file
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'maser-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: availableFeaturesUniprotKB
> ### Title: Query available human protein features in UniprotKB.
> ### Aliases: availableFeaturesUniprotKB
> 
> ### ** Examples
> 
> head(availableFeaturesUniprotKB(), 10)
Warning in file(con, "r") :
  InternetOpenUrl failed: 'A connection with the server could not be established
'
Error in file(con, "r") : cannot open the connection
Calls: head ... availableFeaturesUniprotKB -> urlTracksUniprotKB -> readLines -> file
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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/maser.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/maser_1.4.0.tar.gz && rm -rf maser.buildbin-libdir && mkdir maser.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=maser.buildbin-libdir maser_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL maser_1.4.0.zip && rm maser_1.4.0.tar.gz maser_1.4.0.zip
###
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install for i386

* installing *source* package 'maser' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'maser'
    finding HTML links ... done
    Maser-class                             html  
    PSI-Maser-character-method              html  
    PSI                                     html  
    annotation-Maser-method                 html  
    availableFeaturesUniprotKB              html  
    boxplot_PSI_levels                      html  
    counts-Maser-method                     html  
    display                                 html  
    dotplot                                 html  
    filterByCoverage                        html  
    filterByEventId                         html  
    geneEvents                              html  
    granges-Maser-method                    html  
    mapProteinFeaturesToEvents              html  
    mapTranscriptsToEvents                  html  
    maser                                   html  
    pca                                     html  
    plotGenePSI                             html  
    plotTranscripts                         html  
    plotUniprotKBFeatures                   html  
    splicingDistribution                    html  
    summary-Maser-method                    html  
    topEvents                               html  
    volcano                                 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 'maser' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'maser' as maser_1.4.0.zip
* DONE (maser)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'maser' successfully unpacked and MD5 sums checked